Bosc on Open Bioinformatics Foundation

CollaborationFest 2026

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 13 May 2026 02:30:32 +0000

The OBF/BOSC CollaborationFest (aka CoFest) is a collaborative event where participants get to work together on code, documentation, training materials, challenging analysis problems, use cases, and more. Participants can bring their own project ideas or pitch in on others’ projects.

BOSC has organized CoFests every year before or after ISMB since 2010. This year, CoFest will take place after ISMB 2026 on Friday, July 17 and Saturday, July 18 (9am-5pm each day). The location is in central Washington, D.C. (not far from the ISMB location); the exact address will be shared with those who register. There will be limited opportunities for virtual participation; videoconferencing is not guaranteed but participants will be able to interact on Slack.

CoFest is free, but registration is mandatory, and space is limited. To sign up:

Add yourself to this spreadsheet to help us gauge interest, coordinate topic groups and logistics
Add your project ideas to this document if you have something in mind
Join the #cofest2026 channel in the OBF Slack for discussion before/during/after CoFest!

We’re excited to see you in July at BOSC@ISMB and hope you’ll stick around for CoFest right after.

For more information on CoFest (including updates about planned projects and activities), please visit our CoFest page.

Big thanks to Computercraft for providing the meeting space, and to Seqera, whose sponsorship is helping cover the cost of lunches!

Open Source in the Age of AI

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 30 Mar 2026 02:30:32 +0000

At BOSC 2026, we want to talk about the elephant in the open-source room: Is generative AI an advantage or a hindrance to open source?

We invite abstracts on this topic. Some might be selected to give talks at BOSC (which will be part of ISMB 2026). We may also invite some of the chosen speakers to participate in a panel. The submission deadline is April 9.

For example, here are some possible topics (but don’t feel restricted to these):

Reuse: how can we encourage and facilitate reuse of tools and frameworks when AI makes it easy to code things up from scratch?
Evaluating open source projects: AI tools can generate thousands of lines of code in seconds. The most costly process is now verifying that code for scientific accuracy (https://arxiv.org/abs/2507.09089). What are some good approaches to address this?
Contribution guidelines: balancing scale and utility of AI-assisted development with community-building
- How should an open source project assess pull requests from AI agents?
- Are zero-tolerance bans on submissions generated using AI reasonable? (e.g., https://medium.com/@livewyer/ai-disruption-to-open-source-software-oss-377f10be2d8a)
- How can humans and AI agents best work together?
Attribution and credit:
- How should we recognize contributions in an age of AI-assisted commits?
- Transparency: Should there be mandatory requirements to disclose AI use, including models and prompts used?
- Human ownership: should authors always remain legally and ethically accountable for the outputs of their code?
- Licensing: do open source licenses still mean anything when coding agents can translate or reimplement code?
Sustainability: who does the long-term hard work of maintaining open source projects when AI does the “easy” work?
Credit for training data: part of what AI proposes is reusing existing human-coded work without crediting it. Can there be a way to fairly credit the contribution of an open source project to the (often non open-source) models?
When AI is the user: should open source projects be designed for machine consumers?
The deadly feedback loop: models are trained on what they produce. Does this really work?
Open data in the AI era: balancing access with protection from misuse

We look forward to seeing your thoughts on these topics! Please be sure to submit your abstract by April 9 if you want to be considered for a talk.

Financial support options for attending BOSC 2026

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 04 Mar 2026 02:30:32 +0000

BOSC is part of the big ISMB 2026 conference, so you need to register for ISMB to participate in BOSC.

We recognize that the high price of travel and registration can be a barrier. Below are some ways to apply for financial assistance to attend ISMB / BOSC.

OBF Event Fellowships

The Open Bioinformatics Foundation (OBF)’s Event Fellowships are aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities…such as BOSC.

Awards are made three times a year; the next deadline is April 1, 2026 (note that this is earlier than the ISMB submission deadline of April 9).

BOSC Registration Fee Support

Authors who submit their work to BOSC can request ISMB registration fee support on the abstract submission form (these requests are not seen by reviewers). This initiative is funded by sponsorships.

Only presenting authors whose abstracts are accepted for talk or poster presentation are eligible for this fee support, and not all requests will be granted.

Requests from early-career applicants and people from underrepresented geographical areas will be given priority. Applicants will be notified about whether their request was granted shortly after abstract acceptance notifications go out in early May.

ISCB Conference Fellowships

The ISCB (the organization that runs the ISMB conference) offers a limited number of conference fellowships that cover the registration fee to help students and postdocs to present their work at ISMB.

These fellowships are only open to those who have a Proceeding, Talk, or Poster (not late poster) accepted for presentation at ISMB. The application will be sent automatically to eligible people on May 5. The number of awards is limited; not all eligible applicants will receive awards. Please consult the ISMB page for more information.

Apply to be Event Staff at ISMB

You can apply to work at ISMB 2026 for approximately 20-24 hours in exchange for free registration and time-based pay. (When you’re not working, you can attend talks.) The application deadline is May 1, 2026.

Call for Comments on BOSC 2026 Keynote Speaker Candidates

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 18 Dec 2025 00:00:00 +0000

We thank our community for the excellent keynote speaker suggestions for BOSC 2026. The next phase of our selection process invites you to share any concerns about the suitability of the nominated individuals. Our invited speaker selection process and criteria outline the factors we consider when selecting speakers for BOSC 2026, including characteristics that will exclude a speaker.

Please use this anonymous form to submit any concerns, including as much detail as you are comfortable providing, by Friday, January 9th, 2026.

This year’s nominees are:

Katy Börner
Anne Carpenter
Ishwar Chandramouliswaran
Kyunghyun Cho
Francis Collins
Medha Devare
Casey Greene
Eric Green
Susan Gregurick
Lukas Heumos
Mikhail Kolmogorov
Heng Li
Thomas Leitner
Marcia McNutt
Alondra Nelson
Sandra Orchard
Francis Oullette
Cyril Pommier
John Quackenbush
Heidi Sofia
Paul Thomas
Kirstie Whitaker
Maryam Zaringhalam

The BOSC Organizing Committee will extend invitations for keynote speakers using the community-nominated list after the comment period closes. Since the Committee cannot guarantee a speaker’s acceptance, they may need to consider individuals not on the original list without repeating the entire nomination process. However, the Committee remains open to community input if a speaker is believed not to meet the established standards.

Call for Nominations: BOSC 2026 Keynote Speakers

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 04 Dec 2025 00:00:00 +0000

BOSC 2026 is planned for July 14-15, 2026, as part of ISMB 2026 in Washington, DC.

We invite our community to nominate potential keynote speakers who would be of interest to our community. You may submit as many nominations as you wish. The form may be filled out multiple times. Please submit nominations by December 15, 2025.

Why this matters

Keynote talks are always a highlight at BOSC. We traditionally open and close the conference with invited speakers—prominent contributors or emerging leaders whose work resonates with the bioinformatics open-source community.

About the selection process

Prior to 2023, keynote selection was handled internally by the BOSC Organizing Committee. In 2023, we introduced a more consistent, transparent, and community-aligned process, including a public rubric for evaluating candidates. The results were excellent, and we are continuing this open nomination process for 2026. (See our selection rubric: https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md)

Key Dates

December 15, 2025 – Deadline for keynote speaker nominations
December 19, 2025 – Nomination slate posted for community review
January 9, 2026 – Deadline for community comments on the slate

Nominate a keynote speaker!

BOSC 2025: Report and Videos

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 24 Sep 2025 00:00:00 +0000

Whether you attended BOSC 2025 or missed it, you can read about it (with lots of photos!) in our report published in F1000Research.

We are also pleased to announce that videos of the BOSC 2025 talks are now available on our schedule page, as well as on our YouTube channel. Enjoy!

Financial support options for attending BOSC 2025

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 30 Mar 2025 02:30:32 +0000

We recognize that the high price of travel and registration can make it hard for some people to attend BOSC/ISMB. Below are some ways to apply for financial assistance to present your work at BOSC 2025.

OBF Event Fellowships

Awards are made three times a year; the next deadline is April 1, 2025 (note that this is earlier than the ISMB/ECCB submission deadline of April 17).

More info about applying for an OBF Event Fellowship

Left: Awardee Ruth Nanjala and her poster at ICHG 2023

BOSC registration fee waiver

Authors who submit their work to BOSC can request ISMB registration fee support on the abstract submission form (these requests are not seen by reviewers). This initiative is funded by sponsorships.

Only presenting authors whose abstracts are accepted for talk or poster presentation are eligible for this fee waiver, and depending on the number of applicants, not all requests will be granted.

Requests from early-career applicants and people from underrepresented geographical areas will be given priority. Applicants will be notified about whether their fee waiver request was granted around the same time that abstract acceptance notifications go out (May 14).

ISCB Conference Fellowships

The ISCB (the organization that runs the ISMB conference) offers a limited number of conference fellowships for students and postdocs to present their work at ISMB.

Rules for the ISCB conference fellowships (these are not BOSC-specific):

Eligibility is limited to students or postdocs, plus early career researchers from Low through Upper-Middle Economic countries. Postdocs and employees of any US federal agency are not eligible.
Only open to those who have a Proceeding, Talk, or Poster (not late poster) accepted for presentation at ISMB/ECCB.
The applicant must be the presenting author of the work.
Applicant must be a current ISCB member
Applicant must be able to pay all expenses of attending the conference up front, including conference registration fee, travel, accommodations, and meals.
The application will be sent automatically to eligible people on May 14 (the day after talk/poster acceptances go out).
The number of awards is limited; not all eligible applicants will receive awards.

Apply to be Event Staff at ISMB/ECCB

You can apply to work at ISMB/ECCB 2025 for approximately 20-24 hours in exchange for free registration and time-based pay. (When you’re not working, you can attend talks.) The application deadline is May 9, 2025. Note that Event Staff have to already be ISCB members.

BOSC and BOKR to join forces at ISMB/ECCB 2025

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 17 Mar 2025 00:30:32 +0000

We are pleased to announce that BOSC and the newly-renamed Bio-Ontologies and Knowledge Representation (BOKR) will join forces for a day at ISMB/ECCB 2025! The joint session will include talks chosen from abstracts submitted to BOSC or BOKR, plus a keynote speaker who is well known in both the ontology and open science communities (stay tuned for an announcement soon!).

BOSC and BOKR are two of the longest-running COSIs (Communities of Special Interest) at ISMB: BOSC started in 2000 and BOKR (then called Bio-Ontologies) in 1998. BOKR focuses on the FAIR development and application of ontologies and other Linked Open Data resources and the organization, presentation and dissemination of knowledge in biomedicine and the life sciences. BOSC covers the full spectrum of open source, open science, open data and open standards in the life sciences.

(Right: Melissa Haendel was the keynote speaker at the BOSC/Bio-Ontologies joint session in 2022.)

You can submit relevant abstracts to either BOSC or BOKR (please do not double-submit the same abstract). The Program Chairs of both COSIs will consider appropriate abstracts for the joint session.

BOSC 2025 will take place July 21-22, and BOKR will be July 22-23. The joint session will be part or all of the day on July 22.

Join us at ISMB CollaborationFest 2025!

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 07 Mar 2025 01:30:32 +0000

CollaborationFest 2025 will be a two-day collaborative work event at which participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. Bring your own project ideas or come ready to collaborate with others on their projects!

BOSC has held CollaborationFests (aka CoFests) every year before or after ISMB since 2010. This year, we decided to hold the CollaborationFest as part of ISMB/ECCB and open it to all registered ISMB/ECCB participants. It will take place during the last two days of ISMB/ECCB.

ISMB CollaborationFest 2025 is co-organized by volunteers from four COSIs:

Bioinformatics Open Source Conference (BOSC)
Bio-Ontologies and Knowledge Representation (BOKR)
Function COSI
3DSig

Due to space constraints, participation in CollaborationFest is limited. To indicate your interest in participating, register for ISMB/ECCB 2025 by June 20 and sign up for CollaborationFest as an “add-on” during the registration process. We will contact you by June 23 to request a few pieces of information to help us organize the event. Last-minute walk-ins may be possible for ISMB participants if we are not at capacity.

A limited number of ISMB registration waivers will be available for trainees (students and postdocs) who would like to participate in the CollaborationFest and are willing to work as volunteers during the first two days of ISMB. More info here about applying to volunteer at ISMB.

Limited remote participation in CollaborationFest will be possible, but the amount of interaction that is possible will be highly dependent on the people and projects active on the day. We expect to have a video feed from the room available; joining will require you to have registered as a (virtual or in-person) ISMB/ECCB attendee.

BOSC 2025 potential keynote speakers–community comment period open

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 18 Jan 2025 00:19:29 +0000

We invited our community to nominate potential keynote speakers for BOSC, and we were delighted with the many excellent suggestions received. In the next stage of this process, we’re providing you with an opportunity to express any concerns regarding the suitability of any nominated individuals as BOSC Keynote Speakers.

Our invited speaker selection process and criteria include examples of potential reasons for exclusion. If you have concerns about any of the individuals on our list, please share them (with as much detail as you feel comfortable providing) through this anonymous form by Friday, January 24, 2025.

And the nominees are…

Aitana Neves
Alondra Nelson
Aviv Regev
Catalina Lopez-Correa
Chris Mungall
Christine Orengo
Dorrie Main
Francis Ouelette
Guanming Wu
Heidi Sofia
Helen Parkinson
Joslynn Lee
Kari Jordan
Lincoln Stein
Lisa Bowleg
Mallory Freeberg
Robert Aboukhalil
Rowland Mosbergen
Susanna Sansone
Susheel Varma
Sushma Naithani
Tanya Berardini
X. Shirley Liu

Following the close of the community comment period, the BOSC Organizing Committee will use this list as a starting point for extending invitations to potential keynote speakers. As we cannot predict which speakers will accept the invitation, we may need to consider individuals beyond those nominated. In such cases, we will not repeat this nomination process. However, community members are always encouraged to inform the Organizing Committee if they believe a speaker does not align with our established standards.

Announcing BOSC 2025; seeking keynote speaker nominations

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 09 Jan 2025 06:33:54 +0000

We invite you to join us for BOSC 2025, a vibrant gathering at the forefront of open-source bioinformatics and open science!

Location: Liverpool, UK, and virtual
Dates: July 21-22, 2025
Website: /events/bosc/
LinkedIn: https://www.linkedin.com/groups/14344023/
Bluesky: https://bsky.app/profile/bosc.bsky.social
Slack: https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew

Key Dates

January 16, 2025: Deadline for community nominations of keynote speakers
April 17: Deadline for submitting talk/poster abstracts
May 13: Talk/poster acceptance notifications
May 15: Late poster submission deadline
July 20-24: ISMB/ECCB 2025
July 21-22: BOSC 2025 (the first two full days of ISMB/ECCB 2025)
July 23-24: ISMB CollaborationFest

About BOSC

Since 2000, BOSC has provided a forum for sharing ideas and results in open-source bioinformatics and open science. Our annual two-day program includes keynote talks, talks chosen from submitted abstracts, posters, a panel discussion, and more!

Exciting news for 2025:

BOSC 2025 will include a joint session with the newly renamed Bio-Ontologies and Knowledge Representation COSI!

Plus, our popular collaborative work event (CollaborationFest, or CoFest) will be held as part of ISMB, with participation open to all. Don’t miss this great opportunity to connect with fellow researchers, contribute to groundbreaking projects, and shape the future of bioinformatics!

Nominate a keynote speaker!

We would like to assemble a diverse list of potential BOSC 2025 keynote speakers (see our open selection process and rubric). We invite the community to nominate keynote speakers using this form by January 16. After that, we will share our list and solicit comments from the community prior to finalizing the speakers.

Submit an abstract! (But not yet!)

Abstract submission will open around the end of January. We encourage you to submit abstracts (due April 17– no extensions) on any topic relevant to open-source bioinformatics or open science. Some abstracts will be selected for lightning talks, longer talks, or posters.

BOSC topics include (but are not limited to):

Open Science and Reproducible Research
Open Biomedical Data
Citizen/Participatory Science
Standards and Interoperability
Data Science
Workflows
Open Approaches to Translational Bioinformatics
Open Science
Developer Tools and Libraries
Inclusion, Outreach, and Training
AI/ML: open approaches

Registration fee assistance is available (more info on that soon).

We hope to see you (in person or virtually) at BOSC 2025!

BOSC 2024 Videos Now Available

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 17 Sep 2024 17:52:12 +0000

The talk videos from BOSC 2024 are now available on YouTube. They are also linked from the BOSC talk schedule (scroll down to “Talks”).

Stay tuned - our full report on BOSC 2024 will be published soon!

My Amazing BOSC 2024 Experience

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 02 Aug 2024 18:00:06 +0000

By Beatrice Mihalache

Examining open source projects has been most useful to me while I am sharpening my coding skills, so I was excited to learn about the Bioinformatics Open Source Conference – BOSC. I am a rising senior at UCLA, studying biophysics and data science. I strongly believe in open source, so I submitted the work I’d done with my PI and my grad student collaborator for a poster presentation at BOSC. My research lab at UCLA allocates conference participation funds only for graduate students, therefore I also included a request for fee waiver with my conference submission. I was excited when a few weeks later I received notification that not only I was accepted as a poster presenter, but that I also got free registration to both BOSC and to the entire ISMB (Intelligent Systems for Molecular Biology) conference!

Attending BOSC and ISMB was such an incredible experience. On Saturday and Sunday I attended different sub-conferences at ISMB including multiple talks on deep-learning applications to biological problems such as enzyme design and protein function prediction. I was stoked and humbled by how much I learned. The coffee and lunch breaks were a super welcome opportunity to network and talk to other poster presenters about their research.

Palais de Congress, the conference venue, at night. The colorful window architecture is cool.

On Monday, BOSC kicked off with Melanie Courtot’s keynote about the necessity for better quality data. I learned more about Findable, Accessible, Interoperable, Reusable (FAIR) code, as this was never explicitly mentioned in any of my computer science classes at school.

Tuesday’s talks were also very cool, the most memorable to me being Andrew Su’s keynote, specifically the part where he had us imagine what AI would be like in the future. In a world that is changing at an accelerated pace, this is a difficult exercise, but a valuable one that also gives insight into the skills that will be most valued in future researchers such as creativity and linking interdisciplinary applications together well.

Me in front of my poster at BOSC, enjoying this most awesome experience

One of my favorite conference experiences was going to dinner with some of the conference attendees. Monday night we ate at LOV McGill, an impressively delicious vegan restaurant. It was so valuable to personally connect with people. I sat between Andrew Su, a professor and researcher at Scripps who would be giving the next day’s keynote, and Bhavesh Patel, the founder of the FAIR data innovations hub. It was nice to learn about people’s personal experiences, about how they got to where they are, and also random snippets and stories.

I am most grateful to BOSC’s sponsors Seqera, NIH ODSS, the Chan Zuckerberg Initiative, and GigaScience for helping me attend BOSC. This experience has been invaluable. I am inspired and energized by it. I look forward to applying the things I’ve learned to new projects. I will make sure that all my future projects’ code is FAIR.

The conference was hosted in Montreal, and I had never been there before, so I took this trip as an opportunity to do some sightseeing and exploring, by staying a few extra days after the conference. I was impressed by how well Montreal blends the old architecture with the modern. I climbed the stairs of Mont Royal, ate poutine with some friends I made at the conference, and visited the Museum of Fine Arts and the Archeology and History Museum.

Join us for CoFest 2024!

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 14 Jun 2024 18:20:58 +0000

This year will mark the 15th edition of the BOSC-associated CollaborationFest, or CoFest for short. At these events, participants work together on code, documentation, training materials, use cases, and analyses.

CoFest 2024 will take place on July 17-18, right after ISMB and BOSC 2024. This will be a hybrid event, hosted at UQAM | Université du Québec à Montréal and online. Many thanks to Abdoulaye Baniré Diallo , BF Francis Ouellette, and Karen Reynard for finding and donating the use of this venue!

Interested in joining us to discuss and contribute to open-source and open-science projects? Registration is free but mandatory. More information, and link to register, is available at /events/bosc-2024/obf-bosc-collaborationfest-2024/

BOSC 2024 Review Committee

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 12 Apr 2024 16:09:48 +0000

BOSC is an entirely volunteer-run event. We have an organizing committee of 8 people (see /events/bosc-2024/), and we are assisted by a larger review committee. The review committee is responsible for reading all the submitted abstracts and assessing them for quality and appropriateness to BOSC. You can read more about our review process here.

Our tentative review committee for 2024 is listed below. If you have any concerns about anyone on the list, please contact us at bosc@open-bio.org (that mailing list is private to the organizing committee and is not accessible to the larger review committee) or private-message any of the organizing committee members by email or in Slack.

Review Committee (tentative): Arpita Joshi, Aziz Khan, Bastian Greshake Tzovaras, bhavesh patel, Christopher Fields, Emmanuel Adamolekun, Hervé Ménager, Hilmar Lapp, Ian Simpson, J. Harry Caufield, jenea adams, Karsten Hokamp, Kartik Khosa, Konstantin Okonechnikov, Monica Munoz-Torres, Nehemiah Ongeso, rachel torchet, Seth Carbon, Suruchi Ahuja, Surya Saha, Swapnil Sawant, Tazro Ohta, Titus Brown, Tyrone Chen

Gemma Turon's ISCBAcademy talk available on video

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 26 Mar 2024 03:44:24 +0000

Gemma Turon, PhD spoke at an ISCBacademy webinar on March 5, 2024. Her talk was entitled “Ersilia, open source AI/ML for (antimicrobial) drug discovery”. The talk video is now available on YouTube: https://www.youtube.com/watch?v=xcEkCuJpZbw. Dr. Turon’s bio and talk abstract can be found in this blog post.

Early Poster Acceptance Round 2024

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 18 Feb 2024 23:20:16 +0000

Abstract submission for BOSC 2024 is now open! Since some people can’t get conference travel approval from their institution until they get confirmation that their abstract has been accepted for a presentation, we started offering Early Poster Acceptance last year, and we are continuing the experiment this year. If you submit your abstract by March 21, 2024, we will notify you by March 29 whether it has been accepted or not for (at least) a poster.

When you submit your abstract, you can choose to apply for a poster, or to try for a talk. If you choose talk, then after the Early Poster Acceptance round your abstract will stay in the pool for the regular review round and you will find out on May 13 whether your abstract was chosen for a talk – but you will still get early notification on March 29 that you got at least a poster slot!

After you submit an abstract in our Early Poster Acceptance round, you are free to update it in the EasyChair submission portal until the regular deadline on April 19! So, you don’t lose anything by submitting early and securing your poster acceptance.

Key dates March 21: Early Poster Acceptance submission deadline March 29: Notification of poster acceptance April 19: Regular submission deadline May 13: Notification of talk (or poster) acceptance

FAQ

Q: How do I submit my abstract for the Early Poster Acceptance round? A: The same way all abstracts are submitted to BOSC: via the ISMB EasyChair submission portal. Please see /events/bosc-2024/submit/ for instructions and submission link.

Q: Can I submit in the Early Poster Acceptance round if I want to be considered for a talk? A: Yes, though you won’t get early notification about whether your abstract was chosen for a talk. All abstracts submitted early will be reviewed for possible talk acceptance in the regular review round, and you will be informed on May 13 whether you got a talk.

Q: Will I get a full review of my submission in the Early Poster Acceptance round? A: No, you will just get “accepted for poster” or “declined for poster”. However, your abstract will get a full review in the regular round, and the reviews will be sent to you on May 13.

Q: What are the criteria for poster acceptance in the Early Poster Acceptance round? A: Please see /events/bosc-2024/submit/ for the criteria, but note that early submissions will receive a streamlined review in the Early Poster Acceptance round. They will go through a full review in the regular round.

Q: What are the possible outcomes in this Early Poster Acceptance round? A: 1. Accepted for poster (to be considered for talk in the regular round, if you requested a talk) 2. Declined (not suitable for presentation at BOSC) 3. Deferred (we can’t decide; you will need to wait for a full review in the regular round). (We do not expect many submissions to fall into category #3.)

Q: Can I submit updates to my abstract? A: Yes! After you submit an abstract (whether in our Early Poster Acceptance round or the regular round) to update it in the EasyChair submission portal until the regular deadline on April 19!

Q: Can I present a talk AND a poster at BOSC? A: In the past you could, but ISMB has instituted a new rule for 2024: a presenting author may present NO MORE THAN ONE talk or poster. If you want to present your work as both a talk and a poster, you have to do a separate poster submission with a different author. Note that this is unaffected by early submission.

Q: Are other COSIs also doing an Early Poster Acceptance round? A: Probably not, but we don’t know; you’d have to check with them. (But it was BOSC’s idea first.:-)

ISCBacademy: Gemma Turon on open source AI/ML for (antimicrobial) drug discovery

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 08 Feb 2024 17:32:56 +0000

Gemma Turon, PhD (CEO and co-founder at Ersilia Open Source Initiative) will present on March 5

BOSC and the OBF will host an ISCBacademy webinar on March 5, 2024, at 8am PST (16:00 UTC). Gemma Turon (see bio below) will speak about “Ersilia, open source AI/ML for (antimicrobial) drug discovery”.

Abstract

The Ersilia Open-Source Initiative is a non-profit organisation whose mission is to equip laboratories, clinics and universities in lower and middle income countries (LMICs) with artificial intelligence (AI) tools for infectious disease research. The goal of our mission is to strengthen the research capacity in those countries where these diseases are predominant, supporting the in-country drug discovery pipelines for neglected and infectious diseases. Since its foundation in 2020, we have collaborated with several institutions in the Global South as well as international consortiums. In this introductory talk we will present our computational approach and infrastructure, including the Ersilia Model Hub, a unified platform offering ready- to-use AI models to researchers worldwide, and how we have used it across multiple projects, offering a perspective on how AI/ML can transform drug discovery and contribute towards a more egalitarian world of biomedical research.

About the speaker

Trained as a molecular biologist, Gemma Turon completed a PhD in colorectal cancer and stem cells at IRB Barcelona in 2019, before taking a one-year break to focus on working and volunteering in the third sector. This shifted her scientific interest to global health and neglected diseases, and the existing barriers to tackle some of the most urgent health issues in developing countries. With Ersilia, she aims to explore new ways of community building and engagement in the scientific arena, at the intersection between academia, biotech start-ups and NPOs.

ISCBacademy

ISCBacademy is a series of free webinars sponsored by the International Society for Computational Biology. They are open to all, including those who are not ISCB members. ISCB members can access the webinars via the ISCB Nucleus platform: https://iscb.junolive.co/. Non-members need to register for Nucleus: https://iscb.swoogo.com/ISCBnucleus-registration

Community comment period open for potential BOSC 2024 keynotes

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 19 Jan 2024 06:48:09 +0000

We asked our community to nominate potential BOSC keynote speakers, and we were pleased with the great suggestions! In the next phase of our process, we’re giving you a chance to let us know if there is anything that makes any of the nominated individuals NOT appropriate as BOSC keynote speakers.

Our invited speaker process and rubric gives examples of some possible reasons for exclusion. If you have concerns about any of the people on our list, please let us know (with as much specificity as you feel comfortable providing) via this anonymous form no later than Thursday 2024-01-25.

And the nominees are…

Andrew I. Su
Anne Carpenter
Chris Evelo
Chris Mungall
Emma Hodcroft
Gary Bader
Gemma Turon
Heng Li
Inioluwa Deborah Raji
Laura Ación
Melanie Courtot
Noah Fahlgren
Ziad Obermeyer

After the community comment period closes, the BOSC organizing committee will draw on this list to extend invitations to potential keynote speakers. Since we cannot know in advance which speakers might accept the invitation, we may have to go beyond the list of those nominated. In that case, we would not rerun this process, but community members will always be encouraged to inform the Organizing Committee if they believe any speaker does not meet our standards.

Submit anonymous feedback

Nominate a keynote speaker for BOSC!

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 10 Jan 2024 21:30:32 +0000

We are seeking a diverse list of potential BOSC keynote speakers. We invite you, our community, to nominate people you think would be appropriate (and at least somewhat likely to accept the invitation – for example, it is extremely unlikely that we would get a ‘yes’ from a recent Nobel Laureate). Please submit your nominations here (as many as you like; you can fill out the form more than once to submit additional suggestions) by the end of the day on Wednesday 2024-01-17.

Keynote talks are a highlight at BOSC. BOSC typically bookends keynotes at the beginning and end of the conference. These invited speakers are prominent individuals or emerging leaders who are accomplished in their fields, and whose work is likely to be of interest to the bioinformatics open source community. Before 2023, the process of selecting appropriate keynote speakers was done by the BOSC Organizing Committee. Last year, we realized that making the process more consistent, fair and transparent would better align with our values of openness and inclusivity; we therefore developed an open process and rubric for choosing keynote speakers. This process worked well, so we will use it again in 2024.

Nominate a keynote speaker!

BOSC CollaborationFest 2023 Report

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 29 Sep 2023 22:08:37 +0000

CollaborationFest, CoFest for short, is a collaborative work event that has been held each of the past 13 years as a satellite event of BOSC. At these free events, held right before or after BOSC, participants gather in small groups to exchange ideas and work together on projects including but not limited to hacking. Participants were encouraged to submit their project ideas in advance to facilitate collaboration.

CoFest 2023 took place during the two days just before BOSC, which was part of ISMB/ECCB 2023 in Lyon and online. It was the first in-person edition after several online-only CoFests, due to Covid pandemics. It was hosted by Jérémy Just at the nearby École Normale Supérieure de Lyon, which provided space and infrastructure, with funding from Complex Systems Institute for lunches and coffee breaks. Free virtual machines were made available by the French Institute for Bioinformatics and the Pôle scientifique de modélisation numérique.

List of the projects submitted in advance by the participants for BOSC CoFest 2023.

CoFest brought together 29 in-person participants as well as numerous online participants, experts in fields as diverse as plant biology and personalized medicine.

We were pleased to have many local and first-time attendees participate in this edition of CoFest.

A 360° webcam, kindly lent by Elixir for the CoFest, allowed remote attendees to see the whole meeting room during work sessions.

As in previous years, CoFest participants engaged in a wide variety of projects focused on topics such as the documentation of existing software, the review and discussion of novel technologies, the improvement of existing tools, and several FAIR-related projects.

In total, the participants worked on ten different projects, with tangible accomplishments for several subtasks of these projects. In addition, cross-project discussions facilitated progress on many projects, exchanging perspectives and pointers between participants. The synergies and discussions between the various groups were remarkable.

We would like to thank the entire OBF community for maintaining the positive atmosphere that makes such events a reproducible success!

A few pictures of lunches during BOSC CoFest 2023, in the ENS gardens.

Some advances made during CoFest 2023

(Many thanks to Hervé Ménager for keeping track of the projects during the CoFest, and for his warm encouragement during all the preparation for the event!)

New features added to iCn3D protein viewer

Proposal

iCn3D is a web-based 3D structure viewer synchronizing 1D, 2D, and 3D view, e.g. https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=1TUP&showanno=1&show2d=1. The 1D sequence view shows all kinds of annotations ( e.g. domains, SNPs, etc) in tracks. This project will show the start and end positions of exons in the sequence, and show the sequence of isoforms of the protein and their exons. Thus users can clearly see the exon skipping and potentially relate the exon skipping to the protein functions.

What was done

During the CoFest, the iCn3D viewer got a new feature to show isoforms and exons as tracks with the button “Add Track” in the “Sequences & Annotations” window via the menu “Analysis > Sequences & Annotations”. One example is at https://structure.ncbi.nlm.nih.gov/icn3d/share.html?pA3pPu7LxdiuZDVX7:

Users can also predict structures from sequences using ESMFold directly in iCn3D via the menu “File > Predict by Seq. > ESMFold”. Other features of iCn3D are listed in its GitHub page: https://github.com/ncbi/icn3d.

The BLAST book from 2003 (cover).

Updating the BLAST book

Proposal

The BLAST book, by Ian Korf, was published in 2003. It provides a lot of “recipes” for Blast searches in different contexts. Since then, however, the syntax of most tools from the Blast suite has changed, with the introduction of Blast+ in 2009. The wrapper currently distributed with Blast+ to convert the old syntax (blastall) has quite limited features. My idea is to update the command examples in the book to the new syntax, explain new options, and identify places that need more in-depth updating.

The main author, Ian Korf, had been contacted in advance: he’s not against a new book about Blast, but he doesn’t want to be involved. Two hard copies of Korf’s book will be available during CoFest.

What was done

Scoping discussion on Slack (when should we contact the original publisher?),
Side-by-side option table ( old vs new options),
Practical testing of old examples from the book using the new syntax.

Future work

Write down the updated examples as a web page,
Contact O’Reilly, the publisher of the book, and see if they are interested in a new edition. In any case, the updated examples will be available to the community on a webpage (GitHub or better).

Progress on various Biopython projects

Proposal

Peter Cock will be attending remotely, but as one of the regular Biopython contributors will try to match any newcomers with suitable projects/issues. He hopes to work on migrating the Tutorial documentation from LaTeX to RST to simplify and automate it for each release (see PR 4371). See the #cofest-biopython channel on BOSC Slack.

What was done

Progress on LaTeX to RST/Sphinx conversion of Tutorial (tables, citations).
Improvements to a script dealing with big FASTQ files: speed up reads extraction (6x faster).

Future work

Try to get the converted Tutorial to build without errors.

Question to CoFest group

What file format would you prefer for the Tutorial (HTML, PDF, eBook…)?

MultiK parallelization using `Future`

Proposal

MultiK is a R package built upon Seurat that objectively selects multiple insightful numbers of clusters ( K) in a single-cell RNA-seq dataset.

However the main function of the package is very expensive both in computing and in time since it is not parallelized.

The idea would be to attempt to parallelize it using the Future package (which is already used by Seurat) in order to speed up scRNA-Seq workflows making use of it.

What was done

The first main loop (out of two) was parallelized:
- works when used locally & remotely on a small dataset,
- 10x performance for the whole function.

Future work

MultiK crashes when processing the whole dataset remotely (“ Error: Detected a non-exportable reference ('externalptr') used in the future expression”): we plan to investigate further on that,
Parallelize the second main loop of MultiK.

Make installation of Bionano tools easier

Proposal

Bionano is a technology to create optical maps from HMW DNA. One major problem is the lack of tools options for analysis since there are only tools provided by Bionano Genomics : Bionano Access (server and GUI) and Bionano Solve (analysis software).

The installation of Bionano Solve is clumsy : it uses a docker image to install dependencies. My idea is to retrieve all the dependencies used from the docker image to create a bioconda recipe in order to easily install and maintain Bionano Solve software dependencies.

What was done

Installation of currently available Bionano docker image,
Inspection of Bionano tools installation script.

Future work

Detailed list of dependencies, starting from Python / R packages and software present in the docker image,
(Bio)Conda recipe documentation exploration.

Applications of open source LLMs in bioinformatics

Proposal

This group aims to explore the applications and promotion of open source large language models (LLMs) in the field of bioinformatics. LLMs have gained popularity, and the community seeks models that offer accessibility and transparency. Strategies for collaboration and community engagement, including the use of shared repositories and benchmarking frameworks, will be discussed. Ethical considerations such as data privacy, bias, and interpretability will also be explored.

Sharing resources and ideas:

https://docs.google.com/document/d/1fxA3JCtPkScm7vXSFQqPJtgP6OEZgAwN7-o_pKtoH5c/edit?usp=sharing

What was done

Shared documentation to collect ideas and useful links:
- Tips for choosing/testing open source LLMs,
- Some ideas for applications and benchmarking of the models.

Future work

Summarize the document and merge it into the paper being prepared by the LLM group from BioHackathon Japan that will be submitted to BioHackrXiv :
- BioHackJP 2023.

FAIR Biomedical Research Software (FAIR-BioRS)

Proposal

Most would agree that making biomedical research software (code, scripts, desktop software, Jupyter Notebooks, etc.) reusable is essential to prevent duplicate effort, enable building on top of existing work, and ultimately increase the pace of discoveries and innovations for improving human health. The question then is, how do we make biomedical research software reusable? The Findable, Accessible, Interoperable, and Reusable principles for Research Software (or FAIR4RS principles) published in 2022 provide high-level instructions to achieve that. It is the result of a large-scale effort and is backed by a large community of research software developers. However, just like the original FAIR principles, the FAIR4RS principles remain aspirational and do not provide clear actionable instructions. To address this, we have established the FAIR Biomedical Research Software (FAIR-BioRS) guidelines, that provide clear, actionable step-by-step instructions for making biomedical research software reusable in line with the FAIR4RS principles. Our idea here is to discuss the current version (v2.0.0) of the FAIR-BioRS guidelines, identify if/how they can be improved, brainstorm on how they can be maintained going forward, etc. so as a community we can start adhering consistently with the FAIR4RS principles to make our software reusable and also provide clear guidelines to do so especially for the next generation of biomedical software developers.

What was done

Worked with some attendees to explore how the guidelines would apply to their project,
Scope discussion, and at least one pull request merged,
Notes from discussion available at https://etherpad.osuosl.org/p/Cofest2023-fair-BioRS,
Discussion to wrap up on the paper and plan for future outreach/communication effort.

That’s the second CoFest edition this project is worked on (already in 2022), and its outcome is now published in a peer-reviewed paper:

Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool. Bhavesh Patel, Sanjay Soundarajan, Hervé Ménager and Zicheng Hu, Scientific Data 10:557 (2023). doi:10.1038/s41597-023-02463-x

Future work

Outreach/communication effort.

Question to CoFest group

Would you use the guidelines to make your research software reusable? If not, why, how can they be improved?

Next release of Common Workflow Language

Proposal

108 proposed clarifications to the Common Workflow Language v1.2 standards need summarizing before release v1.2.1.

What was done

All done!

See:

Future work

Get these changes reviewed & merged.

Questions to CoFest group

Reviews are very welcome! (Especially by those with CWL experience)

SPARQL WR RO-Crate queries

What was done

Made SPARQL queries to answer provenance questions from ro-crate-manifest.json.

Future work

Add more queries to the list.

Question to CoFest group

How to use SPARQL queries as unit tests?

WfExS-backend changes to support `envvars` and get conformant to Workflow Run RO-Crate 0.2

What was done

Added support to describe environment variables needed by a workflow execution.
Integrated used environment variables as inputs in Workflow Run RO-Crate, using FormalParameter. There is no standard way to signal which FormalParameters are a traditional workflow parameter and which are environment variables (besides the id).
(partially implemented) Output files and directories are not using an nih URI any more.
(work in progress) Better representation of CWL workflow dependencies, so the usage of an external ontology does not appear as a “hard” dependency itself.

Our sponsors

We are grateful to all the sponsors who allowed us to host the BOSC CoFest 2023 in Lyon in excellent conditions and made it so successful:

Complex Systems Institute Rhône-Alpes École normale supérieure de Lyon Laboratoire Reproduction et développement des plantes French Institute for Bioinformatics

We would also like to apologize to all our colleagues who would have liked to attend but had holiday date constraints this summer. Keep updated for next editions!

Our suppliers

All the catering was purchased from local providers and carried by bike. They will probably not deliver abroad, but if you pass by Lyon and feel hungry, you can for sure trust them:

Main caterer for lunches: Cyril Nitard,
Baker: boulangerie Ondo-Vernin,
Cheese-seller: fromagerie Les Trois Jean,
Fruits and fruit juices: Cerise et Potiron Monplaisir (have a look at some creations).

We did our best to minimize waste, by using reusable containers for lunches and coffee breaks (including drink bottles, glasses, cups, plates, silverware…).

Coffee break

Happy participants at lunch

ISCBacademy webinar Oct 3

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 18 Sep 2023 05:31:52 +0000

Sierra Moxon to speak about “LinkML: an open data modeling framework, grounded with ontologies”

[If you missed the webinar, the video is here and the slides are here.]

BOSC and Bio-Ontologies are pleased to co-host an ISCBacademy talk on October 3, 2023, at 8am Pacific Daylight Time (15:00 UTC). Sierra Moxon (see bio below) will speak about “LinkML: an open data modeling framework, grounded with ontologies”.

Abstract

The Linked data Modeling Language (LinkML, https://linkml.io) is an open, extensible modeling framework that allows computers and people to work cooperatively to document, validate, and distribute data that is reusable and interoperable. It provides a flexible yet expressive standard for describing many kinds of data models from value sets and flat, checklist-style standards to complex normalized data structures that use polymorphism and inheritance. LinkML enables even non-developers to create data models. It is designed to allow software engineers and subject matter experts to communicate effectively in the same language, while also providing the semantic underpinnings to make data easier to validate, understand and reuse computationally. LinkML has an active and growing user community, and has seen uptake by projects including cancer data harmonization, environmental genomics, microbiome data, knowledge graph integration, ontology mappings and language profiles.

In this talk, which expands on the short talk I gave at BOSC 2023, I will describe the LinkML framework and give examples demonstrating how to use it for biological data modeling, ontology-supported validation, conversion, and serialization. I will discuss how LinkML was used to create the Biolink Model, a unifying data model that brings together heterogeneous datasets to answer novel biomedical questions. I’ll also introduce the role the Biolink Model plays in the NCATS Biomedical Data Translator project.

About the speaker

Sierra Moxon is a software developer in the Biosystems Data Science group at the Lawrence Berkeley National Laboratory. Sierra’s work focuses on designing and developing reusable software to harmonize diverse scientific research data into findable, accessible, interoperable and reproducible (FAIR) formats, with applications ranging from biomedicine to the environment.

Sierra leads the Data Modeling Committee for the NCATS Biomedical Data Translator project, which aims to accelerate the path from biomedical research to clinical trials. She is a lead developer of the LinkML data modeling framework and the LinkML-based knowledge graph standard called Biolink Model, which forms a core part of the Translator infrastructure. Additionally, she is the Data Harmonization Lead for the Alliance of Genome Resources project, and she writes software used by the Gene Ontology, one of the most widely used ontologies in biology.

BOSC 2023 Report

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 14 Aug 2023 20:24:33 +0000

The 24th annual Bioinformatics Open Source Conference, BOSC 2023, took place as part of ISMB/ECCB 2023 in Lyon, France, and online. ISMB/ECCB attracted a near-record number of attendees, with over 2100 in person and about 900 more online.

Most of the BOSC organizing committee (missing: Jessica Maia and Chris Fields)A full room at BOSC 2023

The opening session of BOSC kicked off with a welcome from chair Nomi Harris. An overview of BOSC’s parent organization, the Open Bioinformatics Foundation, was presented by OBF Board member Bastian Greshake Tzovaras.

Hervé Ménager presented the projects undertaken at the pre-BOSC CollaborationFest, a collaborative work event (including but not limited to hacking) hosted by Jérémy Just and the nearby École Normale Supérieure de Lyon, with 29 in-person participants, plus more online. In-person participants enjoyed the lavish lunches organized by and underwritten by CoFest sponsors Complex Systems Institute, ÉNS de Lyon, and Laboratoire Reproduction et Développement des Plantes (with additional support from French Institute of Bioinformatics and PSMN to provide free virtual machines to attendees).

Lunch at CoFest 2023

The first BOSC keynote was delivered by Sara El-Gebali, who spoke inspiringly about “A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration,” with case studies showing how open collaboration can strengthen inclusive scientific communities and vice-versa. For example, 95.5% of genomic research participants in GWAS are people of European heritage; this has led to the development of drugs that don’t work for most of the people in the world. Sara made many points that resonated with the BOSC audience, such as the need to revamp research reward systems to take into account open science practices, not just one-dimensional publication metrics.

BOSC 2023 keynote speakers Sara El-Gebali and Joseph Yracheta

The second day of BOSC started with a thought-provoking keynote by Joseph Yracheta (presented virtually due to a last-minute family emergency) entitled “The Dissonance between Scientific Altruism & Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution”, which examined thorny questions about the current open data environment and how it impacts American Indian / Native American communities. Joe, the founder of the Native BioData Consortium, discussed our ethical responsibilities as people who work on open source tools and open bioinformatics research to ensure that indigenous data is ethically sourced and used.

Beyond keynotes, BOSC had seven themed sessions with talks chosen from submitted abstracts, including Translational bioinformatics; Workflows; Data analysis and visualization; and a new BOSC session on AI/ML. The FAIR and Open Data session set the stage for the closing panel, while a session on Open Science reflected the breadth of BOSC topics, including talks relating to open infrastructures and ecosystems, citizen science, training, outreach, and reproducibility. A well-attended joint session brought together BOSC and the Bio-Ontologies COSI for talks relating to standards (including, of course, ontologies) and frameworks for open science. 49 posters were presented at an overflowing poster session. The complete BOSC schedule is available at /events/bosc-2023/bosc-2023-schedule/.

BOSC 2023 participants

BOSC 2023 closed with a panel on Open and Ethical Data Sharing that expanded upon some of the points made by the two keynote speakers, including the observation that there’s no published ethical code for bioinformaticians, and the idea that we individually, and our scientific societies, can be advocates for better practices in ethical data sharing. Along with moderator Monica Munoz-Torres, the panel featured our two keynote speakers (Sara El-Gebali and Joseph Yracheta) along with Verena Ras of the University of Cape Town and Bastian Greshake Tzovaras, who’s a leader in organizing citizen science projects.

Panelists Verena Ras, Sara El-Gebali, Bastian Greshake Tzovaras, and Monica Munoz-Torres

Two well-attended evening events got BOSC participants mingling: a dinner at a casual food court, and a jam-packed party hosted by our sponsor GigaScience (see their ISMB/BOSC writeup at http://gigasciencejournal.com/blog/going-large-language-models-at-ismb2023/).

Julie McMurry and her dog at the GigaScience party

Speaking of sponsors, we are grateful to our BOSC 2023 sponsors: Platinum Sponsor Chan-Zuckerberg Initiative, and Silver Sponsors GigaScience, Genevia, and Software Sustainability Institute. With their help, we were able to offer free registration to 15 BOSC participants, 13 of whom are from groups that are underrepresented in our communities.

BOSC 2023 Chair Nomi Harris thanking Platinum Sponsor, the Chan-Zuckerberg Initiative

We hope to see you (in person in Montréal, Canada, or online) at BOSC 2024, which will be part of ISMB 2024 from July 12-16, 2024!

Spotlight on diversity: Jenea Adams

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 10 Jul 2023 21:25:30 +0000

Diversity, inclusion and accessibility (also known as Diversity, Equity and Inclusion, DEI) are a major part of BOSC’s mission and core values, and we pursue these goals in multiple ways. BOSC 2022, for example, included a panel on Building and Sustaining Inclusive Open Science Communities, with panelists who not only were experts on the topic but also themselves belong to various groups that are typically underrepresented in our community. And with generous support from our sponsors, each year we provide free registration to 10-20 BOSC participants as part of the OBF Event Fellowship program), which aims to increase diverse participation at events related to open source bioinformatics and open science.

Jenea Adams, a Presidential Ph.D. Fellow in Genomics and Computational Biology at the University of Pennsylvania, epitomizes our commitment to fostering diversity and inclusion in the open source bioinformatics community. Jenea served as one of the panelists on the Building and Sustaining Inclusive Open Science Communities panel, and her registration fee and travel expenses were covered by an OBF Event award.

Jenea commented, “BOSC not only showcased the remarkable strides made in computational biology but also emphasized the power of collaboration and inclusivity. Through my participation in the panel on Building and Sustaining Inclusive Open Science Communities, I witnessed the true potential of harnessing diverse perspectives to drive innovation and create a sustainable foundation for open science.”

In addition to her PhD studies, Jenea is the Founder and Executive Director of The Black Women in Computational Biology Network, which aims to amplify the voices and foster community among Black women in computational biology. Jenea observed, “Having support to attend BOSC 2022 made it possible for me to connect with new and familiar faces in person while providing a platform to share the work and progress of The Black Women in Computational Biology Network.”

Jenea summed up her thoughts about BOSC – thoughts we strongly agree with – as follows: “This conference reinforced the notion that by being intentional about accessible science and sharing knowledge, resources, and ideas openly, we can collectively advance the field of computational biology and pave the way for transformative discoveries.”

We thank Jenea for contributing her knowledge and community-building spirit to BOSC, and wish her the best in all her endeavors!

Above: Panel on Building and Sustaining Inclusive Open Science Communities: Jason Williams (moderator); panelists Jenea Adams, Monica Munoz-Torres, Rachel Torchet, and Gary Williams; BOSC Chair Nomi Harris

Hannah Wei webinar video now available

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 17 Mar 2023 23:50:15 +0000

On March 14, 2023, we held a webinar (hosted by ISCBacademy) about “Re-Thinking the Patient’s Role in a Learning Health System: Lessons from the Patient-Led Research Collaborative” presented by Hannah Wei, co-founder and technologist at the Patient-Led Research Collaborative. See the webinar announcement for a full description.

BOSC organizing committee member Monica Munoz-Torres introduced Ms. Wei and fielded a lively Q&A session. The webinar recording is available on YouTube at https://youtu.be/M2vAotWKd_Q.

The ISCBacademy is a series of free webinars offered by the ISCB, which runs the annual ISMB conference, through the ISCB Communities of Special Interest (COSIs), which include BOSC/OBF. Each COSI gets two webinar slots per year, so watch for our next one in fall 2023!

BOSC Early Poster Acceptance

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 09 Mar 2023 17:57:56 +0000

ISMB/BOSC is around the corner! We can hardly wait for the abstracts to start pouring in!

We realize that some people can’t get conference travel approval from their institution until they get confirmation that their abstract has been accepted for a presentation.

To help you, this year we have decided to offer Early Poster Acceptance: if you submit your abstract by March 31, we will let you know by April 6 whether it has been accepted or not for (at least) a poster. (The regular abstract submission deadline is April 20, and authors who submit in that round will be informed of poster/talk acceptance on May 11.)

When you submit your abstract, you can choose to only apply for a poster, or to apply for a poster and a talk. If you choose poster+talk, then after the Early Poster Acceptance round your abstract will stay in the pool for the regular review round and you will find out on May 11 whether you got a talk slot.

Ready your keyboards, and good luck!

Key dates March 31: Early Poster Acceptance submission deadline April 6: Notification of poster acceptance April 20: Regular submission deadline May 11: Notification of talk and/or poster acceptance

FAQ

Q: How do I submit my abstract for the Early Poster Acceptance round? A: The same way all abstracts are submitted to BOSC: see /events/bosc-2022/submit/ for instructions and submission link.

Q: What are the criteria for poster acceptance in the Early Poster Acceptance round? A: Please see /events/bosc-2022/submit/ for the criteria, but note that early submissions will receive a streamlined review in the Quick Check round. They will go through a full review in the regular round.

Q: What are the possible outcomes in this Early Poster Acceptance round? A: 1. Accepted for poster (to be considered for talk in the regular round, if you requested a talk) 2. Declined 3. Deferred (we can’t decide; you will need to wait for a full review in the regular round). (We do not expect many submissions to fall into category #3.)

Q: Can I present a talk AND a poster at BOSC? A: Yes! In fact, all abstracts accepted for talks are also invited to present a poster on the same topic. This is unaffected by early submission.

Q: Are other COSIs also doing an Early Poster Acceptance round? A: We don’t know; you’d have to check with them. (But it was BOSC’s idea first.:-)

ISCBacademy webinar on Patient-Led Research

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 07 Mar 2023 10:53:00 +0000

Date and Time: Tuesday, March 14, 11am EDT/ 15:00 (not 16:00!) UTC Location: Online webinar hosted by ISCB and free to the public. (Video now available at https://youtu.be/M2vAotWKd_Q) Speaker: Hannah Wei, co-founder and technologist at the Patient-Led Research Collaborative Topic: Re-Thinking the Patient’s Role in a Learning Health System: Lessons from the Patient-Led Research Collaborative

The ISCB, which runs the annual ISMB conference, is offering a series of ISCBacademy webinars hosted by the Communities of Special Interest (COSIs), which include BOSC/OBF. These webinars are now open to the public; you’ll just need to create an ISCB Nucleus account to register for the webinar.

So often, a patient’s role in research has been limited to the donor of data and receiver of care, limiting the possibilities in between for participatory methodologies and open science collaboration.

This webinar will be a case study of the patient-led research model. We will explore how the model was formed under the context of those with COVID-19 developing their own research capacity to study Long COVID, or Post-Acute Sequelae of COVID (PASC). We will present the levels of patient-involvement, data ownership and access principles, and accommodations for disabled contributors from our community. We will further discuss how patient-generated data can guide research direction and inform research hypotheses, while patients’ lived experiences, experiments and own research can enrich a learning health system. We will suggest ways to incorporate patient-led research models into open science innovations.

The talk will be delivered by Hanna Wei, a patient-researcher, co-founder and technologist at the Patient-Led Research Collaborative, a multi-disciplinary, patient-run organization dedicated to placing patient voices at the forefront of Long COVID research.

Hannah Wei is a co-founder at the Patient-Led Research Collaborative, an international organization of Long-COVID patient-researchers and advocates at the forefront of the Long COVID patient-led movement.

Since the beginning of the pandemic, PLRC has brought together an interdisciplinary team of patients with backgrounds in medicine, neuroscience, participatory design, public policy, cognitive science, research engineering, data science, biostatistics, virology, psychiatry, neurology, pediatrics, and social epidemiology. PLRC has collaborated with the Long COVID taskforce at the WHO, CDC and co-authored over a dozen papers, including the paper on Characterizing long COVID in an international cohort: 7 months of symptoms and their impact published in the Lancet.

Hannah’s background is in computer science and leading data-driven products for the technology industry. Before the pandemic, Hannah was running field research in frontier communities of West Africa and Southeast Asia for product innovation teams at Fortune 500 tech companies. She became a Long COVID patient after getting infected on an airplane in March 2020. Since then, she has dedicated her efforts to running projects PLRC and innovating on the patient-led research model.

Register for the free webinar

Comment period on potential BOSC 2023 keynote speakers is now open

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 10 Feb 2023 22:44:40 +0000

We asked the community to nominate potential BOSC keynote speakers, and we were pleased with all the great suggestions! Now it’s time for the next phase of our process: we’re giving the community a chance to let us know if there is anything that makes any of the nominated individuals NOT appropriate as BOSC keynote speakers.

Our invited speaker process and rubric gives examples of some possible reasons for exclusion. If you have concerns about any of the people on our list, please let us know (with as much specificity as you feel comfortable providing) via this anonymous form no later than February 16, 2023.

The nominees (in alphabetical order by first name) are…

Anne E. Carpenter (Broad Institute)
Bérénice Batut (University of Freiburg / Open Life Science)
Emma Hodcroft (University of Bern)
Ishwar Chandramouliswaran (NIH)
Joseph Yracheta (NativeBioData)
Kevin Matthew Byrd (University of North Carolina, NIH/NIDCR, and the American Dental Association Science & Research Institute)
Kizzmekia Corbett (Harvard T.H. Chan School of Public Health)
Laurie Goodman (GigaScience)
Maria Nattestad (Google Health)
Mark Robinson Rechavi (University of Zurich and Swiss Institute of Bioinformatics)
Meag Doherty (National Institutes of Health)
Michael R. Crusoe (Common Workflow Language project)
Nico Matentzoglu (semanticly)
Nicolás Palopoli (University of Quilmes, Argentina)
Sara El-Gebali (SciLifeLab Data Centre, FAIRPoints)
Sofia Forslund (ECRC (MDC & Charité joint center), Berlin)
Stephen Klusza (Clayton State University)
Susanna Sansone (University of Oxford)

After the community comment period closes on February 16, the BOSC organizing committee will draw on this list to extend invitations to potential keynote speakers. Since we cannot know in advance who will accept the invitation, we may have to go beyond the list of those nominated. In that case, we will not rerun this process, but community members are always encouraged to inform the Organizing Committee if any speaker does not meet our standards.

Nominate a keynote speaker for BOSC 2023!

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 02 Feb 2023 06:06:58 +0000

BOSC usually includes two or three keynotes. We want these invited speakers to be prominent individuals or emerging leaders who are accomplished in their fields, and whose work is likely to be informative and of interest to the bioinformatics open source community. Please see our invited speaker rubric for more information about our keynote speaker selection process and criteria.

We would like to assemble a diverse list of potential BOSC 2023 keynote speakers. We invite the community to nominate keynote speakers using this form by February 9.

We seek candidates who:

Work on topics relevant to the bioinformatics research community Can contextualize their work with the open source bioinformatics community Have gained acclaim in their field Can inspire the BOSC community with new ideas and/or challenge them to think deeply about new topics Offer diversity in terms of gender, ethnicity, or geographical location

Please submit your keynote speaker nominations by 2023-02-09!

Crowdsourced highlights from BOSC 2022

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 16 Aug 2022 00:08:42 +0000

Going home after attending BOSC was a little bittersweet. It’s my favorite conference because it brings together such a welcoming group of people, and the lineup of talks typically offers a great balance of technical learning and community-building insights. So on my flight home, I was coasting on dopamine from the good times, but also getting a little sad that it was over for this year. With the help of a few fellow BOSC enthusiasts (special shout-out to Nomi Harris for the event summary notes, photos and help recruiting contributors), I put together this little recap of the conference, with highlights and personal accounts contributed by a number of other participants. I couldn’t fit everything people shared into the blog post, but you can find the full quotes in the original google doc.

The 4-1-1 on BOSC 2022

If you’re not already familiar with it, BOSC stands for Bioinformatics Open Source Conference, and we just completed the 23rd edition — BOSC 2022 — as a “COSI” track, or Community Of Special Interest, within the ISMB meeting of the International Society for Computational Biology (ISCB). It was a hybrid conference, with the in-person component hosted in beautiful Madison, Wisconsin (USA). Presenters are encouraged to publish their slides and/or posters as part of the BOSC collection on F1000 Research. This year’s BOSC included two joint keynotes with the Education and Bio-Ontologies COSIs, which multiple people highlighted as some of their favorite parts of the conference. Given the overlaps in terms of interests and methodologies between these COSIs, I thought it was especially great that the Education COSI itself took place the day before the BOSC COSI. To my delight I was able to catch a number of their talks without having to make tough track-preference decisions. (I loved to see how many people are creating portable materials using Jupyter Notebooks, in some cases with the explicit goal of distributing them on the cloud.)

Day 1: Education, standards, tools and more

The first day of BOSC proper kicked off with a welcome from chair Nomi Harris and an overview of BOSC’s parent organization, the Open Bioinformatics Foundation, by Chris Fields, who highlighted some opportunities to get involved with the OBF. I may have volunteered to be the new OBF Newsletter editor; you’ll know it’s for real if I ever manage to get the post-BOSC newsletter out!Next was a joint keynote (BOSC/Education COSI) by Jason Williams entitled “Riding the bicycle: Including all scientists on a path to excellence”. Jason discussed principles for making short-format training (aka “bootcamps”) more effective and persistent. Next was a joint keynote (BOSC/Education COSI) by Jason Williams entitled “Riding the bicycle: Including all scientists on a path to excellence”. Jason discussed principles for making short-format training (aka “bootcamps”) more effective and persistent. Let me do you a big favor here and point you to a recorded version of the same talk that Jason posted on Youtube, because googling “jason williams riding the bicycle” will not give you the results you’re looking for (unless you’re into stories about cycling for charity — but it’s a different Jason). You should also check out Jason’s blog post on lifesciencetrainers.org, which summarizes the concept of the “Bicycle Principles” and calls for community involvement. As Hilmar Lapp commented, “Jason Williams set the perfect tone with his keynote: trying to be as professional as you can about whatever your pursuit is matters, for yourself and those who your work affects, and don’t ever forget to regularly laugh and have fun while doing it. A timely reminder after both got increasingly crowded out by a pandemic of other concerns.“After the keynote, BOSC had themed sessions about “Standards and Practices for Open Science”, “Analysis tools & approaches”, “Data access and visualization”, and “Standards for Open Science”. There were too many great talks to mention all of them, but I will say I was excited to see that several talked explicitly about leveraging GA4GH standards. Brian Repko, echoing this sentiment, called out the Phenopackets schema in particular, which provides a human and machine-readable way to structure phenotypic data about a patient or individual. As Monica Munoz-Torres announced joyfully in her talk, Phenopackets version 2.0 was released earlier this year as a major upgrade to the original schema, which represents the culmination of a huge amount of work — so congratulations to the Phenopackets team on their achievement!During the lunchtime poster session, participants checked out 42 BOSC posters and learned about a variety of bioinformatics tools and initiatives. Connections were made, cards and emails were exchanged, and perhaps next year we’ll hear talks about new collaborations that were sparked here.

Day 2: Workflows, ontologies and inclusion

The second day of BOSC started with a session about “Workflow Management Systems”, including a number of talks related to CWL, aka the Common Workflow Language that grew out of a BOSC CodeFest in 2014. In that same session, I gave a talk about WDL, the Workflow Description Language that grew out of the Broad Institute’s GATK pipeline engineering group and is now stewarded by the OpenWDL community project. Check out my blog post and recording (+ slides on F1000) if you’re interested in a method for deciphering any WDL workflow handed to you by a perfect stranger. The workflows session was delayed by some technical issues, but session chair Hervé Ménager kept his cool throughout the back and forth with the local A/V team. Hervé himself commented “Despite the many technical issues we had with running the Workflow Management Systems session of BOSC, I was really impressed with the patience and understanding of the audience and the speakers, who all went out of their way to try and keep us on track, so that every presenter could get the opportunity to speak.” And it’s true, the BOSC crowd stayed pretty chill when things went, uh, pear-shaped. Ahem. The session after lunch was a joint session with the Bio-Ontologies COSI, featuring a keynote by Melissa Haendel, “The open data highway: turbo-boosting translational traffic with ontologies.” Melissa discussed ways to bridge the translational divide by leveraging semantics and robust ontologies — with the caveat that in most cases, if you think you need to invent a new ontology, you actually don’t. Her talk was very well received and highlighted by multiple people as a conference favorite; though for my money, Brian Repko said it best: “My internal notes for Melissa’s keynote literally says ‘HOLY COW THIS IS GREAT’". BOSC ended with a panel entitled “Building and Sustaining Inclusive Open Science Communities” moderated by Jason Williams, with a fantastic roster of panelists known for their work advancing diversity and inclusion. Being themselves members of groups that are underrepresented in our field, they spoke eloquently of challenges and opportunities that we can all tackle as a community. As Nicole Vasilevsky noted, “Jason did a great job facilitating and the discussion was very thought provoking”. Among key takeaways, “the panel reminded us that we all have much more agency than we think in making spaces welcoming to everyone who wants to enter,” reflected Hilmar.The high level of enthusiasm for the panel was palpable both during the event and in the comments we collected afterward. I read this as a clear sign that the majority of the participants genuinely care about inclusion, which in itself suggests that this community is on the right track. As a long-time community member, Nomi commented, “I’m pretty sure this was the first BOSC, maybe even the first ISMB, where one of the attendees was a [service] dog. Which of course is great regardless, but more seriously, it represents tangible progress in our efforts to make BOSC more inclusive and accessible.” Early feedback from newcomers certainly seems encouraging. “As someone who got into bioinformatics just before the pandemic, it was great to finally be around ‘my people’” wrote Bhavesh Patel, first-time BOSC participant, adding “All the talks were great, but I especially loved the panel discussion on diversity and inclusion. It is a wonderful initiative and I hope it becomes a frequent occurrence at all conferences.“And that is a really nice note to end a conference on, isn’t it?

Add-on #1: Scheduled dinners

But wait, there’s more! BOSC folks are a surprisingly social group, for a bunch of bioinformatics nerds (no offense y’all). So in addition to the daytime conference programming, the organizing committee had organized (as they do) two outdoor dinners for BOSC participants to get together and keep the conversations going. Just about everyone who attended the dinners raved about how great they were, to a point that might be borderline obnoxious to anyone who didn’t go; but I can tell you from first-hand experience it’s all justified. And to be clear, it was “pay-your-own-way” (aka BYO wallet), so the enthusiasm wasn’t about getting a free meal on the dime of some corporate sponsor — it was all about the friendly company and congenial atmosphere. “The dinner was […] a great opportunity to interact with other participants in a laid-back setup,” wrote Bhavesh. As Nomi noted, we were very lucky with the weather, so we were able to hang out, dine and socialize on the outdoor patios until well after nightfall. There was definitely a sense that this felt especially good because we had all been deprived of this kind of interaction for over two years. Nomi shared that for her, “the best moments [of the conference] were not the talks (though of course those were great!) but the personal interactions that I have missed so much the last few years.” As Hilmar pointed out, “The BOSC socials and CoFest showed how much it is worth even to just be together again. Not that we didn’t know, but knowing and understanding are not always the same thing.” This sentiment, which almost everyone who was there in person echoed in some way, does raise the question of how we can provide quality social interaction for those in our community who cannot yet come back to in-person events — or for those who have never been able to do so due to the circumstances of their lives or their geography. As Tazro Ohta remarked eloquently, “What I learnt during the pandemic was: The power of online meetings that connect people and the power of time differences that prevents me from attending them helding in a western time zone.” That is a topic I expect we will have to explore as we iterate on the hybrid event models that are likely to shape the future of scientific gatherings.

Add-on #2: Collaboration Fest (CoFest)

Ok we’re almost done, but I still have to tell you about CoFest, a two-day “collaboration fest” that takes place informally after the conference, in which a subset of BOSC participants stick around for a couple of days to work together on some projects. Those projects can involve coding, but also documentation or other non-coding activities, so anyone can contribute regardless of their technical background. In fact, for my CoFest project, I started working on the upcoming OBF newsletter issue. You can see the full set of projects that were undertaken at this year’s CoFest in the status update slide deck. Out of the six projects that were proposed this year, three were worked on by remote CoFest participants while the other three were worked on by the in-person group. Those of us who attended CoFest in person worked at the Madison Public Library on the first day, and we had ourselves a nice little sunset social on the waterfront with beer and brats. On the second day, we relocated to the airport to accommodate the group’s wide range of departure times, and “cofested” variously from the pre-security lounge, from our respective gates, and from the air, because sometimes it’s just that hard to let a good thing go. In-person CoFesting from the Madison airport lounge. Don’t judge me, I only took off my mask for the photo! In my experience, CoFest is as much about community building as it is about making progress on a project. As Bhavesh, our BOSC first-timer who also attended CoFest, observed, “The cofest was my favorite part as it provided a very informal setting to get to know all the participants on a personal level. It also gave me a unique opportunity to discuss personally with experts of the field and get one-on-one feedback on my work.” In fact, he added, “I would highly recommend anyone new to BOSC to join the cofest!“So don’t miss your opportunity to get in on the fun, and make sure to add BOSC to your must-go list of conferences for next year (whether remotely or in-person). BOSC 2023 will be part of ISMB/ECCB 2023 and will be held in Lyon, France between July 23-27 (exact dates TBD).I hope to see you there/onscreen!

Festus Nyasimi: Journey to the ISMB/BOSC 2022 conference

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 01 Aug 2022 15:45:40 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Festus Nyasimi, A co-founder and lead of the Bioinformatics Hub of Kenya Initiative (BHKi), attended the ISMB/BOSC conference 2022, supported by this fellowship granted to him in the first round of 2022.

In mid-May, I attended a different conference where I shared my experience with community building in the bioinformatics space with one of the attendees. I had a chance to brief them about the BHKI community we are building and growing in Africa. Immediately they suggested I should check out the ISMB/BOSC conference happening on July 11th - 14th, 2022.

I looked into it immediately, and I was lucky to find the late abstract submission round was still on. I sent in an abstract on our community, its activities, and the progress we have made in the region. A few weeks later, our abstract was strongly accepted for poster presentation and iced up with free registration. Bam!!! This felt like a Lebron James slam dunk or Steph Curry swish three point shot. Never felt this happy to go share our work with a larger bioinformatics community.

In the happy moment, the rush to plan for the conference set in; this included travel, accommodation and misc stuff. The rest of the team and I worked on the presentation alongside our training activities; this is one amazing team. Considering we are a young and growing community mostly running training through volunteering and small grants to cater for the training, we had to find a source of funding to cater for the conference fee and that’s where the OBF Event fellowship showed up perfectly. Honestly, I least expected this but I didn’t discount myself and gave it a shot; I always tell myself, “ if I don’t knock, I will never know the answer”.

Fast forward, here I am at the conference; I got to attend some sessions i.e. BioInfo Core, NetBio, Varl, MLCSB and Educational COSI, where I learnt many new skills in Bioinformatics the BOSC track started. Some of the things I learned I will propose to the organizing team we develop tutorials for the community to learn from. The opening day of BOSC was the peak of the conference for me; I had an opportunity to learn more about open-source software, how to efficiently contribute to ongoing projects and how to help communities grow. I also had a chance to join the GA4GH VRS hackathon at the conference. I had a good opportunity to represent the BHKI community on what we are doing and received great responses from attendees who visited my poster. The light was shining on our community; I hope the spotlight will be on and attract more collaborators to help us achieve our mission of a collaborative and inclusive hub.

Some of the cool people I meet at BOSC: panelist Jenea Adams and keynote speaker Jason Williams.

I learned how to advocate for our community to grow well towards achieving Diversity, Equity and Inclusion (DEI) goals; these are necessary for a strong, welcoming and collaborative community. Interacting with attendees at the conference provided me with an opportunity to learn more about leadership and how to be a good leader from a different perspective. I look forward to keeping in touch with other communities to grow further collaborations, especially in community empowerment.

Generally, the whole conference turned out to be the best one I have attended in many months through the pandemic, and I am so thankful to OBF, all organisations and team members who made it possible for me to attend the conference. Looking forward to more of these sweet moments.

This Twitter post got my notifications blowing a trumpet! While you are here, check out the BHKI website and Twitter we have some cool stuff. :)

Post-BOSC CoFest will be online

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 09 Jun 2022 18:31:46 +0000

’ello Co-Fest Friends!

After failing to find a good spot for an in-person CoFest, we decided to have the CoFest remotely! I was really excited to meet you all at this event (and have you all meet each other) in the real world, but we’ll have to settle for doing that at BOSC (for those who are there).

By all means, don’t let this stop your in-person innovations! Want to meet up and work at a café? Do it! Hotel room? It’s your room! Get some of your newest friends together and collaborate!

In order for that to happen, I’d LOVE (and so would others) to see what the projects are planning to be this year. If you are looking to help a project OR lead one, please add your name to the participation spreadsheet and your project idea to The Slides!

We’ll put together an agenda in the #cofest channel of the BOSC Slack (which everyone should join) and make that our main point of communication moving forward.

Thank you all for taking part and increasing the spirit of collaboration!

–Thomas Schlapp, CoFest 2022 organizer

CollaborationFest 2022

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 17 May 2022 18:53:30 +0000

Guest post by Thomas Schlapp, CoFest organizer

This year we’re looking to have another post-BOSC CoFest! Last year (my first year being involved in BOSC at all) showed me just how collaborative and innovative this community can be. I’d absolutely LOVE to see more of it again. Last year we saw six very fascinating projects see progress (look them over HERE!). Let’s see if we cannot do just a few more in the name of innovation and collaboration!

CoFest 2022 will take place the two days after BOSC/ISMB: July 15-16, 2022. We are trying to determine whether there is sufficient interest in holding the CoFest in person in Madison, Wisconsin; if not, it will be virtual.

Please please please REGISTER if you want to be a part of this awesome community remote or on-site! Do you have a project to add? Great! Are you alone but want to help in some way? Equally awesome! Head over to this set of slides ( Submissions!) and add yourself or your project!

Thank you again BOSC community for allowing me the opportunity to help CoFest manifest.

BOSC and Bio-Ontologies: Even better together!

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 02 Mar 2022 04:52:45 +0000

We are excited to announce that BOSC and Bio-Ontologies will join forces for part of a day at ISMB 2022. The joint session will include talks chosen from abstracts submitted to BOSC or Bio-Ontologies, plus a keynote speaker who is well known in both the ontology and open science communities!

BOSC and Bio-Ontologies are two of the longest-running COSIs (Communities of Special Interest) at ISMB: BOSC started in 2000 and Bio-Ontologies in 1998. Bio-Ontologies focuses on the FAIR development and application of ontologies and other Linked Open Data resources and the organization and dissemination of knowledge in biomedicine and the life sciences; BOSC covers the full spectrum of open source, open science, open data and open standards in the life sciences.

You can submit relevant abstracts to either BOSC or Bio-Ontologies (please do not double-submit the same abstract); the Program Chairs of both COSIs will consider appropriate abstracts for the joint session.

Both BOSC and Bio-Ontologies will take place July 13-14, 2022. The time and date of the joint session will be announced in May.

Watch the recording of the ISCBacademy webinar on growing open source communities

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 23 Feb 2022 08:27:54 +0000

Yesterday we hosted the OBF/BOSC contribution to the ISCBacademy webinar. Our former OBF-board member and Open Life Science co-lead Yo Yehudi presented how internship programs such as Google Summer of Code or Outreachy can be a great way to grow your open source community. If you missed the event, you can now watch the recording on YouTube.

Lalit Narayan, who is an undergraduate student at the Indian Institute of Technology Mandi, was a first-time webinar attendee:

“This was my first time attending a webinar from OBF and I enjoyed it. Yo was a really great speaker and it was fun to get guidance from them. I had done industrial internships in the past but not any formal research internships. I really liked the idea of getting connected to like-minded people and working together in a team to work on an interesting research idea. In a team environment we learn from peers and spend time together which eventually leads to a great network.”

ISCBacademy webinar Feb 22: Yo Yehudi

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 20 Jan 2022 22:12:00 +0000

Date & Time: Tuesday, February 22, 2022, 15:00 UTC / 11am EDT

Location: online webinar hosted by ISCB

Speaker: Yo Yehudi, Open Life Science (former OBF board member and Google Summer of Code admin & mentor)

Topic: Growing open source communities with internships

The ISCB, which runs the annual ISMB conference, is offering a series of ISCBacademy webinars hosted by the Communities of Special Interest (COSIs), which include BOSC/OBF. These webinars are free to ISCB members.

If you are not an ISCB member but would like to register to attend this webinar, and the fee (which ranges from $5-$135) is a barrier, please fill out our application for a fee waiver.

Building communities for your open source computational tooling requires more than just technical expertise, and often isn’t as straightforward as building the tool itself. Having a community of contributors and users can make a big difference in many ways - additional community members will spot opportunities and bugs in your code that previously you didn’t notice, and may be able to offer unique skill sets to your team.

One effective way to grow your community can be via internships. Programs such as Google Summer of Code and Outreachy offer the chance to work with interns for 6-12 weeks, working on individual supervised projects whilst getting paid for their work.

This webinar will cover the ins and outs of participating in internship programs like this, from the perspective of a mentoring organisation. Topics will include:

1. Getting started with internship programs - finding mentors and defining a set of projects

2. Time commitments for mentors, before the application period and after interns are selected.

3. Funding for internship programs! (It’s not as tricky as you may fear - others handle this bit!)

4. Keeping interns engaged during the program and bringing them in as long-term contributors afterwards.

This webinar will be run by Yo Yehudi, who has been a mentor and organisation administrator for interns in GSoC and Outreachy since 2017, supervising over 35 interns for various open source organisations, and who co-leads Open Life Science, an organisation dedicated to training open research community builders.

ISCBacademy webinar: Open Sourcing Ourselves - Together (Mad Price Ball)

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 10 Sep 2021 11:19:00 +0000

The ISCB, which runs the annual ISMB conference, is offering a series of webinars hosted by the Communities of Special Interest (COSIs), which include BOSC/OBF. These webinars are free to ISCB members.

The first BOSC/OBF ISCBacademy COSI webinar will take place on Tuesday, September 14, 2021, at 15:00 UTC / 11am EDT, and will feature Mad Price Ball of the Open Humans Foundation speaking about “Open Sourcing Ourselves - Together.” Before Dr. Ball’s talk, BOSC 2021 Chair Nomi Harris will give a brief overview of the OBF and BOSC.

If you missed the webinar, you can watch the video on YouTube: https://www.youtube.com/watch?v=vjMb19NxjdM

Open Sourcing Ourselves - Together

Mad Price Ball (Open Humans Foundation)

September 14, 2021 at 15:00 UTC / 11:00AM EDT

ABSTRACT: “Open source” refers to the practice of making software freely available, re-usable, and adaptable. We might also ask: how can we apply “open source” to understanding ourselves as humans – our genomes, health, or behavior? While navigating concerns about privacy and consent, the principles of “open” should also prompt us to consider what we can do to enable others. How can we make it more “open” for people to research themselves? Open source communities have come to understand that it takes more than just sharing code: it requires building a community. These same principles also apply to individual and collective research about our health. Drawing on my work with the Personal Genome Project and Open Humans, I share insights and lessons I’ve learned in efforts to collect, share, and analyze our personal data to better understand ourselves.

BIO: Mad Price Ball is Executive Director and President of Open Humans Foundation and co-founder of Open Humans, and Affiliate Faculty at the Center for Research and Interdisciplinarity (CRI). Their work focuses on enabling people to access and use their health and personal data. They explore methods for sharing tools, ideas, and data to advance individual understanding, collective empowerment, and research. This work occurs through Open Humans and its associated nonprofit, and with the Peer Produced Research Lab at the CRI. Mad’s past experience and research has included work in genomics and biotechnology, bioethics, digital technology and advocacy, as well as participatory and participant-centered research. More about Mad

Ariel Mundo Ortiz: My participation at BOSC 2021 sponsored by the BOSC-OBF Event Support

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 08 Sep 2021 02:43:46 +0000

The BOSC-OBF 2021 Event Support Fund was awarded to Ariel Mundo Ortiz, a researcher from the University of Arkansas, to participate in BOSC 2021, an annual conference hosted by the Open Bioinformatics Foundation (OBF). Based on the OBF Event Fellowship program, this fund aimed to facilitate the participation of diverse researchers from historically underrepresented groups at BOSC to help wider awareness and adoption of open source bioinformatics practices in the biological research community. Find more information here.

A while ago I came across a Twitter post that mentioned the Bioinformatics Open Source Conference (BOSC). A quick Google search took me to the BOSC website, and I was thrilled to see that one of the core concepts of the conference was to promote open science. Personally, I have been working over the last year to make my work reproducible and accessible, and the fact that BOSC provided talks and workshops focused on open science sparked my interest; I decided that although I did not have material for a presentation, I still wanted to attend the conference.

Fortunately enough, BOSC offered this year the BOSC-OBF 2021 Event Support Fund, with the aim of increasing the participation of members from groups otherwise underrepresented in BOSC. I suspected the number of applications for the Support Fund was going to be high, but nonetheless, I decided to submit my own application.

On July 10th, I received an email notifying me about my successful application! That was excellent news, and now I was sure I would be able to attend the event. One personal challenge with the Conference this year was the time zone; all the sessions started at 5:30 am! (In my time zone).

Day 1

The challenge of time zones quickly became a minor thing after attending the first keynote session by Dr. Christie Bahlai (from Kent State University) on July 29th. Her keynote was titled “Significant heterogeneities: Ecology’s emergence as open and synthetic science” and it covered the historical background of Ecology, and how significant changes over the last two decades have moved the focus of the field, enabled Dr. Bahlai and other researchers to conduct research that is grounded in collaboration and openness.

Her keynote resonated deeply with me; I could see how her path was similar to my own academic path. For instance, trying to analyze noisy data gathered through my research (that never looks like the “example data” from statistical books) was challenging. I was inspired by her talk, and it reinforced in me the desire to make my future work open and to continue to refine my statistical armamentarium.

Day 2

The keynote for the second day of BOSC 2021 was delivered by Dr. Thomas Hervé Mboa Nkoudou (from the African Institute of Open Science and Hardware) titled “Contribution of the maker movement to biotechnology in Africa: An open science perspective”. This keynote covered the democratization of biotechnology in Africa, and how the maker movement (a community-based movement that democratizes access to tools and technologies) has proven successful by promoting Biomakerspaces where African researchers can replicate existing protocols and locally produce enzymes, for example. This keynote was very interesting to me because it allowed me to appreciate a different perspective of the open science movement and the impact that reproducible research has in other parts of the world.

That day I was also able to attend the Sessions on Visualization and Translational Bioinformatics. The talk “Robust variant interpretation in precision oncology using a graph knowledge base” by Caralyn Reisle (UBC) was a talk I enjoyed very much, as it emphasized the use of graph-based knowledge to enable the discovery of molecular pathways in cancer; this talk made me better understand the importance of the use of big data to treat and diagnose cancer, which I think will become extremely important in the future.

Despite the challenges of 2021, and not being able to travel much, I feel BOSC 2021 was a wonderful experience. It allowed me to interact with people from around the world that believe that openness is a central theme in science, and I was able to learn about new tools, statistical analyses, and to get a better understanding of where the open science movement currently stands. I look forward to a (hopefully in person) rewarding and motivating experience for BOSC 2022!

David Twesigomwe: My BOSC 2021 Experience

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 07 Sep 2021 10:24:48 +0000

The BOSC-OBF 2021 Event Support Fund was awarded to David Twesigomwe, a PhD student based at the Sydney Brenner Institute for Molecular Bioscience (SBIMB) - South Africa, to participate in BOSC 2021, an annual conference hosted by the Open Bioinformatics Foundation (OBF). Based on the OBF Event Fellowship program, this fund aimed to facilitate participation of diverse researchers from historically underrepresented groups at BOSC to help wider awareness and adoption of open source bioinformatics practices in the biological research community. Find more information here.

Attending the Bioinformatics Open Source Conference (BOSC) has definitely been one of my highlights for 2021 so far. I am so grateful to have received a registration fellowship as part of the global initiative supported by the BOSC-OBF 2021 Event Support Fund. From the research point of view, nothing beats getting together (albeit virtually) to talk all things bioinformatics and open science with such a welcoming BOSC community as we continue adapting to new routines and work-life balance during the COVID-19 pandemic.

Pre-BOSC

The first thing that stayed with me about BOSC 2021 was the detailed critique and useful comments we received from the reviewers of our abstract. As an up-and-coming bioinformatics scientist, it was wonderful to get such actionable feedback on our pipeline ( StellarPGx), and suggestions on how we can promote open source contributions to the code. One of the reviewers even went the extra mile and submitted the very first issue in the GitHub repository :)

Overview of the conference

BOSC 2021, which was one of the tracks of ISMB/ECCB 2021, was really exciting despite it being a virtual event – kudos to the organising team for putting the conference together aa nd navigating all the technical issues. In particular, I enjoyed the session on workflow management systems, which included a fascinating talk by Paolo di Tommaso on the evolution of Nextflow – the workflow management system of choice for a number of students and senior scientists at the SBIMB. I also enjoyed the session on analysis tools, where I got the opportunity to present StellarPGx, and I learned a great deal from the other sessions as research reproducibility was rightly championed to all the talks.

Furthermore, it was quite exciting to round off the days with virtual round table and happy hour group meetings with incredible role models (Chris Fields, Nomi Harris, and Geraldine Van der Auwera to mention but a few).

Welcoming community

Even though BOSC 2021 (the first BOSC for me) was held virtually, the warm welcome I received from the community – be it on the remarkably active Slack channel or in the round table meetings – was quite uplifting. Special mention to Nomi Harris and the entire organising team for dedicating a lot of time and effort in organising such an engaging conference.

Next steps

I am looking forward to incorporating the ideas and suggested open source best practices arising from BOSC 2021 in the next phase of development for StellarPGx. I will forever be grateful for being awarded the BOSC-OBF 2021 Event Support Fund which enabled me to attend and present at #BOSC2021. I hope to be an active member of the BOSC-OBF community for years to come and to volunteer in some of the upcoming OBF activities.

Join us for BOSC 2021!

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 28 Jul 2021 14:28:50 +0000

BOSC 2021, which is a track (COSI) of ISMB/ECCB 2021, will take place online the 29th and 30th of July. The complete schedule is here.

The event is being held in the Showcare platform – check out our tips for making the most of your online conference experience.

We invite all attendees to join us at the pre-BOSC happy hour at the BOSC [roundtable](http://All attendees are invited to our pre-BOSC happy hour today from 17:30-18:30 UTC! Look for us at the BOSC roundtable. https://ismbeccb2021.showcare.io/roundtables/) on Wednesday, July 28, from 17:30-18:30 UTC!

We encourage participants to take screenshots of the event and share them with us! Also, if you’d like to write a blog post about your experience at BOSC, we’d be happy to post it on our blog!

Happy BOSCing!

Birds of a Feather at BOSC 2021 (deadline June 25)

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 15 Jun 2021 19:06:36 +0000

Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of shared interest.

BoFs at ISMB/ECCB 2021 will take place each day of the meeting except the last day, at the same time as the poster session (not ideal, we know–but there are only so many viable hours in the day), from 15:20-16:20 UTC. We recommend that you choose either Thursday, July 29 (the first day of BOSC) or Wednesday, July 28 (the day before BOSC).

Any ISMB/ECCB participant is welcome to propose a BoF! All you need is a topic, a leader, and a brief description. Submit your BoF proposal at https://www.iscb.org/cms_addon/conferences/ismbeccb2021/bof/ no later than June 25.

If you’re organizing a BOSC-related BoF, let us know! We’ll list it on our website ( /events/bosc-2021/bosc-2021-schedule/) and tweet about it!

BOSC-OBF 2021 Event Support Fund

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 11 Jun 2021 12:00:00 +0000

Thanks to funding from our sponsors, we are opening a special call for applications to the BOSC-OBF Event Support Fund. This fund aims to increase participation of members from groups otherwise underrepresented in BOSC or in bioinformatics community events in general, including but not limited to underrepresented demographic groups (country of residence and citizenship), ethnic background (historically underrepresented and other minority groups), career stages, gender identity and expression, people with disabilities and members from low income/resource organisations.

A limited number of qualified applicants will be chosen to receive free registration for ISMB/ECCB 2021. No other financial support (for example, for internet access or headphones) will be included.

The application deadline is 30 June 2021, and decisions will be sent out by 8 July 2021. Apply at https://forms.gle/aDVSHpq7Gs46CNDb6.

We hope you’ll join us at BOSC! For more #BOSC2021 news, follow us on Twitter!

BOSC late poster abstract deadline is June 3!

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 28 May 2021 22:17:49 +0000

There’s still a chance to submit your abstract in the Late Poster round, which closes June 3 at 11:59pm ET!

What about late-breaking lightning talks? Unfortunately/fortunately, we got so many high-quality abstracts in the early round, we were not able to save any talk slots for the late round. Talk slots will open up only if some early-round speakers decide not to attend the conference.

Abstract format. To be considered for a poster, you only need to submit a 200-word short abstract. However, you should feel free to add a PDF (2 pages max) that better describes your work! Your PDF should include the title, author name(s), open source license, and code or project URL (even though this information is also requested on the submission form). Accepted abstracts are published on the BOSC website as-is.

Registration. This year, BOSC is a track (also called COSI) of ISMB/ECCB 2021online. There is no partial registration option; BOSC participants must register for the full ISMB/ECCB meeting.

Fee assistance. With help from our sponsors, we are able to offer registration fee assistance to some presenters. If the cost of registration is a barrier to your participation, just check a box on the abstract submission form to request registration fee assistance!

How posters will work. Authors whose poster abstracts are accepted will be able to upload content to the ISMB/ECCB virtual conference platform between July 19-23, including your full abstract, PDF of your poster (it doesn’t have to be poster-sized!), and a short (max 7 minutes) talk as a .mov or .mp4 file. Poster presenters will be able to host “video demo rooms” (with up to 15 participants) and engage in live Q&A with attendees during the poster session. The BOSC poster session is from 15:20-16:20 UTC on Thursday, July 29.

 Join us on Slack! Our BOSC Slack workspace is open to the community!
 Follow us on Twitter! @OBF_BOSC, #BOSC2021

Introducing the BOSC 2021 Organizing Committee!

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 09 May 2021 21:07:13 +0000

BOSC is organized entirely by volunteers. We are lucky to have these amazing people on the Organizing Committee this year!

Jason Williams( @JasonWilliamsNY) is a new member of the BOSC Organizing Committee, though he’s been a BOSC participant and an abstract reviewer for years. Jason was a BOSC panelist in 2015 on a panel about increasing diversity in open source bioinformatics, and again in 2018 for a panel about training and documentation in open source bioinformatics.

Jason works for Cold Spring Harbor, where he’s the Assistant Director of External Collaborations for the DNA Learning Center and Lead for CyVerse Education, Outreach, and Training. Jason provides training and support to scientists and educators, as well as serving on several committees and boards for projects that advance science and science education including the Software Carpentry Foundation. In his spare time, Jason plays the cello and whips up amazing multi-course dinners. Read more about Jason and his CSHL journey here.

Malvika Sharan( @MalvikaSharan)joined the BOSC Organizing Committee in 2021. Malvika was elected to the Board of the Open Bioinformatics Foundation in 2019, where she runs the OBF’s Event Fellowship program. Malvika is the Community Manager for the Turing Way at the Alan Turing Institute, and a Co-Founder of Open Life Science, a mentoring and training program focusing on open science projects. She is also a fellow of the Software Sustainability Institute.

Malvika is known as a community builder, open science educator and facilitator of open source projects, and is passionate about enabling collaborative culture, accessibility and inclusive practices in research. She is a frequent speaker on these topics, at BOSC and beyond. When she’s not traveling to conferences, Malvika loves to learn about food history. Read more about Malvika at her website.

Monica Munoz-Torres( @monimunozto) has been part of the BOSC Organizing Committee since 2017. She has also chaired several BOSC panels: Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community (2015), Growing and sustaining open source communities (2016), and Open Data: Standards, Opportunities and Challenges (2017).

Moni is an Associate Research Professor at the University of Colorado School of Medicine. She is Director of Operations for NIH/NCI’s Center for Cancer Data Harmonization and Program Director for the Phenomics First Resource - an NHGRI CEGS. Moni has a strong background in biocuration; she has served as the Chair of the International Society for Biocuration (ISB) and a Steering Committee member for the global initiative to sequence and annotate the genomes of 5,000 arthropods (i5k Initiative).

In her spare time, Moni co-leads the Healdsburg Citizens Organized to Prepare for Emergencies (COPE), a neighborhood safety organization in Sonoma County, CA, and loves to take care of her garden roses.

Karsten Hokamp joined the Organizing Committee for BOSC 2015, which was held in his hometown, Dublin, Ireland. In 2020, Karsten was the force behind BCC2020’s move to an online platform called Remo.co, designing every detail of the virtual conference space, down to the decorations in the online “party room”. Karsten was the Technology Chair for 2020 and is the co-chair for 2021.

Karsten holds the role of Bioinformatics Research Officer at Trinity College Dublin, where he looks after several open source bioinformatics software packages. He likes to unwind with a swim in the sea or a vigorous game of tennis and wouldn’t refuse a freshly pulled pint of stout afterwards.

Chris Fields( @cjfields) has been on the BOSC Organizing Committee since 2011. He’s also the Secretary of the Open Bioinformatics Foundation.

The Director of the High Performance Computing in Biology Group at the University of Illinois Champaign-Urbana, Chris is also known as one of the founders and lead architects of BioPerl, one of the earliest “Bio*” projects that formed the core of the OBF.

Chris is also a big proponent of open science efforts in Africa through his current collaboration with H3ABioNet. His current work focuses on day-to-day tasks with a bioinformatics core, keeping up with current sequencing technologies, and generally just trying to stay sane in an ever-changing research and analysis landscape. He looks forward to having a pulled pint of stout with Karsten and others at some future point.

Peter Cock( @pjacock) has been involved in BOSC organization since 2011, and co-chaired the conference from 2014-2016. He is currently the President of the OBF, having previously served as Secretary and Treasurer.

Peter is a senior bioinformatician at the James Hutton Institute in Scotland, and one of the core developers of Biopython since getting his PhD. He moved to Scotland in part to be closer to the mountains, but since starting a family has not been able to visit as often as before.

Nomi Harris( @nomiharris) helped to plan the very first BOSC in 2000, and has chaired or co-chaired the meeting since 2011. She also serves on the Board of the OBF.

Nomi is a Program Manager at Lawrence Berkeley National Laboratory, where she helps to coordinate a number of large open source bioinformatics projects. Previously, she was a bioinformatics software developer.

Nomi loves music, and organizes both a Renaissance vocal quintet and a folk music circle. During the pandemic, she has been volunteering for Help Berkeley and fostering kittens for the Berkeley Humane Society.

BOSC Abstract Parties!

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 09 Apr 2021 16:58:44 +0000

Are you thinking of writing an abstract for BOSC? We’re here to help! The BOSC Organizing Committee is holding two “abstract parties” that will be fun collaborative work sessions. We’ll start by giving some tips for writing a great BOSC abstract, and then open the floor to questions and “workshopping”: show us your in-progress abstract, and we’ll give you helpful suggestions. Or you can just attend and work on your abstract in silent solidarity with others!

We’ve chosen two different times for worldwide coverage:

Thursday, April 15, 22:00 UTC (3pm PT / 6pm ET / 8am (Friday) AEST): Zoom link
Thursday, April 22, 14:00 UTC (7am PT / 10am ET / 15:00 BST): Zoom link

We hope you’ll put on your writing hat and meet us there! (And join us on our Slack channel as well!) If you can’t make it to either of the parties, you can look at these slides, which explain what you need to know to put together a good BOSC abstract!

Join us at BOSC 2021!

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 24 Mar 2021 21:21:52 +0000

BOSC 2021 will take place July 29-30, as part of ISMB/ECCB 2021 Online.

Key Dates

May 6, 2021 (11:59pm EDT): Deadline for submitting one-page talk/poster abstracts May 27: Talk/poster acceptance notifications June 3: Late poster (and Late-Breaking Lightning Talk) submission deadline June 10: Late poster / LBLT acceptance notifications July 29-30: BOSC 2021 Online (part of ISMB/ECCB 2021 Online) July 31-Aug 1: CollaborationFest (CoFest)

About BOSC 2021

BOSC is returning to ISMB in 2021, after a successful partnership with Galaxy for the first Bioinformatics Community Conference last year (BCC2020 online). Originally slated to take place in Lyon, France, ISMB/ECCB 2021 will be held online, and features over a dozen tracks, including BOSC. As usual, BOSC will include keynote talks, longer and shorter (lightning) talks from submitted abstracts, posters, Birds of a Feather, and more!

Timing

BOSC 2021 will take place the last two days of ISMB/ECCB: July 29-30. Our usual free collaborative work event, CoFest, will be held July 31 - August 1.

The complete ISMB/ECCB schedule is available here. The core hours for talks will be 11:00-15:30 UTC, with poster sessions and ISMB keynotes from 15:30-17:30 UTC. The core hours correspond to:

13:00-17:30 CEST (Europe) 12:00-16:30 BST (UK/Ireland) 7:00-11:30am EDT (East coast of North America) 4:00-8:30am PDT (West coast of North America) 9:00pm-1:30am AEST (East coast of Australia)

Abstract submission

We encourage you to submit abstracts on any topic relevant to open source bioinformatics or open science. After review, some abstracts will be selected for lightning talks, longer talks, or posters. The deadline for abstract submission is May 6th (11:59pm EDT / 03:59 (May 7th) UTC)!

BOSC session topics include (but are not limited to):

Open Science and Reproducible Research Open Biomedical Data Citizen/Participatory Science Standards and Interoperability Data Science Workflows Open Approaches to Translational Bioinformatics Open Science for Global Health Developer Tools and Libraries Inclusion, Outreach and Training Bioinformatics Open Source Project Reports (about new or existing projects)

Requesting registration fee assistance

We realize that the cost of ISMB/ECCB may be prohibitive for some. If you are submitting an abstract to BOSC and would have difficulty covering the cost of registration, you can request registration fee assistance. To make it easy, this request can be made right on the abstract submission form. (Only the conference chairs will see these fee assistance requests – the abstract reviewers will not.) We regret that we will not be able to offer registration fee assistance for those who are not submitting abstracts. (But you should consider submitting an abstract! Even if your work is preliminary, it may qualify for a poster.)

Stay in touch!

Learn more about BOSC: /events/bosc/ Join our BOSC announcements mailing list: https://groups.google.com/forum/#!forum/bosc-announce Chat with us on Slack: https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew Find us on Twitter at @OBF_BOSC and use #BOSC2021 for this year’s conference.

We hope to see you online at BOSC 2021! Please share this announcement with people or groups who might be interested. We are particularly interested in reaching out to diverse communities who may not yet be aware of BOSC!

Call for applications for OBF Event Fellowship, Round 1 of 2021

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 19 Feb 2021 10:36:38 +0000

The call for applications for the OBF Event Fellowship 2021, round 1 is now open. The deadline for this round is 1 April 2021. Applications should be submitted via this Google Form.

We invite applications from candidates who are seeking financial support to attend or host virtual events in 2021. The selected awardees can use the OBF Event Fellowship to cover conference registration fees and potentially additional expenses associated with attending or hosting the event, such as small hardware (microphone, speaker, webcam), childcare for the duration of the event and high-speed internet. Like last year, in this round, we will consider applications to attend or host virtual events only. This decision has been made due to the ongoing Coronavirus pandemic induced lockdown and restricted travels. Expenses that will be incurred by remote participation have to be justified in the application and will be evaluated on a case-by-case basis.

Group applications are not in scope, but: if multiple members of the same group would like to attend the same event, each member should send their application separately. If members of an organising committee would like to apply for support for hosting an event, the application should be sent by one person (preferably the lead organiser).

Planning to attend BOSC 2021 ? You can request a registration fee waiver/reduction when submitting your abstract for a talk or poster directly via the BOSC abstract submission form. If you would like to participate without a talk or poster, please fill the OBF Event Fellowship application form providing your motivation and expected outcomes from attending BOSC 2021.

More details regarding the fellowship application, review, and reimbursement process can be foundon our website: /event-awards/. If you have questions, please contact the OBF board by emailing board@open-bio.org.

Learn about the OBF Event Fellowship Awardees from 2020!

Round 1 (1 April 2020)

As part of the fellowship process, all OBF Event Fellowship awardees write blog posts that are posted on the OBF website ( see here). Below are the blog posts by the awardees from 2020 application rounds.

Using his OBF Event Fellowship Award, Armando Blondel Djiyou Djeuda hosted the H3ABioNet‘s Introduction to Bioinformatics course (IBT) in Cameroon for the first time. Read his report in this blog post.

Gigi Kenneth and Edidiong Etuk attended the Bioinformatics Open Source Conference (BOSC) track at the Bioinformatics Community Conference 2020. It was a first-time opportunity for them to attend bioinformatics and open science workshops at an international conference. Read their posts: A Software Engineer’s Experience at BCC 2020 (by Edidiong) and Getting introduced to Bioinformatics and Open Science through BCC 2020(by Gigi).

Pengfei Fan from Queen’s May College in London attended the Conference on Lasers and Electro-Optics 2020 and shared his experience in this blog post: Smart computational imaging.

Round 2 (1 October 2020)

Siddhant Sharma, an undergraduate student from India, received the OBF Event Fellowship to participate in the International Student Conference 2020 (IEEE, EMBS). A post will be shared soon.

BOSC 2021 will be part of ISMB/ECCB 2021 (online)

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 12 Feb 2021 06:22:49 +0000

BOSC is returning to ISMB in 2021, after a successful partnership with Galaxy for the first Bioinformatics Community Conference last year ( BCC2020 online). Originally slated to take place in Lyon, France, ISMB/ECCB 2021 announced today that the conference will be virtual. This news may be disappointing to some, but for others it offers an opportunity to participate in a conference that they would not have been able to travel to attend.

Registration for the ISMB/ECCB 2021 virtual conference is for the full conference only – there will not be an option to register for only some of the days, as there has been in the past. Registration fees are based on your status as a working professional, postdoc, or student, as well as what country you work in (or your home country for students).

Requesting registration fee assistance

We hope to see you online at BOSC 2021!

Planning an online vs. an in-person conference: which is harder?

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 01 Sep 2020 04:10:19 +0000

Online. By at least a factor of two.

Our recent article entitled Lessons learnt from organizing a virtual conference discusses some of our technology choices and how we leveraged them to put on a successful online meeting. That article touches briefly on some of the challenges we faced, but it doesn’t fully convey how much work it was–both in advance and during the event.

Before we go any further, who are you? This post was written by Nomi Harris, the long-time (co-)chair of BOSC, and the co-chair (along with Dave Clements) of BCC2020 (the Bioinformatics Community Conference, a collaboration between the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference (GCC)). The perspective expressed in this post is mine alone, and does not necessarily reflect the views of others on the BCC2020 organizing committee. Also, although BCC2020 was an equal partnership between BOSC and GCC and the planning was done jointly (except for abstract reviews), my perspective is naturally BOSC-centric.

Me, with a fake bookshelf backdrop and a pear facemask. (The BCC2020 sign only appeared backwards to me, not to the viewers.)

What was the original plan for BCC2020, and wha t changed? BCC2020 was originally going to take place in Toronto. The organizing committee made the decision in March to move it online, and it became increasingly clear with every day that passed that there was no way we could have held the conference in person in Toronto as originally planned.

The original BCC home page showed the Toronto skyline at night.

Who runs these meetings, anyw ay? One thing to understand about BCC2020 is that aside from a few Galaxy people for whom planning conferences is part (a small part) of their job, all the organizers are volunteers. We have regular jobs, and we work on conference organization during our evenings and weekends.

The BCC2020 organizing committee

Many of us on the BCC2020 organizing committee have been involved in BOSC or GCC organization for years. (I, for example, was involved in planning the very first BOSC in 2000, started co-chairing it in 2010, and have chaired or co-chaired it every year since then.) So we are pretty used to doing the huge amount of work involved in planning an in-person BOSC. None of us had ever organized a large online meeting before, so there was a big learning curve. Our recent article entitled Lessons learnt from organizing a virtual conference discusses some of our technology choices and how we leveraged them to put on a successful online meeting. That article touches briefly on some of the challenges we faced, but it doesn’t fully convey how much work it was–both in advance and during the event.

The organizing committee met almost every week during the spring and summer.

There must be things that are easier with an online m eeting , right? Yes, a few, but not a lot. There’s no travel required for an online meeting, so there’s no need to book plane tickets or research hotels–but that’s true for everyone who participates in a meeting, not just the organizers. As meeting organizers, we don’t plan travel for anyone other than ourselves, so that doesn’t really count towards lightening our organization duties. We didn’t have to worry about handing out name tags or T-shirts, but those tasks are also not the direct responsibility of the organizing committee. An online meeting doesn’t involve food or coffee–but the volunteer organizing committee doesn’t generally have to do any planning for those; they are handled by the venue. So are the projector, wifi, air conditioning, the chairs in the conference rooms, etc. Basically, only if we for some reason decided to hold our conference in an empty warehouse would the organizational overhead come close to the difficulty level of planning an online meeting.

Why was organizing an online meeting so hard?

This was our first online meeting. We’d never done this before, so we had to figure out a lot of things. It almost certainly wouldn’t be quite this hard to organize another online meeting next year, particularly if we stick with the same technology choices. Karsten postulates that online conferences probably have a higher “reusability factor” than in-person ones, from a planning perspective.

More options to consider. For an in-person meeting, many of the choices and the responsibility for supporting those choices fall on the venue. For example, there are many different kinds of video projectors. Some are better than others. Some are more expensive than others. Which one should we choose for our meeting? Fortunately, we never had to make that choice: the venue has whatever projectors they have. With an online meeting, we not only had to (metaphorically) choose a projector, we had to set it up and run it ourselves. And the projector was only part of the story: we had to make choices and configure and support a variety of tech platforms that would not be required at an in-person meeting (such as a chat app).

We were early adopters. Admittedly, we made our job harder by choosing a video conferencing platform (Remo.co) that was new to us and to our attendees. Some things would have been simpler if we’d just run the meeting as a bunch of separate Zoom rooms. We wouldn’t have had to do as much training (of the organizers, the workshop leaders, the speakers, and the many volunteers), nor would we have had to write as much documentation. We wouldn’t have had to design floor plans for each of our virtual “buildings” (though actually Karsten Hokamp, who is a total hero, did all of that, as well as preparing most of the documentation and leading most of the training sessions. Seriously, he deserves to be knighted or something.)

The fact that Remo was new and still in active development led to some issues (for example, shortly before the conference, their system for registering attendees broke; at another point, private messaging stopped working). But overall, despite the challenges, we felt (and most of the participants agreed) that Remo offered an online conference experience that was more fun and more reminiscent of an in-person meeting. The reasons why we chose Remo, and the challenges and opportunities it presented, are covered in more detail in the article mentioned earlier ( Lessons learnt from organizing a virtual conference),

Chatting at one of the “tables” in Remo.

Tangent: serendipity at online meetings–it happens. While I’m on that subject, let me share an anecdote that didn’t make it into the “lessons learnt” post. One evening during the conference, I needed to talk to Dave Clements, but I wasn’t sure where he was. He wasn’t answering email or responding in Discord. But as I wandered through our virtual buildings, I happened to spot him in the poster building. He was at one of the sponsor tables, chatting with someone there (I could tell that they were talking because of the little microphone icons on their photos). I could choose to approach the table and break in on their conversation, or wait until they were done. It was uncannily similar to wandering through a conference center and serendipitously seeing someone you knew.

I ran into some old friends at the pre-meeting open house.

How do you walk and talk at a virtual meeting? That story might give you a sense of one reason running an online conference is hard: you have to come up with substitutes for things that you get for free in real life, like walking around a conference center and using your voice to talk to people. We couldn’t find a single technology platform that supported threaded, persistent chat in addition to video conferencing, so we ended up using Discord as well as Remo.

Online talks: what could possibly go wro ng? Another big challenge was how to present the talks. At an in-person meeting, the speakers just show up and talk. We realized pretty quickly that it would be way too risky to have all the speakers give their talks live during our online meeting. So many things could go wrong. They could get confused about the time zone and fail to show up. Their internet connection could be spotty, or could fail completely. Their computer could decide to reboot in the middle of their talk. Their toddler could toddle into the room and yank their headset off their head (this happens regularly to one of our organizing committee members). Things can and do go wrong at in-person talks, too (the video projector not working is a popular one), but online talks present a whole new array of possible fails.

We decided to have presenters pre-record their talks and share the videos with us. Actually, I have to admit that I was pretty sure that at least a few presenters would fail to get their videos done on time (or at all), but we had amazingly high compliance, and only a few speakers who brazenly went over their allotted time. We had to check all the videos to make sure the volume was ok (sometimes it wasn’t) and that the beginning and end of the video wasn’t truncated (sometimes it was). We then had to upload all the videos to a site from which they could be streamed–we chose Vimeo rather than YouTube because YouTube’s terms of service don’t allow you to stream videos for an audience. That was a lot of work, but once again, Karsten did it. (Is he a saint or WHAT?) We also added the video links to the online schedule, so that attendees could watch them asynchronously if they wanted to, which was a nice thing to do but again involved more work.

During the talk sessions, the session techs had to start each talk video at the appropriate time. We discovered as the meeting proceeded that different latencies in attendees’ internet connections meant that for some people, the video took longer to play, and therefore when the next talk started, they hadn’t yet finished watching the last one. This was one of a number of challenges we faced with the talk video presentations.

Working harder for inclusivity. In some cases, we made choices that created more work for the organizers but which helped to make our meeting more inclusive and accessible. For example, we decided to run the sessions twice each day, once at a time convenient for people in the Western hemisphere, and again 12 hours later at a time convenient for people in Asia and Australia.

Another thing we did to increase accessibility was to pay for (with the help of a sponsor donation) closed-captioning all the talks, including the live keynotes as well as the pre-recorded talks. This was a cool feature, but it also took time to set up. We paid a company to do the actual captioning, but we had to provide the pre-recorded videos to them and get back the captioned videos, as well as coordinating the captioning of the live talks. Was it worth the expense and effort? I think so. 25% of the respondents to our post-conference survey said that they’d made use of the CC, and there were many positive comments about it (for example, “Fantastic, very helpful. I have good hearing, but it helped me digest more effectively anyway.”).

Time zones are hard. One of the things that makes online conferences complicated to organize is time zones. At an in-person conference, there is only one time zone to deal with. We had participants joining us from all over the world, representing an array of time zones that included some that are, unbelievably, off by half an hour. Every schedule we dealt with had to list multiple time zones. That would have been hard enough, but since we ran the whole conference in two hemispheres, we had to list the times for every event in two hemispheres, translated into multiple time zones.

A portion of one of the spreadsheets we used to deal with multiple time zones.

Many volunteers were needed. To successfully run our online conference, we required the help of dozens of additional volunteers in addition to the people on the organizing committee. Volunteers (for whom we are extremely grateful!) were needed to help staff the Help Desk, to stream the videos during the parallel sessions, to monitor the various chat forums, and to help visitors to the poster building figure out how to find the posters they wanted to see. All of the volunteers had to be trained, and we had to assemble huge spreadsheets to organize who was volunteering when (with multiple time zones listed, of course).

Karsten explaining the BCC2020 setup in Remo during one of the many volunteer training sessions.

Stress displacement: during the conference vs. in adva nce. When I plan an in-person meeting, most of the planning happens ahead of time. The meeting itself is somewhat stressful and exhausting, but also a lot of fun (last year, for example, I got to float down the Rhein with a bunch of other conference attendees). There is some pressure on the session chairs, who have to manage the Q&A and make sure speakers don’t go on too long. But the “on-the-ground” stress at an online meeting is so much higher. The session techs (who were responsible for starting each video at the appropriate time) had a particularly nail-biting time of it. (Conversely, the speakers, who had already done the hard work of preparing their talk videos in advance, found the online meeting relatively unstressful.)

Did I mention that planning an online meeting is a lot of work? All in all, I would say that I personally spent about 2x as much time on BCC2020 organizational activities as I do organizing an in-person BOSC–and that’s a substantial amount of time. And that’s just me. Karsten alone probably spent more time on BCC2020 preparation than there are actual hours in the days leading up to the meeting. (But his job in particular would be easier next time if we chose to run another online conference in Remo.)

One of many organizational spreadsheets we created to help us keep track of everything. This one (which listed details for each session, including session chair, session tech, talk titles, presenters, talk lengths, video URLs, Q&A times, and more) was nicknamed “the colorful spreadsheet”

Why am I going on about how haaaaard it is to plan an online meeting? It’s not because I want praise or sympathy (though those are always appreciated), but because we want to manage expectations for next year’s conference. We know that many people would like us to offer an online conference even if next year’s meeting is physical. Here are a few such comments from the post-conference survey:

“Please make next year’s meeting virtual/hybrid not F2F only.”

“Please keep some aspect of this virtual if it goes back to face-to-face. I may only be able to attend virtually for the foreseeable future. Having this inexpensive option makes this community more accessible and more inclusive.”

“Would really appreciate keeping this conference virtually accessible in the future, at least a hybrid approach maybe!”

So will we make the next BOSC both virtual and in-person? We’ll see what we can do–we sincerely do want to make the conference as accessible and inclusive as possible. But at the same time, there are only so many hours in the day, and all of the organizing committee members have other jobs that pay the rent. If putting on an online conference is 2x the work of an in-person one, running a hybrid event would be 3x as hard, which is simply not feasible. We don’t yet know whether BOSC 2021 will be online or in-person, but whichever it is, we will not be able to support both a full in-person and a full online experience. We hope you understand, and we hope you will join us if you can.

Some of the attendees at the online BOSC party–the next best thing to being there!

A Software Engineer's Experience at BCC 2020

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 16 Aug 2020 11:55:53 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Edidiong Etuk (Eddie), an open-source lover and a software engineer from Nigeria, was supported to take part in Bioinformatics Open Source Conference 2020 by this fellowship granted to him in the application round-1 of 2020. Find more information here.

TL;DR This post is about my experience at Bioinformatics Community Conference 2020.

Before attending the Bioinformatics Community Conference (BCC) 2020, I had zero experience with Bioinformatics. But, after the conference, I am more confident in my ability to tackle bioinformatics-related tasks, challenges and discussions. I enjoyed every moment of BCC2020 virtual conference, hung out with a lot of cool folks through the Remo conference platform, and got introduced to new concepts in bioinformatics through workshops, keynotes, short talks, poster sessions and community interactions. In this post, I am summarising my experiences and lessons learned from this conference.

BCC Pre-Conference Workshops

I registered for two workshops: Dockstore Fundamentals: Introduction to Docker and Descriptors for Reproducible Analysis and I must say I found them easy to understand as a beginner. I had an idea of what Docker was but the tutors made working with Docker so easy. They also switched up and explained Descriptors (focus was on Workflow Description Language). It was a good introduction to Dockstore.

Next, I attended Reproducible Analysis in the Cloud with Dockstore and Terra, where I got introduced to Terra, Anvil, and learned more about Dockstore. The ability to access data, run analysis, and use the cloud all from Terra while fostering collaboration is what this training was about. All experiments I toyed with, worked and results could be seen easily and tracking bugs or experiment failure was seamless.

One regret I had during the workshops is the number of sessions I missed. All the sessions were so interesting that I wished I could attend all training and workshops. All the training materials and notes were made available, so I guess I’d have enough resources to start with when learning them on my own.

Main Conference

I attended the West sessions of the 3-day main conference as this favored my timezone. As a volunteer for BOSC, I spent a lot of my time in the BOSC building (yes a virtual building). There were several interesting talks during the conference about research and a variety of open-source tools which I can’t point to, but some of those I describe below.

Day 1

Day 1 started with a keynote from Lincoln Stein who showed us how Open-Source has improved the biomedical world.

The presentations were all short and precise and though some were very technical, I got a thing or two from them. The most memorable presentation was Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI genome data science Analysis, Visualization, and Informatics Lab-Space (ANVIL).

It was very relatable and I applaud the creativity behind the presentation, bravo Michael!!

Poster sessions were cool and were held in a different virtual building from Galaxy and BOSC tracks. This was a good opportunity for me to see innovative work by the researchers in various bioinformatics communities. I also had a chance to chat with the representatives of the sponsors at the sponsor tables.

Day 2

On Day 2, Prashanth N Suravajhala gave the keynote on the importance of mentoring students. It was sad to hear that the building he was delivering his keynote from had some emergency situation during the presentation, but kudos to him for delivering an excellent keynote.

Another memorable session was Building open source communities and empowering new contributors by Yo Yehudi. This talk was important as without Yo’s mentorship from Outreachy, I wouldn’t be here (Thanks Yo!). Although that session clashed with a Galaxy session, luckily the recordings were made available so I got to watch The cloud-native Galaxy: Galaxy on Kubernetes. I’m interested in everything Kubernetes so the session, of course, interested me.

Day 3

Day 3 hit closer to home due to my work at Popper, everything about workflow management seemed understandable. Although I gotta add, there are a lot of workflow engines out there for reproducibility in research.

It would make a lot of sense if they all came together to do a conference to ensure we’re all going in the same direction and not competing with each other. Of course, there were a lot of interesting posters which I got to check out.

Welcoming Community

Everyone at BCC 2020 was very welcoming, Birds of a Feather session at the virtual-bar was a great addition to the event. I had my drink with me, and of course, we all drank responsibly (lol!). I enjoyed switching tables and going to different floors on Remo where I got to interact with warm and friendly people during the conference.

The Bioinformatics community is the most welcoming out there! Special shout out to everyone who made me feel welcome, Michael R. Crusoe, Dave Clements, Emmy Tsang (who pronounced my name very well), Nomi Harris, and others! You were all fun to hang with and I hope next year I can meet y’all in person!

BCC exemplified diversity in tech and I loved it. BOSC Happy Hour West was thrilling as we had 18 people on the stage (please don’t try this on Remo! 😬).

Next Steps

Due to my interest in Bioinformatics, I am working to dockerize DoBlastzChainNet and popperize it to make it reproducible. This is going great and I’ll appreciate any help.

Thanks to OBF for this amazing opportunity! Till next time!

Lessons learned from organizing a virtual conference (BCC2020)

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 13 Aug 2020 19:28:41 +0000

BCC2020 (the collaborative BOSC + GCC meeting) was held online, with over 800 people registered for some part of the meeting. We used Remo.co as the technology platform, along with Discord for chat. Read about why we chose those, how it worked out, and our tips for others who are organizing virtual conferences here.

“Table view” in Remo during BCC2020

BCC2020 pre-conference open house

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 08 Jul 2020 04:06:07 +0000

After much discussion, the BCC2020 organizing committee has decided to hold the meeting on Remo.co, which is similar to Zoom but offers a more conference-like experience, with “floors” and “tables” where you can mingle with other attendees. It has great small group and presentation support, including for posters and demos. It’s also more fun than most online conference platforms.

Because Remo is not familiar to most BCC participants, we are holding two open houses, one in each hemisphere, the day before BCC training starts. These walk-throughs will introduce participants to Remo’s features and demonstrate how to navigate between sessions, poster/demos, BoFs, training and everything else.

All registered participants will receive invites by email the day before the open houses. If you’re not already registered, remember that the early registration discount ends on July 10, and registration will close on July 15.

The events below show up in the Eastern US timezone (ET) but you can follow the instructions to switch to your local timezone.

Western hemisphere open house (Thursday, July 16)
Eastern hemisphere open house (Friday, July 17)

We are looking forward to showing you the BCC venue. (But you’ll have to bring your own snacks.)

Help us make BCC2020 a rewarding online experience!

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 22 May 2020 18:31:38 +0000

We’re old hands at organizing in-person BOSC s (some of us were involved in planning the very first BOSC, in 2000), but this is the first time we’re attempting an online conference, and we want your help to make BCC2020 a rewarding experience for all.

We know many of you have attended other virtual conferences recently, and we’re interested in hearing what worked well and what didn’t. In particular, we are trying to figure out how to make virtual posters work, and how to run Q&A (with audio, or just typed? live, right after the talks, or asynchronous?). We’re also interested in ideas for adding fun social elements to what could otherwise be a pretty dull extended videoconference.

To share your ideas with us, we invite you to join one or both of our public gitter chat rooms: BOSC: https://gitter.im/OBF/BOSC_community BCC: https://gitter.im/bcc2020/community

Or, if you prefer, you can email us at bosc@open-bio.org.

We look forward to your suggestions, and hope to see you at BCC2020!

BCC2020 (inc. BOSC 2020) abstracts due this week

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 03 May 2020 12:28:23 +0000

We look forward to receiving lots of abstracts by the end of this week from people interested in presenting at the online Bioinformatics Community Conference (BCC2020), which combines the Galaxy Community Conference, and our own Bioinformatics Open Source Conference (BOSC). The BCC2020 abstract submission deadline is Friday 8 May 2020.

Some of the recent round of the OBF Travel Fellowships will be supporting BCC2020 attendees with video conferencing costs (headsets, web-cameras, etc), full announcement coming soon.

In Memoriam: Galaxy's co-founder, James Taylor

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 03 Apr 2020 23:08:56 +0000

The Open Bioinformatics Foundation was shocked and saddened to learn that our colleague and collaborator James Taylor, a professor of biology and computer science at Johns Hopkins University, died on April 2, 2020. James was one of the creators and PIs of the Galaxy Project, which is among the most widely used platforms in open bioinformatics. The Galaxy community has created a tribute page for James.

We have close ties to James and the Galaxy project via our flagship conference. BOSC, which was first held in partnership with the Galaxy Community Conference (GCC) in 2018, will again be co-hosted with GCC at the online Bioinformatics Community Conference (BCC2020) this July.

OBF joins many others in mourning the loss of a pillar of the bioinformatics community.

BOSC 2020 will be online

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 24 Mar 2020 16:29:18 +0000

The 2020 Bioinformatics Community Conference (BCC2020), which brings together the BOSC and Galaxy communities, will take place online–more info here.

The online meeting will still be held July 18-21. Registration will open in a few weeks, and fees will be lower than for an in-person meeting. Abstract submission will open soon and will close April 30th. We will follow the usual submission and review processes.

We are discussing how to arrange the schedule to allow for participation across the globe. We welcome your input on how to make our first Virtual Bioinformatics Community Conference a success.

OBF Travel Fellowship 2020: Round 1 and BCC 2020

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 17 Feb 2020 09:00:00 +0000

We are currently accepting applications for the first application round for the OBF Travel Fellowship 2020. This fellowship aims to promote the conference/event participation of attendees who advocate and present their work related to open-source bioinformatics software development and open science in the biological research community. In 2019, a total of 9 applicants received OBF travel fellowships to attend various conferences across the globe to present their work, gain new skills and promote Open Science practices in their respective areas of life science.

Apply for round 1 of 2020 here.

(Image on Unsplash by @timmossholder)

If you are unsure of your eligibility for this fellowship or want to understand the fellowship process better, check the details on our website and read blog posts of past recipients.

The Bioinformatics Open Source Conference (BOSC) will be joining the Galaxy Community Conference at BCC2020 - the Bioinformatics Community Conference. The main conference will take place from 19 to 21 July 2020 at Victoria University in Toronto, Canada. The optional pre-conference training day will be 18 July and the CoFest and CoFest Encore days will span from 22 to 25 July. Registration for BCC2020 will open in March 2020 ( see details).

The fellowship application deadline for this round is 1 April 2020, midnight in any part of the world. Those who plan to attend BCC2020 or other conferences related to open source / open science, and whose presence would promote diverse skills and perspectives, are encouraged to apply.

Call for OBF Travel Fellowship is Open until 1 December 2019

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 14 Nov 2019 16:50:13 +0000

The call for OBF travel fellowship to select the next round of awardees is officially open! Please submit your application by filling out this form. Deadline for this round is 1 December 2019.

This fellowship aims to support our community members in attending events that promote open source software development and/or open science in the biological research fields. As the organiser of Bioinformatics Open Source Conference (BOSC) since 2000, OBF understands the role of such conferences and wants to support people who can benefit from showcasing their work, learn from each other and promote open science at BOSC or similar events.

Applications are particularly encouraged from members from historically underrepresented groups, who work in low-income research environments and strive to promote diversity and inclusion in their communities. The conference or event that the applicants intend to attend must take place in 2020 (preferably during the first half of the year) and should provide them with a platform to learn or promote open science.

Since 2018, OBF has offered this fellowship to 12 awardees to defray or subsidize their travel-related cost of up to $1000 each. You can read their blog posts in OBF blog where they have shared their experiences from attending different events as OBF travel fellows.

In 2020, there will be two application calls that will close on 1 March and 1 September 2020. [ NOTE: This was later changed to 1 April and 1 October.] Please read more details on the fellowship program and feel free to contact the committee by writing an email to board@open-bio.org.

Computational biology without borders

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 15 Oct 2019 20:52:03 +0000

This is a guest blog post from Aziz Khan, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the ISMB/ECCB and BOSC 2019 meeting in Basel, July 2019. The OBF’s Travel Fellowship program aimed at increasing diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Find more information here.

Computational tools and software are now becoming the core of scientific discovery, and making it open source and sharing it freely with the community helps to take scientific discoveries to the next level. We live in an era where international and interdisciplinary collaborations become very central to answer big scientific questions. Given science is becoming more collaborative and data-intensive, we need intelligent and robust computational algorithms to help us to understand and interpret such big-data.

Biology is no longer limited to PCR or gel electrophoresis. The high-throughput approaches to DNA sequencing at the genome and exome level are the state-of-the-art. For example, genomics and epigenomics are shifting from bulk sequencing to single-cell sequencing, which produces even more and sparse data. The (epi)genomics at single-cell can help us to understand the molecular mechanisms more precisely to understand disease and tumor biology. Integrative methods and software are needed to interpret multi-omics data at bulk and single-cell resolution to better understand the heterogeneity between cells, patients, or multi-region biopsies from a tumor. All these require open-source bioinformatics software and resources that are free and accessible for everyone.

The international community that develops such software and methods need a diverse and multidisciplinary platform to meet and share the latest developments in the field, fostering fresh dialogues and perspectives to learn about and shape the future of bioinformatics. And such a platform is provided by ISCB’s Intelligent Systems for Molecular Biology (ISMB) and European Conference on Computational Biology (ECCB) when they both meet in Europe every second year with diverse Communities of Special Interest (COSI) such as the Bioinformatics Open Source Conference (BOSC).

ISMB/ECCB is the world’s largest bioinformatics/computational biology meeting. I’ve been very lucky to attend three of those so far. I started my ISMB/ECCB journey when I was a Ph.D. student at Tsinghua University, China. In fact, first I joined the ISCB Student Council, a wonderful forum for early career researchers (ECR) in bioinformatics. I was part of the web-committee and later served as co-chair of the committee. I helped the community to organize and review student symposiums. If you’re an ECR in bioinformatics, I would definitely recommend joining the community. So, back to ISMB/ECCB, it was July 2015, I was accepted to present a poster and also to volunteer at ISMB/ECCB 2015 in Dublin. Of course, I saved the registration fee by volunteering but it also gave me an excellent opportunity to network. I met some of the great people in that meeting and we’re still connected. My second ISMB/ECCB was in 2017 in the beautiful city of Prague. Again, I signed up to volunteer and had a wonderful meeting and presented one of our open-source projects both at the Student Symposium and at the Regulatory and Systems Genomics (RegSys) COSI.

This year, 2019, the ISMB/ECCB came to Basel, a city in the heart of Europe, which shares its borders with France and Germany.

The tripoint (Dreiländereck) where the borders of France, Germany and Switzerland meet.

I knew I wanted to attend, especially my favorite ISMB/ECCB COSI on the Regulatory and Systems Genomics (RegSys). And this year, my PI Anthony Mathelier was one of the organizers of RegSys. I always wanted to attend BOSC, so I submitted our community initiative, ECRcentral, that aims to bring ECRs together to discuss funding opportunities, share experiences, and create impact through community engagement. ECRcentral was accepted for a long talk and on top of that, I got a travel fellowship from the Open Bioinformatics Foundation (OBF) to attend #ISMBECCB2019 and present @ECRcentral at #BOSC2019. What else do you need, right?

Welcome to Basel! We arrived in Basel on July 21st from Oslo, Norway.

In Basel for #ISMBECCB19! My 3rd #ISMBECCB conference, looking forward to meet the community and 4 days of exciting science.

— Aziz Khan (@khanaziz84) July 21, 2019

Basel was on fire (~40°C), compared with 20°C in Oslo. While walking from the train station towards the hotel, we passed through a bridge (Basel has many bridges over the river Rhine) and saw many people floating down the Rhine to escape from the heat. For a while, it felt like liquid-liquid phase separation in biology, or maybe solid-liquid!

People are escaping from the heat by floating down the Rhine. Picture credit

I quickly checked-in, got fresh and ran to the conference venue. The conference kicked off in the San Francisco hall at Congress Center Basel with over 2,000 participants from all over the world, mainly from developed countries. I love the idea of naming conference rooms of Congress Center after different cities around the world like you could bump in Montreal from Delhi without border control. Anyway, I am not sure how many researchers couldn’t make it due to visa denials or solely due to lack of funding. I made it because as a European resident I don’t need a visa to enter Switzerland.

I found that at this year’s ISMB/ECCB “ 3” was my lucky number. As I mentioned earlier, this was my 3rd ISMB/ECCB meeting with 3 participations (2 posters and 1 talk). And surprisingly, three of my mentors were in Basel for the meeting who came from three different continents, Asia, Europe, and North America. My former Ph.D. advisor Xuegong Zhang from Tsinghua University, my current Postdoc PI Anthony Mathelier from the University of Oslo and my next PI Christina Curtis from Stanford University. This is the beauty of ISMB/ECCB, which connects us without borders although many of us have to cross several man-made borders. By the way, I am joining the Curtis lab this fall at Stanford as a research scientist. And congratulations to Xuegong on getting elected as ISCB Board of Directors. Back to lucky number 3, I visited three countries (Switzerland, Germany, and France) in one day with a lunch in Switzerland, dinner in Germany and went for a walk to France.

Anyway, the first day of the conference started with an exciting keynote talk by Nikolaus Rajewsky from MDC Berlin on the principles of gene regulation in space and time at single-cell resolution. He also shared a great European research initiative, The LifeTime Initiative which aims to use single-cell multi-omics and machine learning techniques to map disease progression to improve medicine.

We started the second day with a fascinating keynote by William Stafford Noble of the University of Washington on traveling across spaces: the power of embedding genomic and proteomic data into a latent space. He shared three powerful applications of machine learning and deep learning to make sense of complex genomic or proteomic data into latent representation.

After the keynote, participants started traveling to different “cities” to attend their favorite COSIs. My favorite COSI at ISMB has been SysReg. But this time, I stayed in San Francisco (the main hall) to attend the first keynote of HiTSeq COSI by Christina Curtis from Stanford University on quantifying the rates and routes of metastasis.

After Christina’s talk, I was back to RegSys which was on in the Singapore room with a great line of keynote speakers in the field of gene regulation. The exceptional keynote talks demonstrated the power of using model organisms for important discoveries including interpretation of genetic variants and characterization of different roles and usages of cis-regulatory regions. Other talks highlighted novel experimental and computational methods for characterizing the 3D organization of the genome, TF co-binding, chromatin accessibility, and linking them to different cellular and molecular outcomes. Transcriptional enhancers and their diverse roles in gene regulation were common themes across many talks highlighting the importance of studying these non-coding regulatory regions.

The Singapore room is full on the 2nd day of RegSys’s morning session on single-cell. Photo by @ferhatay

The second day of RegSys started in the Singapore room with sessions on the bleeding edge developments in the field of single-cell and transcription factor binding. The three amazing keynotes and other selected talks were full of exciting discoveries enabled by comparing single-cell data from different organisms or by integrating multi-omics such as scRNA-seq and scATAC-seq. Other talks demonstrated the power of machine learning and deep learning techniques at the base-pair resolution, in enabling a better understanding of gene regulatory programs through refined characterization of transcription factor binding.

On the 4th day, BOSC 2019, the 20th annual Open Source Bioinformatics Conference, was kicked off in Delhi room by BOSC Chair Nomi Harris followed by an introduction to the Open Bioinformatics Foundation by Heather Wiencko. This was my first official BOSC meeting although I dropped by at the BOSC 2015 in Dublin and BOSC 2017 in Prague while volunteering at ISMB/ECCB. This year the BOSC community presented some excellent open-source bioinformatics resources, tools, and workflows through talks and poster sessions. Nicola Mulder of the University of Cape Town gave a keynote talk on building infrastructure for responsible open science in Africa. She discussed the technical, ethical and social challenges of sharing data in Africa. She said, “It’s really hard to convince people to share their data and their tools when they have such a history of being exploited”. She and her team under the umbrella of H3ABioNet consortium are making progress in building a Pan-African bioinformatics network.

And then came the fifth and last day of ISMB/ECCB 2019. It was also the second and last day of BOSC 2019 which started with interesting talks on open-source, open science and reproducible research using containers and workflows. The last session of BOSC 2019 was on Building Open Source Communities, where I was given the opportunity to introduce our community initiative, ECRcentral. I made my slides and poster publicly available on F1000 Research.

https://twitter.com/khanaziz84/status/1154329690154438656

ECRcentral is a community-driven initiative for early career researchers to find research fellowships and travel grants and to share experiences, resources and get feedback.

Read more here…

I co-founded ECRcentral as part of eLife Ambassadors program in collaboration with other eLife Ambassadors. We are a group of ECRs advocating for best practices in science to make science open and reproducible. As an advocate for open science and open-source, I do share all of my code on GitHub and also the source code for the ECRcentral platform is openly available on GitHub.

My talk about ECRcentral was well received by the community!

https://twitter.com/yoyehudi/status/1154390803248287746

And ISMB/ECCB 2019 concluded after an inspiring keynote talk by Bonnie Berger of Massachusetts Institute of Technology on Biomedical Data Sharing and Analysis at Scale. Bonnie Berger started her talk with a powerful statement to emphasize the importance of computational biology. She said:

“Biology used to be biology. Now biology is inseparable from computer science.”

Bonnie Berger

I loved it and tweeted right away!

https://twitter.com/khanaziz84/status/1154410102901923841

And I would say that this inseparable biology now needs to be more open and reproducible without borders.

Along the lines of openness to science, ISMB/ECCB and BOSC are setting an example for many other conferences and organizations by recording talks and making those publicly available with the consent of speakers licensed under CC-BY 4.0. I have noticed that most of the talks at several other conferences are recorded but sadly these are put behind the paywalls and community need subscriptions to watch these talks later. There is a great need to digitize conferences and make the recorded talks freely available to everyone, and especially for researchers from developing countries who can not attend these events due to lack of funding or visa restrictions.

To conclude, I would like to thank the OBF for providing the travel fellowship to participate in ISMB/ECCB and BOSC 2019. This travel fellowship was a great opportunity to connect with open source and open science enthusiasts, and I strongly believe that this community will push the boundaries even further to grow and diversify in the years to come.

https://twitter.com/khanaziz84/status/1155005378079395841

Aziz is a computational biologist interested in gene regulation, machine learning, cancer, and regulatory genomics and epigenomics. He is a strong advocate of open science, open-source, preprints, and reproducible research and often tweets about it. He is also an eLife and ASAPbio Ambassador and co-founded ECRcentral, which is powered by eLife.

5 tips to promote 'water cooler effects' at informal discussion sessions

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 27 Aug 2019 22:36:32 +0000

The Open Bioinformatics Foundation (OBF) sponsors a Travel Fellowship program aimed at increasing diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Malvika’s participation at Bioinformatics Open Source Conference 2019 was supported by this fellowship granted to her in January 2019. Find more information here.

The phrase ‘water cooler effect’ is derived from informal gatherings and connections made around water coolers (or vending machines these days!) at the workplace or other formal situations. Such unplanned encounters lead to genuine connections between people resulting in meaningful and productive collaborations. Many research organizations value the importance of such serendipitous interactions, and actively promote them in their work-culture. Conference organizers also recognize its effectiveness and design their program with longer coffee breaks, dedicated slots for informal discussions and designated venues for breakout sessions.

Image on Unsplash by @productschool

Since 2000, the Bioinformatics Open Source Conference (BOSC) has been bringing together bioinformaticians and computational researchers interested in Open Science, to provide opportunities for them to discuss their projects, exchange ideas, learn about the latest practices in bioinformatics, and collaborate with each other. These meetings are attended by participants with different backgrounds, which provides them with a unique environment to gain multiple perspectives into different technical and social issues within the bioinformatics community. To facilitate informal interactions that promote the water cooler effects, attendees are encouraged to lead or take part in the participant-driven discussion sessions called Birds of a feather (BoF) on topics of interest to them. Since these sessions are very short, session facilitators try to encourage interactions between the participants, while making effective use of the allocated time, welcoming different viewpoints, and finishing the session with some defined outcome or future directions.

Image on Unsplash by @zainulyasni6118

I attended my first BoF on the topic of “Unseminar” at the BOSC 2013, where I first met Aidan Budd who was leading this session. Aidan chose the World Cafe method to facilitate this session, where participants could form smaller groups to discuss related topics and switch groups to join different discussions. This informal setting was quite different from the usual speaker-centric format of conferences because it was participant-driven. Everyone immediately felt welcome and included in this session because the emphasis was on learning about the topic at hand together as a group. For a fresh grad student like me, this was a very special experience because I could truly co-exist as a scientist with people of varying levels of experience without feeling like an imposter or someone who didn’t belong there. This discussion didn’t end with the session itself, but catalyzed a much longer discussion after the conference over emails and shared documents, which finally led to a crowdsourced publication on “Ten Simple Rules for Organizing an Unconference”, several long-lasting collaborations among the participants, and Aidan became my mentor and a close friend.

As a community manager, informal discussion sessions are hands-down my favourite way to connect with others, promote collaborations between the existing members of the community and welcome new members while encouraging active participation from them. Since my first encounter with BoFs, I have participated in and led several discussion sessions. In particular, I facilitated one BoF session at BOSC 2017 in Prague, and one session this year in Basel during my participation at BOSC 2019, which was supported by the OBF fellowship, granted to me in December 2018 application round.

off = BoF* :), i.e. Birds of a feather - where people with a common interest can discuss the topic together.

— Malvika Sharan (@MalvikaSharan) July 24, 2019

Here are my top 5 tips for facilitating BoFs or similar discussion sessions that promote the informal and unplanned aspects of the water cooler effect.

1. Set the ground rules

Start your session by welcoming everyone and highlighting the main points of your organization’s/conference’s Code of Conduct. By choosing an inclusive discussion format (see this post by The Instruction Section, ACRL for ideas) we can provide a platform for our attendees to participate equitably. It is also useful to introduce a few simple tips for effective discussions, for example, by inviting volunteers to take different roles such as notetaker, timekeeper, or chair in different groups to ensure that everyone’s voice is heard and noted (see this role card by Ada Initiative).

2. Get everyone on the same page

State the objective of your sessions clearly so that your participants know what to expect. You shouldn’t assume that participants will know the specific details essential to discuss the topic (we can always ask!), therefore, you can take the first few minutes to briefly introduce the topic and the main terminologies. It’s important to clarify what they will and will not discuss in your session.

3. Manage your time effectively

Be thoughtful and appreciative of people’s time that they invest in your sessions. Conferences can be stressful. Listening to talks, taking down notes, and getting introduced to new topics while coping with the busy schedule, new venues, and jet-lag can be both mentally and physically exhausting. Therefore informal sessions should not demand too much effort from our attendees and should allow them to decompress. To make everyone’s time count, you can share a clear agenda and divide your session into short rounds. When a session is attended by a large number of participants, it’s more effective to split them into smaller groups where they can discuss different aspects of the given topic. We should also encourage people to switch groups to maximize their chances for personal interactions. As facilitators, we should minimize our own contribution but shouldn’t hesitate to bring the focus back to the topic when the discussions derail.

4. Make it truly collaborative

Short sessions are great for brainstorming and generating new ideas. To ensure that these ideas don’t get lost after the session is over, there should be possibilities for your participants to collaboratively explore the topic and take notes. Each group can be provided with pens, sticky notes, flip charts, and/or whiteboards to facilitate note-taking or drawing concept maps. Online documents such as Etherpad, google docs and GitHub are generally used for sharing details of the sessions, offering a place for everyone to exchange their contact information, store their notes, add questions, and refer back to after the session is over. These online tools can be distracting if not balanced well with in-person collaborative activities (see this excellent post on facilitating discussions by University of Waterloo). Each group discussion can be guided by a set of questions or scenarios and the chair of each group can be asked to share the outcome of their discussion with everyone.

5. Communicate your next steps

Even though these events are short, it’s always useful to use a few minutes towards the end of the sessions to bring the entire group together to invite final thoughts and possible directions for the discussed topic and ideas. You can set a few channels of communication that the attendees can use in order to connect with each other and continue the discussion afterward. Since we want to be mindful of the contributions made by our participants, it’s important to let them know where and how the outcome of their discussions will be used, how they can reuse the material, and where they can access them in the future. After the conference, a summary of the session in a collaborative document and further details can be shared with a “Thank You” email.

Picture from a BoF I facilitated during BOSC 2017 on ‘Promoting Diversity at Bioinformatics Conferences’

To conclude, informal discussion sessions are useful for collecting ideas, gaining perspectives, and engaging with others over informal conversations on topics of mutual interests. With a little pre-planning, these meetings can turn an idea discussed over coffee or by the water coolers into useful community-driven projects. I hope you find these tips useful and take advantage of this format at the next BOSC or in your community events.

Do let me know on twitter ( @malvikasharan) which of your favourite tips are missing in the post.

Cordon Bleu Bioinformatics

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 25 Aug 2019 18:08:26 +0000

I attended the Bioinformatics Open Source Conference ( BOSC 2019) organized this year along with ISMB/ECCB in Basel, Switzerland from July 21st-25th. BOSC 2019 was in multiple ways a lot of ‘firsts’ for me. I was attending my first ISMB/ECCB. It also happened to be my first time in Europe. It was the first time I was putting faces and voices to a lot of names. Like in most of the conferences these days, I met a lot of Twitter-verse friends for the very first time. And above all, this was my first ever BOSC. I was funded in part by the Open Bioinformatics Foundation’s Travel Award and ISMB/ECCB’s Travel Fellowship. My travel and the learnings I summarize here would have been impossible without both.

Nomi Harris introducing the 20th BOSC 2019 (Couldn’t capture Nomi at this angle)

BOSC and me

I had been trying to go to BOSC for around three years. I submitted three abstracts over the three years which were all accepted for a lightning talk. However, a lack of funding made it impossible for me to make it to BOSC 2016 and BOSC 2018. I submitted my abstract for a poster and talk about pysradb that was selected for a lightning talk (a short five-minute talk) and a poster.

ISMB/ECCB Single Cell Workshop

I arrived in Switzerland on July 19th, two days earlier than the official start date of the meeting and a day earlier than the Tutorial tracks.

OBF’s Travel award not only covered my ISMB registration but was also generous enough to cover the registration costs for Tutorial(s). ISMB/ECCB 2019 had multiple tutorial tracks spanning the fields of interpretation of deep learning in biology, computational drug discovery, statistical methods for single-cell RNA-seq, biological data visualization, biomarker discovery and tools for reproducible analysis. I decided to attend the tutorial on statistical methods for single-cell RNA-seq primarily to get an overview of the single-cell world, which is not very distant from my current research interest of deciphering translation regulation. The tutorial was very comprehensive and gave an overview of the technology, its nuances and the methods developed to tackle them. I expected it to be a bit more methods oriented, but it is difficult to have the best of everything for a diverse audience.

Keynotes at ISMB/ECCB

ISMB/ECCB being a large conference (owing to the fact that it is two conferences combined into one) is organized into multiple tracks. The upside of a large conference is that there is so much new to learn. An obvious downside is that it could be overwhelming. I followed an “on-the-day” optimization strategy where I would look up schedules for the talks for a day in the early morning. This would have been practically impossible without the ISMB’s conference app. Though there are traditional conference booklets, an app comes in handy in scheduling. Given the multitude of tracks involved, I would keep running from one room to other. The calm dusk at Rhine river came to the rescue after each day’s heated effort, quite literally,

I made sure I attended all the keynotes. Day 1 had Dr. Nikolaus Rajewsky’s keynote on how single-cell RNA-seq is making it easier to improve our understanding of gene regulation on a much granular scale in space and time. Day 2’s Keynote had Dr. William Noble walking us through the applied machine learning world in genomics: an embedding method for inferring the corresponding cells given two biological assays data and an imputation method for learning the latent representation of the epigenome. Day 3 had Dr. Alexis Battle talking about modeling the complex impact of common and rare genetic variation on gene expression. The field of Genomics is full of examples of missing ground truth. On Day 4, Dr. Christophe Dessimoz talked on “Challenges and rewards of benchmarking – how to cope with a biased, incomplete, or even entirely missing ground truth”. I had been aware of Dr.Christophe’s work through his paper on the ortholog-paralog conjecture. Finally, Dr. Bonnie Berger’s keynote introduced me to the perils of data sharing in the genomic world and the solutions her lab has worked on over the years.

Poster Sessions

The poster sessions were spread over 4 days of ISMB/ECCB. With approximately 1000 posters, it is overwhelming to digest all the information you obtain. I again relied on the ISMB/ECCB mobile app to shortlist ones that I really wanted to learn about. I am sure I still missed out on a bunch.

Keynote at BOSC

Dr. Nicola Mulder’s keynote introduced us to the challenges faced by African countries, owing to their history of exploitation and inequitable scientific partnerships.

https://twitter.com/GigaScience/status/1154012905639206912?ref_src=twsrc%5Etfw

H3ABioNet is a Pan-African bioinformatics network that is trying to address this challenge by making the controlled access data findable and interoperable for both data providers and users.

BOSC Takeaways

BOSC happens over two days of the main conference that is often followed by another two days of C oF est. Unfortunately, I was not able to participate in CoFest. BOSC was packed with sessions on data crunching, data modeling and formats, containers, open science, workflows and building open source communities. Besides these sessions there were also independent Birds of a Feather sessions (BoFs) which are informal self-organized meetups on a myriad of topics, spread over the two days. I participated in the “Reimaging the paper” BoF organized by Dr. Emmy Tsang of eLife Innovation. We discussed how the traditional model of publishing is limited in terms of reproducibility. The journals need to define a minimum standard for ensuring reproducibility, but defining what these gold standards should be, still remains a challenge in itself.

Summarizing all the talks at BOSC would be near impossible here. So I will describe the ones that got me super excited. The first one was by Dr. Malvika Sharan, on how promoting inclusiveness in Open Science communities requires an “open by design” approach where information sharing is scalable, the community is welcoming and supportive of newcomers and there are appropriate channels for skill transfer.

https://twitter.com/yoyehudi/status/1154384936893329408

Dr. Devon Ryan’s talk on snakePipes was another talk that stuck around with me as it solves a critical problem that I have faced as a computational biology PhD student. A lot of data analysis requires mundane steps in analysis. snakesPipes is designed to make this useful for everyone with such a need, without forcing them to be familiar with CLI.

https://twitter.com/dpryan79/status/1154277950151372800?ref_src=twsrc%5Etfw

If you are wondering what “eierlegendewollmilchsau” is, to the best of my knowledge (and memory), it translates to “has only advantages, satisfies all needs, meets all demands” and probably fits in well with the ideology behind snakePipes.

Mateusz Kuzak from Elixir in his talk “ELIXIR Europe on the Road to Sustainable Research Software” encouraged everyone to open source their work from day one. No, there is no evidence of your work being scooped if you choose to do so. Here is his advice:

https://twitter.com/morgantaschuk/status/1154326308203257857

I need to mention my fellow OBF Travel awardee Dr. Aziz Khan’s efforts at building ECRcentral that helps early-stage researches find and discuss funding opportunities besides providing them a platform to share their experiences and mentor peers. As an early stage researcher myself, I have found the resources there extremely useful.

Finally, a project that I will keep a lookout on is Biotite by Patrick Kunzmann designed as a comprehensive and efficient computational molecular biology library. But we already have Biopython? Well, yes and no. Extensive usage of numpy and cythonization results in reduced runtimes.

Biotite and Biopython: Open source wins

Biotite’s perfomance compared at multiple tasks

My lightning talk at BOSC

My schedule before leaving for ISMB/ECCB 2019 from Los Angeles was jam-packed. I did the grave mistake of overestimating my ability to make a presentation for a 5-minute lightning talk. You just have to talk for 5 minutes, but then you have only five minutes. My presentation was only complete the night before my actual talk and would not have been possible without the feedback of Meghna Verma, a PhD candidate at Virginia Tech. I met her also for the first time at ISMB. I had a lightning talk on Day 1 where I talked about pysradb, which I built over the last year to help me in my Ph.D. project. In the future, I plan to not overestimate my abilities, they are not worth the potential ill-effects they can have.

https://twitter.com/yoyehudi/status/1153969142665502720?ref_src=twsrc%5Etfw

I also had a poster on pysradb on the day of my lightning talk. I got a lot of visitors and a bunch of feedback. I hope pysradb also gets more contributors in the days to come!

P-01: pysradb poster

Applying for BOSC Travel Award

If you are thinking of traveling to any event promoting open-source bioinformatics software development and open science in the biological research community, OBF covers up to USD 1000 and it is possible to request a higher amount. The application process is one of the smoothest I have ever come across!

Application Deadlines: April 15, August 15, December 15 every year.

Applying for ISMB Travel Fellowship

ISCB also provides Travel Fellowships that can come in handy if your original source of funding is not sufficient. Switzerland travel was a bit expensive, so I had applied for a travel fellowship once I got an acceptance. If you are submitting to ISMB in the future, you will receive instructions via email if you want to apply for a Travel Fellowship. Both the OBF and ISMB applications are very easy to fill out.

Cordon Bleu?

Though more often associated with a dish, I chose the title of this post as such for the high quality of talks at ISMB/ECCB and BOSC. I learned a lot in the span of five days and look forward to participating in the future as well. Again, I can’t thank enough the Open Bioinformatics Foundation and ISMB/ECCB for making this cordon bleu experience possible.

Cordon Bleu - the dish

Dusk at the Rhine river, a few minutes walk away from the conference venue

Meeting report: BOSC 2019, the 20th Annual BOSC

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 01 Aug 2019 20:45:36 +0000

As Europe experienced a record-breaking heat wave, BOSC 2019 attendees stayed cool in the Basel Congress Center (and many took breaks by floating down the Rhine). This was the 20th annual BOSC. In 2018, BOSC partnered with the Galaxy Community Conference in GCCBOSC2018; this year, it returned to ISMB as one of over a dozen “Communities of Special Interest” (COSIs).

BOSC 2019 opened on July 24 with chair Nomi Harris noting that over its 20 years, BOSC has been held in 12 different countries, 6 US states and 2 Canadian provinces. Next, Heather Wiencko introduced the Open Bioinformatics Foundation, BOSC’s parent organization, and Kai Blin discussed the OBF’s participation in Google’s Summer of Code. The two morning sessions focused on data–representing it, storing it, crunching it. Open Data was covered in another session later in the day.

The second day started with Late-Breaking Lightning Talks, which offered peeks at the latest open source / open science research. Next up was a popular new session on Containers, followed by an Open Science session. Our ever-popular Workflows session was followed by a session called Building Open Source Communities (check out the acronym!), which opened with a talk by newly-elected (at the public OBF Board Meeting held during BOSC) OBF Board member Malvika Sharan on Inclusiveness in Open Science Communities.

This year’s keynote speaker was University of Cape Town professor Nicola Mulder, who spoke on “Building infrastructure for responsible open science in Africa.” Sharing data in Africa involves technical, ethical and social challenges (“It’s really hard to convince people to share their data and their tools when they have such a history of being exploited,” she observed), but despite these obstacles, the H3ABioNet Consortium (of which Prof. Mulder is lead PI) is making progress in building a pan-African bioinformatics network.

The two-day meeting included a total of 46 talks and 55 posters. During the meeting, attendees generated over 1500 tweets mentioning #BOSC2019(you can find them in JSON format here).

BOSC closed with an announcement that next year’s meeting will be held in collaboration with Galaxy’s Community Conference as the Bioinformatics Community Conference (BCC 2020), which will be held in Toronto, Canada, July 18-22, 2020. We may return to ISMB in 2021 (this has not yet been decided).

The two days after BOSC, about 50 people participated in the OBF-run CollaborationFest (or CoFest for short), an event at which participants work together to contribute to bioinformatics software, documentation, training materials, and use cases. CoFest 2019 was held at The Swiss Innovation Hub for Personalized Medicine in Basel.

The OBF/BOSC thank our sponsors for helping to support BOSC, the CoFest and our ongoing Travel Fellowship program: AWS, Google Cloud,eLIFE, PLOS Comp. Biol., GigaScience, The Hyve, KNIME. and the Software Sustainability Institute.

Figure 1: The BOSC 2019 Organizing Committee (from left to right: Peter Cock, Karsten Hokamp, Yo Yehudi, Nomi Harris, Monica Munoz-Torres, Heather Wiencko, Michael Heuer, Bastian Greshake Tzovaras; not shown: Chris Fields)

Figure 2: A rapt audience at BOSC 2019

Figure 3: Many people escaped from the heat by swimming in the Rhine, which runs right through the middle of Basel

BOSC late-round abstract submission closes May 15!

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 09 May 2019 23:48:35 +0000

If you’d like the opportunity to present your work at BOSC 2019 (which will take place in Basel, Switzerland, on July 24-25, the last two days of ISMB/ECCB 2019), now’s your chance! The late round of abstract submission is open, and we will be choosing a few abstracts for “Late-Breaking Lightning Talks” as well as posters.

BOSC welcomes submissions about all aspects of open source bioinformatics, open science and open data. More information, and a link to the EasyChair submission portal, can be found at /events/bosc/submit/ .

A few tips to increase your chances of success: 1. Work discussed in BOSC presentations must be open source, with a recognized open source license and a URL for accessing your code. Submissions that don’t meet those requirements will be rejected. 2. We look for impact in building or sustaining open source communities. It’s ok if your project is just getting started–tell us about how it will help the community, and how others will be able to contribute to it in the future. 3. If you submitted an abstract in the first round and didn’t get selected for a talk, you can revise your abstract and make a new submission in the late round. (You can’t just update your previous submission–you must start a new one in order to be considered for the late round.) 4. All submissions must include a 200-word summary. A one- or two-page PDF is also encouraged, though not required for poster-only submissions. We hope you’ll use the extra space to tell us more about your project and how it fits into the bioinformatics open source ecosystem, and maybe add some cool pictures, too!

Note that the deadline for submissions is Thursday, May 15, at 23:59 in the “Anywhere on Earth” time zone, which is UTC-12. That means that for almost everyone, the deadline is effectively the morning of May 16.

Please spread the word about BOSC–we welcome everyone, and are actively seeking to increase the diversity of our participants.

To keep informed, follow us on Twitter or join our public Gitter room.

New OBF logo

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 05 Nov 2018 22:00:53 +0000

We have successfully crowd-sourced a new OBF logo! The process started at the OBF Birds of a Feather meeting at GCCBOSC 2018 when the OBF leaders announced that we were seeking a new logo design. Two BoF participants immediately started sketching ideas, as well as a third community member who was not at the BoF but saw our tweet. The designs (which you can see here) were put up for a public vote. Aleix Lafita’s narrowly won and was adopted as our new OBF logo! We are currently working on possible variations on the logo for special events or causes (for example, a rainbow version).

The OBF is delighted that community members responded to our request for new logo designs with creativity and focus–attributes that are valuable in the open source community.

If you’re interested in joining the OBF and getting on our (low-traffic) mailing list, please fill out a membership application here!

The color of bioinformatics: what is it and how can it be modified?

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 29 Aug 2018 10:33:49 +0000

This is a guest blog post from Tendai Mutangadura, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the GCCBOSC 2018 meeting in Portland, June 2018. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. This was one of three awards from our April 2018 travel fellowships call. Our August call recently closed, the current call closes 15 December 2018, you might want to apply?

When I was selected as one of 3 recipients of the April 2018 OBF Travel Fellowships, I wanted this to signify a turning point in my career. I expected to meet and interact with many great minds in open science and bioinformatics, and the GCC-BOSC 2018 meeting in beautiful Portland exceeded my expectations. Because I was travelling light and had been to Portland once before, I chose to use public transport from PDX to get to Reed College, the meeting venue. This afforded me a mini tour of Portland before getting to the serious but fun business of the meeting. When I stepped off the Reed College bus stop, I flagged down the first person I saw to ask for directions to the registration venue, and this person was none other than Anton, one of the scientists instrumental in the development of the Galaxy project. Great start. As we chatted en route to the registration place, I took the opportunity to brag to him that I had recently figured out the causal mutation associated with a neurodegenerative disease in one of our whole-genome-sequenced dogs using the web-based Galaxy platform.

I attended as many training sessions related to Galaxy on Day 1 of training as I could. I have been a Galaxy platform user for >3 years and had previously attended the GCC 2016, so it was great to meet new and old acquaintances this time round. I even had the opportunity to get help with aspects of my Jetstream account virtual machines during one of the two CollaborationFest days that I attended. I found the CollaborationFest very useful in making new contacts and discussing potential future collaborations.

On Day 2 of Training, the highlights of my training, based my bioinformatics needs, included a 2.5 hour GATK training session and the bcbio workshop. In the latter, Brad Chapman, starring here, talked about and demonstrated how communities can work together to make giant strides in developing robust open source software pipelines and making these freely accessible to anyone, everyone, anywhere. For someone like me, for whom having access to computing resources and setting aside the time to focus on developing or tweaking code as part of my day job can sometimes be an uphill struggle, the bcbio workshop was a godsend. Bcbio allows me to do my day job duties and do bioinformatics too. After the meeting, I immediately contacted one of my XSEDE Extended Collaborative Support Services ( ECSS) team members, Phil Blood, to discuss the possibility of putting together a species agnostic variant-calling pipeline. I have already started this project using my XSEDE start-up grant computing resources allocation on Bridges, at the Pittsburgh Supercomputing Center ( PSC). So far, I have been off to a good start. For those who may not be aware of the many great free computing resources out there, such resources exist, as I have alluded to above, for anyone to take advantage of.

Now, a light-hearted reference to a serious (according to me), but common observation at conferences such as but definitely not limited to GCC-BOSC: the lack of diversity of attendees. This is what prompted me to title my blog post the way I did. My first answer was (metaphorically speaking) that the color of bioinformatics should be ‘rainbow’. But when I googled ‘rainbow colors’ it occurred to me that the colors black and white are not part of the rainbow. I also refreshed my rusty optical physics and got explanations why this is the case. Now, to get back on track, would it not be wonderful if more people of color were involved in this bioinformatics revolution? What can be done to redress this current state of affairs? Thumbs up to the OBF for recognizing and doing something about this lack of diversity by creating the OBF Travel Fellowship! For my part, when and if I complete any pipeline(s) based on bcbio code, I plan to publish a collection of such pipelines online as self-paced tutorials (the website will go live soon) in a very user-friendly format targeted to those who are command line challenged, from any community, to encourage them to get started in bioinformatics analyses, or at least analyze their own data without buying expensive commercial packages. This would be my way, albeit at very small scale, of democratizing bioinformatics. One of the advantages of involving people with as diverse backgrounds as possible with basic training in bioinformatics and genomics is that this may help reduce mistrusts linked to unfortunate historical incidents such as the Tuskegee experiments, not only for countries like the US but anywhere around the world where similar types of mistrust may exist.

City of roses they call it - Portland Oregon (USA)

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 18 Aug 2018 15:27:34 +0000

How should I start describing the fruitful experience in this amazing city… First time ever in Portland, second time attending BOSC… I knew I was signing up for a great time but did not know much about the uncanny beauty of this picturesque city.

First of all, I would like to thank the Open Bioinformatics Foundation (OBF) for providing partial funding to support my travel expenses (though an OBF Travel Fellowship award). I would also like to thank my PhD supervisors Andrew Lonie and Richard O. Sinnott for the remaining expenditure.

I had written a very detailed blog post of my experience in BOSC 2017. The experience was a bit different this time as BOSC was organised in conjunction with Galaxy Community Conference(GCC) this year, unlike previous all times when BOSC was held with ISMB. On a lighter note, the most positive difference (as compared to last year) was the unlimited supply of coffee/tea in the coffee town throughout the conference to keep the morale high. The other difference was the budget-friendly registration costs of the conference this year. The cheaper accommodation options were available in the hostels of Reed College, the beautiful and lush green venue for the conference.

The conference was divided into three cores:

Training days: The first two days June 25th and June 26th were focused on training sessions running in parallel covering various bioinformatics topics such as Galaxy introduction, RNA-seq data analysis (Galaxy and bcbio), Data carpentry workshop, Conda-Containers, Workflow Definition Language( WDL) and Common Workflow Language (CWL) introduction.
Conference days: The next two days June 27th and June 28th were dedicated to parallel sessions of Galaxy and BOSC talks taking place in two different venues with combined keynote speeches.
Core Cofest days: Unlike last year, the intense collaborative hacking sessions were after the conference on June 29th and 30th.
Encore Cofest days: July 1st and 2nd also part of cofest but on a smaller scale with fewer participants.

This year was special in one more aspect that I contributed in the reviewing process as part of the BOSC program committee.

https://twitter.com/farahzk03/status/1011658076900823040

I have attended all 8 days of the conference beginning from the training all the way to end of the Encore cofest. My abstract was accepted for a long talk (and by default for a poster) in BOSC so there was a bit of anxiety until I was done with my presentation on June 28th :). There were so many interesting parallel training sessions and it was quite a tough decision to choose which one to attend. I managed to attend few such as Conda and Containers, Common Workflow Language and Snakemake and Nextflow. During the CWL training session on June 26th, I volunteered to help with the session to answer questions during the training.

https://twitter.com/rvmngr/status/1011701337719857152

Like last year, I decided to print my poster at the venue to save myself from the hassle of carrying it from one continent to the other. Keeping that in mind, I did the same this year. I got the poster printed from a local printing press Minuteman Press. The staff was highly professional, talking over the phone, placing the order over the phone, sending poster via email and paying online saved me from having to visit the shop twice. They checked the poster, called again clarified few things to make sure things are appearing the way they should be. I would say overall the experience was pretty smooth and the print quality was also up to the mark. There were in total two poster sessions, each in the evening of the conference days. My poster was scheduled for the evening session on June 27th. I received the printed copy on the morning of 27th which I arranged on the assigned slot.

https://twitter.com/farahzk03/status/1012073266599489537

The conference on June 27th started with very informative and interesting keynote speech by Fernando Perez on “Sustainable development of scientific open source tools: a view from Jupyter”.

https://twitter.com/farahzk03/status/1012002955053027328

I must admit I was not aware of the functionality of Jupyter notebooks before this and how interactive these are supporting many scripting languages as including Python, R, Julia, and Scala. Fernando was of the view that computational hygiene should be a day to day practice.

https://twitter.com/farahzk03/status/1012013507942891522

Followed by keynote was an interesting talk where four engineers collaborating remotely for the project “FROG”, shared their experiences with the packaging technologies. One of the many lessons emphasized in the talk is " The first step to learn packaging technologies: read the manuals."

https://twitter.com/farahzk03/status/1012019611741577216

An interesting talk in the evening session was given by Ravi K. Madduri on “Reproducible big data science: A case study in continuous FAIRness in which he explained how they demonstrated reproducibility of real-life workflows using Galaxy, minids and BDBags to achieve interoperability in naming and identifier conventions. He emphasized that reproducibility requires patience and discipline but “Reproducibility is like brushing your teeth. Once you learnt it, it becomes a habit .”

https://twitter.com/farahzk03/status/1012079639890546688

Some other talks in this session were Intermine 2.0 by Yo Yohudi, NIH Data Commons Introduction by David Siedzik and Snakemake by Johannas Koster. I rushed from Vollum hall where BOSC talks were organized for the Poster presentation In Performing Arts Building. The poster session was very interactive and the audience enjoyed the tea/coffee walking around and asking the presenters about their work. I think the time went by very fast and we had to rush back for the Panel discussion in Vollum hall which I missed a bit because of the ongoing conversations at the poster venue,

As I arrived late so could attend half of the panel discussion. The panel discussion was on a topic which is of my personal interest as I am working on Provenance of the Bioinformatic workflows. The topic of the discussion was “Training and Documentation in Bioinformatics” where Fernando Perez, Tracy K. Teal, Jason Williams and Berenice Batut were guests.

https://twitter.com/farahzk03/status/1012127092421455872

Also, GigaScience has the coolest Game of Thrones-themed shirts as always :D I got my hands on one last year but this year I could not get one :(.

https://twitter.com/farahzk03/status/1012175720682905605

After the panel discussion, now the time was to prepare for my talk the next morning. I was very anxious but also excited to present what I am passionate about. Michael R. Crusoe was patient to listen to me, very kind to help me with the preparation of the presentation and encouraging that it will all be good. I don’t have a massive public speaking fear but the start is always the hardest.

The highlight of June 28th for me was the presentation which was scheduled for the morning session at 11:40 am. It turned out to be better than I expected :). A huge sigh of relief and then I could really enjoy the rest of the talks without thinking about mine.

https://twitter.com/biocrusoe/status/1012394197121261568

My talk was about CWLProv, a format for the representation and automatic aggregation of workflow enactment, its results and provenance to promote interoperability and reproducibility of methods. The feedback from the live audience during and after the presentation and on twitter was very helpful and encouraging, one of the most outstanding characteristics of the BOSC community :).

https://twitter.com/yoyehudi/status/1012401483776577537

https://twitter.com/farahzk03/status/1012479030979747841

The day got better with many interesting talks such as celebrating that CWL, a project that was founded in 2014 during the discussions in BOSC2014 turned four years old :). It is exciting to see how much the standard has grown and influenced projects all around the globe with more than 20 participating organizations and many individual contributors. CWL is an epitome of “Open Source-ness” and Community-driven projects designed with continuous interaction with the community itself to build a standard for workflow definition which promotes interoperability, portability and reproducibility and resolves the heterogeneity issue in workflow domain.

https://twitter.com/yoyehudi/status/1012395134665703424

Another highlight is the provision of affordable daycare for the participants and encouraging participants from all backgrounds to participate. An example was Cristel Thomas presenting in Galaxy session with the youngest participant with her. That’s the example, this amazing event is set for the other conferences. Encouraging participation if you are eager, no matter what the circumstances are.

https://twitter.com/crstlthms/status/1012054388347555840

The day ended with an open door BBQ conference dinner, the weather, the food, the mood everything was on point. The beauty of the lush green campus and artistic architecture is breathtaking, sad that I was not able to explore much beauty but whatever I saw and wherever I went was telling a story.

https://twitter.com/farahzk03/status/1012528947836276736

A big improvement during Cofest was gender balance which was a bit alarming last year during code fest where only 3 female participants joined in total out of >60 participants. This year the situation improved drastically because of the two communities doing it together. The venue was quite spacious and full of resources to accommodate more than 100 participants working on different projects.

Like always the regular updates from groups were spread throughout the day, in the morning, before lunch and at the end of the day. These update sessions keep you going and motivate you to push yourself for tangible outputs. I worked alongside Michael (CWL) and we refactored the implementation of CWLProv, improved the prototype implementation working continuously for four days of cofest.

I believe in collaborative science without caring about geographical scenarios but with a huge time difference, it does get tricky sometimes to work together on a project. These four days were breath of fresh air discussing long due issues face to face, getting instant help, contributing more efficiently and getting a Pull Request with 338 commits merged into cwltool :). That is the biggest highlight for my participation and I am sure it would have taken much longer if I did not have this opportunity. I encourage everyone to participate in the code fest as it will increase your productivity 10x.

https://twitter.com/farahzk03/status/1016537277160275974

P.S. Some other day, I will write about my experience with food, walks around the city, strolling on the river bank and the non-science talks.

Taking Turns

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 02 Aug 2018 16:55:44 +0000

BOSC 2019 will be part of ISMB 2019 Every year until 2018, BOSC was part of the annual ISMB conference as a community of special interest (COSI, formerly known as a SIG, Special Interest Group). As part of our continuing quest to broaden and deepen the BOSC community, we decided to perform an experiment this year by partnering with the Galaxy Community Conference rather than with ISMB. As we reported, the experiment was a success–participants were overwhelmingly positive about the experience, and the conference did attract a somewhat different mix of attendees than in past years. However, we also concluded that there are some advantages to meeting with ISMB–for example, it attracts more students and postdocs, and the presence of other COSI tracks provides a wider range of scientific topics. Moreover, unlike the GCC 2018 venue, the venue already chosen for GCC 2019 has a number of drawbacks: we wouldn’t be able to run similarly-sized parallel sessions; registration prices wouldn’t be as affordable as in 2018; and the venue would not be able to accommodate the larger (160 people) and longer (four days) CollaborationFest that was one of the highlights of GCCBOSC 2018.For these and other reasons, the BOSC organizing committee concluded that the best way to serve the broadest community of potential BOSC attendees will be to partner with ISMB some years and GCC some years. We therefore plan to hold BOSC 2019 in Basel as part of ISMB. We hope to partner with GCC in 2020 at a North American site to be determined, or in 2021 in Europe.Wherever we hold future BOSCs, you can be sure that they will include a wide range of topics in open science and open source bioinformatics, and we hope that they will draw an ever-diversifying mix of attendees. As always, we welcome your feedback about what you liked in past BOSCs and your suggestions for the future. Feel free to email us ( bosc@open-bio.org) or tweet (@OBF_BOSC).

GCCBOSC 2018 post-meeting report

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 27 Jul 2018 19:52:39 +0000

This year, the Galaxy Community Conference (GCC) and the Bioinformatics Community Conference (BOSC) met together to form the first Bioinformatics Community Conference. At GCCBOSC 2018, participants were able to meet and collaborate with a broad community of bioinformatics developers and users who focus on open, interoperable software tools and libraries that facilitate scientific research.

Held in June 2018 at Reed College in Portland, Oregon, GCCBOSC attracted nearly 300 participants from around the world. The meeting started with two days of training workshops (Figure 1). The main meeting had some parallel sessions and some joint sessions, including well-received keynote talks by Tracy Teal, Fernando Pérez and Lucia Peixoto, as well as a panel discussion about documentation and training. Posters, demos and Birds of a Feather sessions ( BoFs) gave participants opportunities to engage in discussions about topics of mutual interest. After the main meeting, many attendees stayed for up to four additional collaboration days (the CollaborationFest, or CoFest). Figure 1. Participants at one of the GCCBOSC training workshops. (All GCCBOSC photographs in this post are from Bérénice Batut’s Flickr album, under a CC-BY-SA license.) Figures 2,3. Attendees and presenters mingled at the poster/demo sessions.

Figure 4. CoFest attendees assembled for morning meetings before breaking into smaller groups to work on collaborative projects.

There was wide agreement among GCCBOSC participants that the meeting was informative, productive and enjoyable. Comments from participants in the post-meeting survey included, “Loved the mix of communities!”, “Location was great,” and “Nice conference. Nice atmosphere. Nice people. I really enjoyed it. Thanks!”. The training workshops and extended CoFest were mentioned by participants as great features of the meeting. Most of the survey respondents who had previously attended a GCC or BOSC rated this year’s meeting as similar or better than past meetings (Figure 5). The main complaint was that the parallel GCC and BOSC sessions forced attendees to choose between them–an embarrassment of riches.Figure 5: Responses to post-GCCBOSC survey questions from those who had been to previous GCCs or previous BOSCs.Although post-meeting feedback was almost entirely positive, we did receive two reports of behavior at GCCBOSC that the reporter perceived as not consistent with the spirit of the Code of Conduct. These were handled by the GCCBOSC organizing committee, and everyone involved is satisfied with the outcome. The discussions held by the organizers around these issues led us to re-examine the CoC and think about how we might want to revise it for future meetings. Your input on this topic (or anything regarding GCCBOSC) is welcome.We are grateful to all those who helped make GCCBOSC 2018 a success: the organizers, presenters, workshop leaders, participants, and our generous sponsors, including Platinum sponsor Google Cloud and Gold sponsor Lenovo + Intel. Thanks in part to sponsor funding, we were able to offer subsidized child care and an onsite lactation room that enabled a speaker who would otherwise have been unable to attend to bring her four-month-old baby and participate actively in the meeting.Whether or not you attended GCCBOSC 2018, we look forward to interacting with you in the future!

Following up from BOSC's OBF Birds of a Feather meeting

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 09 Jul 2018 15:49:30 +0000

It was really great to meet so many of you at GCCBOSC this year! We will soon have a couple of Travel Fellowship blog posts talking about the conference, so we won’t provide too much of a general overview at this point, but we would like to share a little more about one of the Bird of Feather (BoF) events we ran - specifically the OBF community BoF. The aim of this BoF was to engage anyone who was:

Curious about the OBF
Interested in suggesting ideas
Wanting to help or get more involved with the OBF

The OBF BoF started with a pre-dinner round where we all introduced ourselves and why we were interested in the OBF, and a second round after a quick bite and relocating inside - Portland can get chilly fast in the evening! Motivations for participating in the BoF included a desire to help people who come from a software background learn more about the biology / bioinformatics side of things. Other participants shared the feeling that they loved the conference but weren’t sure how to take home the “open / good practices make for better software and better research” message we were trying to share. We ended up with lot of brainstorming and helpful discussions - here are some of the topics.

OBF logo and site

The OBF logo is over a decade old now and looks a little… dated. When we floated the idea of redesigning it at the meeting, we didn’t expect to have sketches roughed out by several attendees before the end of the BoF meeting! We’ve ended up with three different design sets, which you can check out or comment on in this GitHub issue. We’re also considering updating the entire OBF site, if we can find someone to work on that (possibly a summer intern).

Increasing year-round sense of community

For many people, BOSC and the OBF are approximately the same thing - which makes sense, since BOSC is one of the biggest and most noticable things we do. We’d like to support open bioinformatics all year, though. Possible ways we could do this:

Local OBF / bioinformatics meetups or hackathons. If the OBF created guidelines for this, would you be interested in running a group in your area?
Newsletters with project updates, interesting open / bioinformatics news, events, etc.
“How to be open in bioinformatics” webinar - a sort of “open 101” for projects that are interested in being open but aren’t sure where to start. This would be a nice way to kick-start projects that want to present a poster or talk at BOSC but don’t yet meet the openness requirements. (Note that anyone is allowed to attend BOSC, whether or not they have any open repositories - it’s only presenting that mandates a fully open project.)

Joining the OBF as a project or individual

A pertinent question asked at the BoF was: why join, as an individual? Many people have attended BOSC multiple times and even been heavily involved in the community without officially being in the rolls of registered members. The primary reason to join is the ability for membership to vote on issues pertaining to the OBF. In the next few months, we’re hoping to run a vote on changing OBF bylaws pertaining to how projects join, as well as a plain to adopt a Code of Conduct that may apply to both the OBF and its member projects. If this matters to you because A) you care about a project that might be joining soon (there are a couple!) or B) you’d like to see the OBF adopt a more explicit behaviour standard in the form of a CoC, please join the OBF so you can vote!

Get involved

After reading all this, if you’re interested in helping out with any of the ideas or initiatives suggested, please follow up by any of these mechanisms:

Open an issue on our OBF-docs repo - this is our preferred method as it allows others to chime in easily and is less transient than a tweet.
Leaving a comment on this post!
Tweet to @obf_news

Also - please don’t forget to join the OBF if you haven’t already. Any BOSC attendee automatically qualifies for membership, and even if you haven’t attended BOSC before, if you’re reading this post there’s a good chance you’ll fulfil the requirements anyway. Details are in the form!

OBF-BoF-2018 - 25

OBF-BoF-2018 - 31

Hilmar, Peter, and Yo

OBF Birds of a Feather at GCCBOSC 2018

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 14 Jun 2018 18:11:25 +0000

If you’re going to GCCBOSC 2018, we invite you to join us at the OBF Birds of a Feather on Wednesday, June 27, from 5:40-7:40pm. Come and chat over dinner! Everyone is invited, whether you’re a longtime OBF member or someone who’s never even heard of the OBF. (By the way, anyone who is involved in open source or open science is welcome to join the OBF, and there is no membership fee.) More details at https://gccbosc2018.sched.com/event/FCGp We look forward to seeing some of you there!

GCCBOSC 2018: A Bioinformatics Community Conference - Call for Abstracts

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 21 Feb 2018 10:07:04 +0000

We are pleased to announce that abstract submission and early registration for GCCBOSC2018 are now open. This event brings our annual Bioinformatics Open Source Conference and the Galaxy Community Conference together into a unified week-long event. If you work in open source life science or data-intensive biomedical research, then there is no better place than GCCBOSC 2018 to present your work and to learn from others.

Dates: June 25-30, 2018 Location: Reed College, Portland, OR GCCBOSC website: https://gccbosc2018.sched.com/ BOSC website: /wiki/BOSC_2018 Email BOSC organizers bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Twitter: @OBF_BOSC, #GCCBOSC

Important Dates

Abstract submission deadline: March 16, 2018
Authors notified: April 10, 2018
Travel fellowship application deadline: April 15, 2017
GCCBOSC 2018 Training: June 25-26, 2018
GCCBOSC 2018 Talks: June 27-28
GCCBOSC CollaborationFest: June 29-30

About BOSC

Since 2000, the yearly Bioinformatics Open Source Conference (BOSC) has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.

Why is BOSC partnering with GCC in 2018?

In past years, BOSC has been part of the ISMB conference. Because of our continuing focus on broadening and deepening the BOSC community, we’ve been exploring ways to reach those in the bioinformatics community who aren’t already part of the audience attracted by ISMB. As part of that exploration, we have looked at other organizations and conferences that have been successful at establishing a strong and growing community of participants, such as the Galaxy Community Conference (GCC).

After much discussion and planning, we decided to hold BOSC in conjunction with GCC in 2018. We hope that this will be an enjoyable and productive experience for all participants, and we welcome your feedback before, during and after the event.

As always, BOSC 2018 will include two days of talks and posters, two keynote speakers, a panel discussion, Birds of a Feather, and more. BOSC sessions will run in parallel with GCC 2018 sessions, with some sessions shared. The two days of talks will be preceded by two days of training on topics nominated by the community, and will be followed by a two-day CollaborationFest that merges BOSC’s Codefest and Galaxy’s Developer and User Hackathon Days.

Abstract submission

We encourage you to submit one-page abstracts (due March 16) on any topic relevant to open source bioinformatics or open science. After review, some abstracts will be selected for lightning talks, longer talks, demos and/or posters. Abstract submission instructions and a link to the EasyChair submission portal can be found on /wiki/BOSC_Abstract_Submission BOSC session topics include (but are not limited to):

Open Science and Reproducible Research
Open Biomedical Data
Citizen/Participatory Science
Standards and Interoperability
Data Science
Workflows
Visualization
Medical and Translational Bioinformatics
Developer Tools and Libraries
Bioinformatics Open Source Project Progress Reports

We look forward to receiving your abstract and meeting you at GCCBOSC 2018!

Sincerely,

BOSC 2018 Organizing Committee: Nomi Harris (chair), Heather Wiencko (co-chair), Brad Chapman (co-chair), Peter Cock, Christopher Fields, Bastian Greshake, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres

P.S. Don’t forget to submit your BOSC abstract by March 16 at /wiki/BOSC_Abstract_Submission! Please share this announcement with your colleagues!

BOSC 2017 in Prague, the land of stories (and beer)

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 21 Nov 2017 14:02:57 +0000

This is a guest blog post from Farah Zaib Khan, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend our annual conference BOSC 2017 and its preceding Codefest in Prague, July 2017. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes 15 December 2017, you might want to apply?

So the journey started back in May 2017 when I met Common Workflow Language (CWL) co-founder, Michael R. Crusoe during his visit to our University ( University of Melbourne). I have been working with CWL team since 2015 but it was only then we met in person and discussed various aspects of the CWL standard and how we can collaborate to incorporate principles of Provenance modelling to capture retrospective provenance of CWL workflow enactments. We started working on an idea which led to poster submission and acceptance at Bioinformatics Open Source Conference (BOSC) 2017. I was excited as well as nervous (will explain how this changed later :) ). Excited because this was my very first time attending any BOSC and ISMB conference and nervous because of the feeling that the names that you see at the top of high quality research articles will be there and you get to meet and talk to world class scientists doing wonders.

Nervous and excited I prepared for all the travelling which involved applying for a visa of course (going to Sydney for that) and arranging accommodation, conference registration, booking plane ticket and finally receiving the visa 7 days before my flight. The Czech Consulate was very professional and kind to process the visa in just 7 working days. I left Melbourne to attend 2-Day OBF Codefest followed by 2-Day BOSC and remaining ISMB conference. My Airbnb host was waiting for me when I reached and welcomed me warmly. She had the whole day planned for us as I reached at 9 am July 19th and the codefest had to commence on July 20th. She was keen to learn about my culture, home country, language and research too :). During the day we roamed around the City, had lunch and she shared information about the Czech history and how late 80’s Velvet Revolution changed the economic conditions of the country.

In the evening of my first day, I had a dinner with few members of Seven Bridges team and CWL working group (thanks to Michael for arranging this) at an amazing vegan restaurant in the Old town. We kick started discussion of our work informally during dinner where SevenBridges team introduced their super cool open source toolkit, Rabix for describing the CWL tools workflows. I presented the idea of CWL provenance module which we had planned to work on during the OBF Codefest the very next day. Mostly it was getting to know the teams and getting ready for the next day while enjoying delicious dinner in the heart of Prague Old town.

All geared up, next morning I took a subway from the station right next to Congress center to reach Brmlab which is a non-profit hackerspace self supported by community. The transport system of Prague is commendable as despite the signs written Czech, it was quite straight forward to follow Google maps and take the right subways, trams or buses. When I reached, Brad Chapman, Matúš Kalaš and others were already there making arrangements, providing enough extension cables, arranging food (with many vegan friendly options) and making sure everything is in place. There were more than 60 participants for this open collaborative event to build things and discuss future prospects of research together. The day kick started with introductions and organization into groups to work on related projects. This was followed by coffee and local produce (fruits, bread and pastries) break where people carried on with individual introductions and conversations.

[caption id=“attachment_1782” align=“aligncenter” width=“378”] “Breakfasting” in open air outside the lab. Image was originally shared here.[/caption]

Various groups started working on different projects from 10 am to 1 pm. These projects include MultiQC, biopython, nextflow, Singularity support in CWL, Provenance support in CWL, CWL SDK and Rabix. Our group led by Stian Soiland-Reyes started working on Provenance analysis and had a very useful discussion about what to capture from a workflow run retrospectively and how to structure the Provenance of a CWL workflow run. To start with, we decided to include a provenance module in reference implementation cwltool developed by CWL team. Nervously I started but now it felt like home and we got to work during 10am-1pm work window. I had guidance through out this time by people around me and I would like to thank them once more :) .

[caption id=“attachment_1784” align=“aligncenter” width=“446”] Work in Progress for 10am-1pm session[/caption]

At 1 pm, we took a lunch break but before going for lunch break all the groups gathered and presented their progress so far. A round of applause for the organizers and sponsors who kept the supply of coffee running through out the day. The lunch was delicious pizza with local flavored soft drinks. Again all dietary requirements were accounted for and everyone seemed to enjoy " across-group" discussion and food. After lunch break the group gathered again and started working from 2 pm to 6 pm before leaving for the group dinner. We kept working on our project idea and all the groups reported at 6 pm presenting their progress and headed out for the group dinner. Our group stayed back as Brad graciously offered to stay back if someone wants to continue working. Luckily brmlab was also open 24/7 so we kept working till 9 pm. Late night dinner and headed to the apartment taking the same subway. The city was awake and happening even later in the night. At last the first very productive day came to an end.

July 21st was the second and last day of the Codefest. On my way to brmlab, I stopped at Copy General to get the print of my poster which was required to be displayed the next day. I must admit the staff at this shop was very professional and helpful. They made sure I get the right size of my poster (as it was in landscape orientation) and were quite flexible about the pick up time. Getting done with this important task, I was relaxed and headed to the lab for second day of codefest. The day followed the same pattern as July 20th starting with projects’ updates, plans to be followed for the day followed by coffee and breakfast. Our organizers collected some best quality local produce from a farmer’s market and kept everything organized efficiently.

We further worked on the implementation of a basic Research Object generation as a result of CWL workflow run. By the lunch time we were able to complete the set goals and presented out progress. Everyone was excited and engaged in working with their groups and contributing in every way they could. At 6 pm every group leader wrapped up their progress through out these two days and everyone participated in cleaning the space as it is a community-run space shared by everyone. At the end of these two amazing days, I looked back and realized I was nervous for nothing. As Brad Chapman says and I quote " BOSC is all about getting people together and learning from each other" .

I don’t think anyone can disagree with this statement and the idea of community led projects and open source bioinformatic software feels real and in practice when one interacts and participates in events like OBF-Codefest and BOSC. The codefest ended with dinner at Zly cafe near the Congress center where the next four days are scheduled.

[caption id=“attachment_1787” align=“aligncenter” width=“482”] Dinner at Zly Cafe[/caption]

New day, new tasks.. July 22nd was the first day of BOSC 2017 and at the same time all the posters were required to be hanged in the morning. I rushed to the copy general to collect my poster which was ready the same day. On my way to the shop I met loving and most friendly Monica Munoz-Torres from UC Berkeley who was volunteering as part of organizing committee (presenting Apollo later as well) and was headed to the same copy center. We had good conversation about open source bioinformatics initiatives and her work as volunteer organizing BOSC which she calls her favorite conference :) .

Rushed back to the Congress center, arranged the poster on its designated location along with 100s of amazing posters and headed to attend BOSC opening talks. I was impressed by OBF progression and their support for researchers by providing OBF Travel scholarship and participation in organizing Google summer code camps. Brad presented the summary of Codefest afterwards which had a slide we prepared for our part of work [Provenance Support in CWL]. There were many talks related to CWL application and usage during the whole day. Rabix composer, Rabix Executor, CWL Viewer, bcbio and many more CWL oriented work was presented. We organized a Birds of a feather session during lunch time to discuss what should be captured in a Research Object when a CWL workflow is enacted. This session initiated interesting discussion about different levels and views of Provenance.

In the afternoon Björn Grüning’s talk was very interesting where he empathized on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles for tool deployment and resolving tool dependencies using package managers as Conda and BioConda. Later during this and next day FAIR bingo became a real thing as part of most of the talks. The highlight of the day was indeed the key note speech “Open Sourcing Ourselves” by Madeleine Ball who is working on the project Open Humans. She discussed inspiring Dana Lewis’s story who is creator of “Do-It-Yourself Pancreas System” and made her own continuous glucose monitor alarms louder further leading to the foundation of OpenAPS.

On the second day of BOSC, we had more talks and updates starting with the key note speech " Bioinformatics for Personalized Medicine: Looking Beyond the Genome" by Christoph Bock. He presented few examples from cancer research explaining how epigenomic mutations can be mapped to identify the various aspects of cancer. The topic was of my personal interest and indeed very informative. The ultimate goal is to make the dream of personalized medicine a reality using the available technologies including use of CRISPR for modelling epigenomic factors.

After the key note speech I attended Monica Munoz-Torres’s talk about Apollo, collaborative genomic annotation editor that automatically synchronizes the work of geographically separated research community and establishes a network between the researchers, more like a social network for curators according to Monica. The huge user base working on different genomes interact using Apollo and share the curated genomes. The next talk by Pjotr Prins was about Journal of Open Source Software (JOSS) , an initiative all available on GitHub for accrediting academic software equipped with documentation. In this way, software engineers can publish their software without getting to write a paper about it. It will facilitate the users as the software will be better documented when intended to be published.

Another impressive talk was about " Distance-based, online bioinformatics training in Africa: the H3ABioNet experience" by Nocola Mulder from University of Cape Town. She described the efforts made to bring bioinformatics training to all the places in Africa using a distributed classroom model. Due to internet connectivity issues and other factors, the lectures were recorded beforehand. The lectures were delivered live (online) as well but if there is a connectivity issue, the recordings were available. In addition, various practical assignments were designed to enhance the learning experience. The combination of live lectures, online classes, recordings and practical exercises together results in connectivity and highly interactive environment. Another highlight from the session was release of open source variant calling toolkit GATK4 coupled with WDL and Cromwell.

There were many more talks that I attended and enjoyed such as talk by Ted Liefeld about GenomeSpace, Kai Blin about anitSMASH and Kenzo-Hugo Hillion about BioThings SDK. Oh and during lunch time I attended the BoF session organized by JOSS (was intrigued after listening to the presentation earlier). Later in the day, the panel discussion was worth attending chaired Madeleine Ball, Prof. Carole Goble, Andrew Su and Nick Loman. Carole Goble’s point made perfect sense that the young scientists although are willing to share the data and are open to collaborations where as senior scientists (PIs) consider it more effort with less rewarding results.

Day 2 ended with an amazing closing key note speech by Nick Loman who discussed virus outburst surveillance using the Oxford nanopore minION sequencing technology, using two examples, namely Ebola outburst in Africa in 2015 and the Zika virus in Brazil. “If you can’t move the subjects and samples to the sequencer, bring the sequencer to the subject”.

Oh wait the day actually ended with an end of BOSC dinner ..

but before that we stopped at GigaScience’s 5th birthday for cake and free GOT themed “Data is coming” T shirt which they graciously saved ^_^ (because I reached late). Why did I reach late?

Yes I was there for a poster presentation :) . The poster presentation was from 6-7 pm and was a terrific experience talking about my work and progress we made during code fest earlier.

All in all, everything was amazing, the people, the venue, the city, the knowledge gain, the help you get from peers, the encouragement from fellow researchers. Remember the nervousness I mentioned at the beginning of this post ? ALL GONE after this fruitful experience. Few things that might be helpful in future: We should work towards resolving the issue of gender imbalance that was seen (and usually seen in conferences), discussed and acknowledged during Code fest and BOSC. I think we can advertise the Codefest and the objectives in more detail so people can attend even if they don’t have a group there to start with. This is by no means a complaint or criticism, just something I observed and felt as there were 3 female participants out of >60 total participants of Codefest. I think in future we can make this better and advertise about the welcoming environment of Codefest and BOSC.

Thanks to OBF for covering my air fare by refunding through OBF travel funding. I would also like to thank Data and Software Preservation for Open Science ( DASPOS) (working in developing workflow and provenance tracking for high energy physics) for covering the rest of conference related expenses . In the end, this post will be incomplete if I don’t thank Michael Crusoe for the mentoring, encouragement, guidance, all the support, connecting me with DASPOS and providing prompt feedback whenever I ask :) .

Need a shorter version and more pictures?? –> View the story “BOSC-2017 in the Land of stories” on Storify

P.S. Some other day, I might write about wandering experience in Prague Castle, Old Town, Charles Bridge, local wooden sovereigns, amazing food especially Goats cheese and of course… lemonades :) .

BOSC 2017 report

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 28 Oct 2017 23:01:19 +0000

BOSC 2017 ( /wiki/BOSC_2017) was held in Prague in July 2017 as part of the annual ISMB conference. Nearly 250 people, half of whom were first-time attendees, participated in the meeting. Over 50 talks and a similar number of posters covered topics ranging from workflow tools to a crowd-funded “tree of beers.” This year’s Open Data theme was reflected in the keynote talks by Madeleine Ball and Nick Loman and the panel discussion about the opportunities and challenges of open data.

A report about BOSC 2017 is now available on F1000 ( https://f1000research.com/articles/6-1858/v1), and most of the talk and poster abstracts and talk videos are linked from the schedule page ( /wiki/BOSC_2017_Schedule).

In 2018, BOSC will be partnering with the Galaxy Community Conference (GCC) as an experiment in broadening the BOSC community. We invite anyone who has an interest in open source bioinformatics or open science to join us in Portland, Oregon, June 25-30–see https://gccbosc2018.sched.com/ for more information.

OBF Travel Fellowship - BOSC session of the ECCB/ISMB 2017

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 28 Aug 2017 14:43:53 +0000

This blog post is syndicated from a post on Jonathan Sobel’s blog, originally published July 27, 2017. Jonathan was supported by the ongoing OBF travel fellowship program to attend the 2017 Bioinformatics Open Source Conference (BOSC), held as part of the 2017 ISMB/ECCB meeting in Prague, Czech Republic, in July 2017. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences, workshops, or training events. The next call closes 15 December 2017.

As the lucky recipient of an Open Bioinformatics Foundation (OBF) travel grant, I had the chance to attend to my first Bio-informatics Open Source Conference (BOSC) in Prague the 21 and 22 July 2017.

During the event, I discovered an amazing community of scientists and developers involved in the field of bioinformatics, with a strong open source mindset. “Sharing is caring” and I can tell these guys care a lot! The first day was quite technical with several talks about projects developed during the code fest that happen just prior to the conference. I had the opportunity to discover the FAIR principles (Findability, Accessibility, Interoperability, and Reproducibility) of open data, and several tools aimed at simplifying bioinformatics workflow sharing, visualizing and production. These teams triggered my curiosity towards the Common Workflow Language (CWL) and data standards, notably RABIX, GA4GH and nextflow. Several talks presented very useful tools such as YAMP (Yet Another Metagenomic Pipline!) or MiltiQC for next generation sequencing quality control, and Open MS 2.0 for mass-spectrometry data analysis. One important topic of the day was the reproducibility of bioinformatics piplines and several talks were addressing this question with various approaches, such as containers (Dockers, BioContainers), GNU Guix or package repository such as BioConda.

On the second day, I had the chance to present our BeerDeCoded project in the Citizen Science session of the BOSC. I had the first slot in the morning with an audience of nearly 250 attendees. The beer topic is kind of holy in a geek environment. I had the pleasure to share several important message regarding science conducted outside of academia or industry, in a community laboratory space like Hackuarium. I put some emphasis about science communication between fields and outside of our institutional scientific community. As experts, we have the responsibility to make our knowledge and our researches accessible to a wide audience, and this is exactly our goal with BeerDeCoded and Hackuarium. In addition, I could announce the official release of our first results based on the metagenomic analysis of 39 beer samples. I was able to show our preliminary analysis. The BOSC community was really enthusiastic about the project and attendees tweeted quite a lot about it.

Some background material for @JonathanSobel1’s “BeerDeCoded” talk at #BOSC2017 pic.twitter.com/O52PI6k1hT

— Madeleine Price Ball (@madprime) July 23, 2017

The scientific method reloaded: Analyse data, think, drink, repeat. #BOSC2017 pic.twitter.com/JY0sLuXtzw

— Bastian Greshake (@gedankenstuecke) July 23, 2017

Work in progress for @beerdecoded – really really want @nanopore (so do we!) #BOSC2017 #ISMBECCB pic.twitter.com/FplOglIpb0

— BauhiniaGenome (@BauhiniaGenome) July 23, 2017

In addition, I had some very interesting questions about the interest of breweries in BeerDeCoded, the potential fear of companies that citizen scientist decode their proprietary yeast strain or about the data integration of sequencing with GC/MS in order to study small molecules present in our beer data-set. Moreover, this talk will potentially trigger new collaborations with with Bérénice Batut from the Galaxy training network. Galaxy is an open source, web-based platform for data intensive biomedical research. The Galaxy platform regroups a collection of bioinformatics tools and workflow that can be run without coding knowledge. This program is widely used by biologists to analyze their next generation sequencing data. BeerDeCoded will benefit from this collaboration with a specific instance of Galaxy to make the beer metagenomics accessible to anyone.

Later during this second day, I was impressed by several other talks. One of the greatest initiative is the work of the H3ABioNet, which aim at training bioinformaticians in Africa. I discovered the Journal of open source software (JOSS) that facilitate the publication of bioinformatics software. Then, BioThings SDK and Wikidata presented their API and their knowledge base that allows retrieving efficiently some annotations of biological data. This day was as well the occasion to discuss about data sharing of human data (wearable, clinical, etc.) in order to improve precision medicine and the ethical implication. In addition, second-hand data usage and the problem of re-digitalization of published data in a non-machine readable format was evoked. Finally, Nick Loman gave the closing keynote presentation at BOSC. He gave a great talk about virus outburst surveillance using the Oxford nanopore minION sequencing technology, using two examples, namely Ebola outburst in Africa in 2015 and the Zika virus in Brazil.

In summary my first BOSC experience was very intense and highly interesting. I met with great scientists and developers and I learned about the newest open source software/library/API and practices in this field. I would like to thank once again the BOF committee for allowing me to join this great event and to give me the opportunity to present Hackuarium and the BeerDeCoded project.

#bosc2017 cheers! Thanks for this great conference pic.twitter.com/m6oO8Wbbky

— Jonathan Sobel (@JonathanSobel1) July 23, 2017

Travel award recipients for April 2017

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 05 Jun 2017 14:36:29 +0000

We had a huge response to this round of the OBF travel award. After reviewing the applications, the OBF board selected four recipients. Three applicants accepted awards, and all plan to use the funds to attend this year’s BOSC, to take place July 22-23 in Prague.

Congratulations to our spring 2017 recipients:

Sourav Singh, who will participate in the Codefest and present the Biopython Project Update 2017 talk
Jonathan Sobel, presenting on a citizen science project named BeerDeCoded, carried out by members of the Swiss non-profit called the Hackuarium
Jiwen Xin, presenting the BioThings Explorer project, which integrates genomic data via public APIs

We encourage everyone at BOSC to come out and support our award winners! After BOSC, watch for blog posts from each of the awardees.

The next deadline for travel awards is August 15. You can apply to travel to participate at any event that develops or promotes open source development and open science in the biological research community. See the OBF travel award page for details and link to application.

BOSC 2017 keynote speakers

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 13 Apr 2017 10:28:24 +0000

We’re delighted to announce the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2017, and our first sponsors.

But first a final reminder - today (Thursday 13 April 2017) is our deadline for submitting a full length talk abstract to BOSC 2017.

Dawn Field

Dawn Field is a Lamberg International Guest Professor at Göteborg University’s Department of Marine Sciences. Previously she was a senior research fellow at the NERC Centre for Ecology and Hydrology, Head of the Molecular Evolution and Bioinformatics Group at the Centre for Ecology and Hydrology in Wallingford, UK, and a research associate at the Smithsonian Institution. She is also a founder of the Genomic Standards Consortium, the Genomic Observatories Network and Ocean Sampling Day.

Dr. Field is credited with introducing the concept of a biological code, or “biocode” - the sum of all DNA on earth. In their book Biocode: The New Age of Genomics, she and coauthor Neil Davies describe the rapid rise of genomics, how it is revealing the scale and diversity of life on Earth, and future possibilities and implications.

Dr. Field’s advocacy for open data and interoperability is epitomized by her past leadership of the Genomics Standards Consortium ( GSC), which aims to facilitate genomic data integration, discovery and comparison through international community-driven standards.

The title of Dr. Field’s keynote talk is “Understanding the Biocode: Global Sharing of Data.”

Nick Loman

Nick Loman is known as a vocal proponent of open genomic data in healthcare. A Professor of Microbial Genomics and Bioinformatics at the University of Birmingham, Dr. Loman explores the use of cutting-edge genomics and metagenomics approaches to human pathogens. He promotes the use of open data to facilitate the surveillance and treatment of infectious disease.

Dr. Loman helped establish real-time genomic surveillance of Ebola in Guinea and Zika in Brazil (via the ZiBRA project, which states that “Data will be subject to open release as it is generated”). In another recent project, real-time genomic data was used to analyze a small outbreak of Salmonella enteritidis in the UK. Through this sharing of genomic datasets, researchers were able to confirm that the cases were linked to a larger, national-scale outbreak. Dr. Loman is one of the authors of Poretools, and he regularly shares cutting-edge Nanopore data and protocols for using it. In collaboration with Lex Nederbragt, Dr. Loman is developing an open-source repository of sequencing and bioinformatics benchmarking datasets called Seqbench.

BOSC 2017 Sponsors

We are grateful to and welcome The Hyve (open source solutions for bioinformatics) and Mozilla Science Lab (a community of researchers, developers, and librarians making research open and accessible), as the first sponsors for BOSC 2017.

If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.

BOSC 2016 in Disney World with Donald Docker!

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 21 Jul 2016 14:18:33 +0000

First I would like to congratulate OBF that supports diversity in the community with its travel awards initiative. I was very pleased to be one of the three travel fellowship awardees. Thank you OBF! Ιt was great to attend BOSC 2016 and meet remarkable people and know their work.It was one of the most welcoming meetings I have attended and Ι liked that is was active on the social media and the conference materials and speaker presentations were available online. It made it fun and useful and we could focus less on our notebooks and more on the speakers. Τhis also attracted a lot of positive comments from the other Special Interest Groups. So “Bravo” to the organizers!On the scientific part, it was nice to see Docker making an impression on the bioinformatics community. Everyone was talking about it. It is an awesome way to package bioinformatics applications and the fact that it received so much attention got me pretty excited. I am planning to use it to package CollOS, an open source web application I presented at the conference, that tracks, annotates and barcodes biological samples to facilitate wet lab scientists to locate and identify biological samples.Last but definitely not least, I would like to congratulate Mónica Muñoz-Torres and the organizers for their reference to the recent tragic shooting incident in Orlando.Hope to see you next year in Prague!Dimitra

New BioJava Logo Design Competition

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 14 Jun 2016 17:47:52 +0000

BioJava is organizing a design competition to come up with a new logo. Anybody can participate:

The logo should look modern and be better than the current one (yellow circle)
The logo should be able to be rendered as a favicon, as well as large (e.g. on a t-shirt). Designs that come in two (or multiple) sizes are ok.
Logos shall not look similar in any way to the trademarked Java programming language logo. This means no coffee cups in any way.

Deadline: Deadline for submissions is July 4th.

Announcement of Winner: The winner of the new logo competition will be announced during BOSC 2016.

Prize: We will print t-shirts with the new logo and the designer will get a free t-shirt.

If the designer of the winning new logo will be attending ISMB 2016, the attending BioJava developers will take the winner out for dinner.

BioJava will carry the new logo on its homepage and GitHub Profile

Details: For full details of the competition and how to make a submission please view here:

https://github.com/biojava/logo Result Update:

As announced via the mailing list and at BOSC 2016, the winning logo was by Aleix Latifa:

BOSC 2016 Panel: Growing and Sustaining Open Source Communities

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 27 May 2016 16:45:21 +0000

Every year, BOSC includes a panel discussion that offers attendees the chance to engage in conversation with the panelists and each other. BOSC is all about community, so this year’s panel topic– Growing and Sustaining Open Source Communities–is right at the heart of what we do. Since the first BOSC in 2000, we have focused on bringing together open source bioinformatics developers and users to form and expand collaborations and grow the communities that use and improve their tools and resources.

Community projects have resulted in some of the most popular bioinformatics resources. However, there are many challenges that may be encountered as a community effort develops and evolves. For example:

How can an open source community integrate a diverse set of participants, including people with different levels of experience, different interests, and different demographic characteristics?
How can non-developers (for example, people who primarily write documentation, or who are users of the software) contribute to these projects?
What funding approaches have successfully sustained open source communities after any core funding has run out?
What technologies have helped open source communities coordinate efficient communication and planning across multiple locations?
What organizational models have some of these communities followed?

This panel brings together six people (five panelists plus a moderator) who have worked to sustain open source communities. They will join audience members in an open dialog about challenges encountered during the life cycle of these communities and approaches to addressing them.

Panel chair Mónica Muñoz-Torres is the biocuration lead for Berkeley Bioinformatics Open-Source Projects (BBOP) at Lawrence Berkeley National Laboratory.

Abigail Cabunoc Mayes is the Lead Developer of the Mozilla Science Lab.

Bastian Greshake co-founded openSNP, a crowdsourced/citizen science open data project.

Jamie Whitacre is the technical project manager for Project Jupyter, which grew out of the widely used IPython Notebook.

John Chilton of Penn State is a software developer on the Galaxy project, and one of the co-founders of the Common Workflow Language.

Natasha Wood of the University of Cape Town is the co-founder of the Cape Unseminars in Bioinformatics.

Please see /wiki/BOSC_2016_Panel for more information about the panelists.

First three OBF travel fellowships awarded

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 23 May 2016 16:05:25 +0000

The first round of the Open Bioinformatics Foundation travel fellowship program has granted funds to three open source bioinformatics software developers to help them attend the Bioinformatics Open Source Conference (BOSC) 2016 in Orlando, Florida, this July. The travel fellowship program ( announced 1 May 2016) aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Applications for the first round in 2016 were due on April 15, with two more due dates this year on August 15 and December 15.

Out of more than a dozen applicants from four different continents, the OBF Board chose the following three recipients:

Dimitra Sarantopoulou of the University of Pennsylvania is an open source bioinformatics developer who focuses on web applications for proteomic analysis.
Michael R. Crusoe ( @biocrusoe) is the Co-founder & Community Engineer for the Common Workflow Language (CWL), and previously was the lead developer of khmer.
Anurag Priyam is a self-taught bioinformaticst who has created several successful open source tools, including SequenceServer and oswitch, a Docker-based virtual environment switcher.

The OBF Board congratulates the three winners!

This first round has also shown several points of improvement, both for the program description and the application form. We are in the process of making small adjustments to both, and expect to reopen the application form for the next round of funding at the latest by the time BOSC 2016 rolls around (July 8). We encourage others for whom travel costs are a barrier to participating in open source bioinformatics events to apply for this next round (due date is August 15, 2016).

BOSC CodeFest 2016

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 28 Mar 2016 13:56:07 +0000

The Bioinformatics Open Source Conference (BOSC) is a two day meeting focused on open source bioinformatics. We aim to encourage and support a friendly, open and productive community that helps us work together to answer hard biological questions. We’ll get together this summer, July 8-9, in Orlando, Florida.

Abstracts for BOSC 2016 talks and posters are due this Friday, April 1st. We want to hear about your research and encourage everyone to submit an abstract. We love talks from newcomers to BOSC as well as established projects: no idea is too big or small. We also offer Travel Fellowships for speakers if money would be a barrier to attending.

Prior to BOSC, we organize a free two day collaborative working session called Codefest. We’ll establish friendships and collaborations while helping new members find fun work and extending existing projects. It’s a time to learn, teach, develop and grow. This year we’re kindly hosted by the FamiLAB workspace in Orlando. So in addition to getting to work with fellow OpenBio members, you’ll have the chance to learn about the Orlando maker community.

We hope you’ll join us in Orlando this summer for Codefest and BOSC. Please send in your abstracts before Friday and sign up on the Codefest page.

BOSC 2016 Keynote Speakers

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 22 Mar 2016 12:10:51 +0000

We’re delighted to announce the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2016:

Jennifer Gardy

Dr. Jennifer Gardy is both a scientist and science communicator. She holds a PhD in Bioinformatics, and is an Assistant Professor of Population and Public Health at the University of British Columbia and a Senior Scientist at the British Columbia Centre for Disease Control (BCCDC). At the BCCDC, she pioneered a new way of investigating outbreaks of infectious diseases – “genomic epidemiology”, which uses a pathogen’s genome sequence as a tool for understanding how an infectious disease spreads. Her group was the first to use genome sequencing to reconstruct a large outbreak of tuberculosis, and she is continuing to apply this novel technique to other outbreak scenarios. She is also involved in other genomics-related research, including replacing traditional laboratory microbiology protocols with single genomic analyses. In 2014, she was appointed the Canada Research Chair in Public Health Genomics, and is Senior Editor at the new open data, open access journal Microbial Genomics.

In addition to her career as a research scientist, Dr. Gardy is known for her work in science communication and education, both in print and on TV. She has made regular appearances on CBC’s documentary series The Nature of Things, has hosted CBC’s eight-part science series Project X, and is a regular guest host on Discovery Channel’s Daily Planet science show. She has written and blogged for the Globe and Mail, has written a children’s book – It’s Catching! The Infectious World of Germs and Microbes – and runs a series of workshops on how to communicate science effectively.

Dr. Gardy’s keynote topic is “The open-source outbreak: can data prevent the next pandemic?”

Every century, something comes along that shakes up public health – vaccines, sanitation, antibiotics – and data promises to be the great disrupter of 21st century infectious disease epidemiology. In the last 5-6 years, genomics has dramatically changed how public health agencies diagnose and investigate diseases from food poisoning to tuberculosis, giving us a new tool to understand and control infections. The change is also apparent at a cultural level – genomics and bioinformatics researchers have largely come from an open data, collaborative space and have brought new ways of thinking to public health laboratories, previously secret, closed organizations. In this talk, we’ll explore some of the dramatic changes in public health microbiology that genomics and bioinformatics has facilitated, and look at how future data sharing efforts in areas such as digital disease detection might be the key to preventing future pandemics.

Homepage: Jennifer Gardy, Twitter: @JenniferGardy

Steven Salzberg

Dr. Steven Salzberg is the Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics and the Director of the Center for Computational Biology in the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University. From 2005-2011, he was the Director of the Center for Bioinformatics and Computational Biology and the Horvitz Professor of Computer Science at the University of Maryland, College Park. From 1997-2005 he was Senior Director of Bioinformatics at The Institute for Genomic Research (TIGR) in Rockville, Maryland, one of the world’s leading DNA sequencing centers at the time.

Salzberg’s lab currently focuses on next-generation sequence alignment, genome assembly, and microbiome analysis.They have produced several popular systems for alignment of next-generation sequencing reads, including the Bowtie, Tophat, and Cufflinks systems. All of the group’s software is free and open source, and their systems have been downloaded hundreds of thousands of times.

Dr. Salzberg is a Fellow of the American Association for the Advancement of Science (AAAS) and a Fellow of the International Society for Computational Biology (ISCB). He was the 2013 winner of the Benjamin Franklin Award for Open Access in the Life Sciences, in recognition of his many contributions to open access bioinformatics software and his strong advocacy for open access to data, software and publications.

Dr. Salzberg will speak about “Open source, open access, and open data: why science moves faster in an open world”.

The Human Genome Project established a practice of sharing data rapidly, prior to publication, that has since become a model for many projects in genomics. Data sharing has been slow to penetrate other fields because of many factors, some of which I will discuss in this talk. Nevertheless, sharing of methods, data, and results helps science move ahead faster, and openness is essential for the continual process of checking and self-correction that good science requires. I will discuss some of the successes as well as some noteworthy mistakes that have been discovered thanks to open science.

Homepage: Steven Salzberg, Twitter: @StevenSalzberg1

The BOSC 2016 call for abstracts is currently open, and BOSC/ISMB 2016 registration will open next week. We hope to see you in Florida!

OBF Travel Fellowship Program

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 01 Mar 2016 20:52:10 +0000

We are very pleased to announce our new Open Bioinformatics Foundation (OBF) Travel Fellowship program. The program is designed to enable people, whether long-standing members of our community or newcomers, to participate in eligible events for which costs would otherwise be prohibitive. This includes our annual Bioinformatics Open Source Conference (BOSC).

Although not limited to specific groups of people, the program constitutes another major step for us in our ongoing efforts to increase the diversity in our communities in particular, and in the open source / open science bioinformatics community in general. As explained in the just published BOSC 2015 report, inclusivity was one of the founding principles of the Bio* open-source project communities that came together under the OBF umbrella, and thus also of BOSC, our flagship event. OBF’s bylaws have included a nondiscrimination clause from the outset. OBF’s major member projects have not only always welcomed new participants to their communities, but embraced passing on leadership to people who hadn’t been part of the “inner circle” from the beginning.

However, being on the “inside” can hide the barriers to joining a community as a newcomer. In practice, the demographics of our member community, and therefore also of BOSC, have mirrored the low diversity observed for open-source project communities in general.

We’ve committed ourselves to address this. We simply owe it to our mission, which is predicated on being inclusive. For BOSC 2015 we chose to make increasing diversity the main theme, including the BOSC 2015 panel discussion. When asked for a show of hands of who was there for the first time, nearly half of the attendees’ hands went up! We believe firmly that with enough dedicated and sustained attention, our community can include everyone who shares our mission. We also believe that eventually more diversity at our community events will trickle down to increasing the diversity of participants in our member projects.

To fund the OBF Travel Fellowship program, we have for now committed an annual budget of $5,000 from our existing assets. At this level, we should be able to sustain the program for a minimum of 3 years. We would like to do more, and to commit to the program for at least 10 years. To help us accomplish that, we are calling on donors and BOSC sponsors. You can earmark your contribution to be used specifically for funding this program – simply email the Board if the donation form does not leave enough space.

Special thanks for bringing this program to life go to Karen Cranston, who joined the OBF Board in spring 2015 and shepherded the effort from inception to launch.

BOSC 2016 Call for Abstracts

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 01 Mar 2016 17:42:48 +0000

Call for Abstracts for the 17th Annual Bioinformatics Open Source Conference (BOSC 2016), a Special Interest Group (SIG) of ISMB 2016.

Dates: July 8-9, 2016
Location: Orlando, FL
Web site: /wiki/BOSC_2016
Email: bosc@open-bio.org
BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce
Twitter: @OBF_BOSC and @OBF_News

Important Dates:

Call for one-page abstracts opens: March 1, 2016
Abstract submission deadline: April 1, 2016 - extended to Monday 4 April 2016
Travel fellowship application deadline: April 15, 2016
Authors notified: May 6, 2016
Codefest 2016: July 6-7, 2016, Orlando, FL (confirming venue)
BOSC 2016: July 8-9, 2016, Orlando, FL
ISMB 2016: July 8-12, 2016, Orlando, FL

The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual ISMB conference. It is organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results and software.

We welcome one-page abstracts on any topic of relevance to open source bioinformatics and open science. Presentation formats are lightning talks, longer talks, and/or posters. We plan to offer a limited number of travel fellowships to help offset expenses for some accepted speakers who would not otherwise be able to attend BOSC – please see the OBF Travel Fellowship announcement for more information.

Session topics include:

Open Science and Reproducible Research
Standards and Interoperability
Data Science
Visualization
Translational Bioinformatics
Bioinformatics Open Source Libraries and Projects

If your company or organization is interested in helping to sponsor BOSC 2016, please contact us! Sponsors in 2015 included Google, GigaScience, Curoverse and Bina – we thank them for their support.

BOSC 2016 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Brad Chapman, Christopher Fields, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather Wiencko

BOSC 2015 Panel - increasing diversity

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 05 Jun 2015 10:29:46 +0000

Every year, BOSC includes a panel discussion that offers all attendees the chance to engage in conversation with the panelists and each other. Two months ago we announced the theme of the BOSC 2015 panel would be " Open Source, Open Door: increasing diversity in the bioinformatics open source community". Our complete list of panellists is:

Panel chair Mónica Muñoz-Torres ( @monimunozto) is the lead biocurator at Berkeley Bioinformatics Open-Source Projects (BBOP). She is part of the development teams for Web Apollo (a web-based annotation editor designed to support community-based curation of genomes) and the tools of the Gene Ontology (GO) Consortium. She co-leads the Community Curation group within the global initiative to sequence and annotate the genomes of 5,000 arthropods (i5K Initiative), and is a member of the Executive Committee of the International Society for Biocuration (ISB). As a graduate student, Monica founded the first Southeastern Chapter of the Society for Advancement of Hispanics/Chicanos and Native Americans in Science (SACNAS) at Clemson University; the chapter has since been actively involved in outreach activities to local high schools in an attempt to inspire students to pursue careers in STEM. She is currently working on forming the first professional chapter of SACNAS in the San Francisco Bay area.
Holly Bik ( @hollybik) is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes.
Michael R. Crusoe ( @biocrusoe) is the lead for the k-h-mer project at C. Titus Brown’s Lab for Data Intensive Biology at the University of California, Davis in the School of Veterinary Medicine. A community-minded bioinformatics research software engineer and Software Carpentry instructor, he is also a member of the Debian Med software packaging team. Michael’s social justice background includes a prior seat on the board for the Phoenix, Arizona chapter of GLSEN, the Gay, Lesbian, and Straight Education Network and he is proud to be a supporter of the Ada Initiative.
Aleksandra Pawlik ( @aleksandrana) is a Training Lead at the Software Sustainability Institute at Manchester University, UK. She coordinates training activities and helps develop strategies and curricula for teaching computational lab skills to researchers across disciplines at all stages of their research career. She is a member of the Steering Committees for Data Carpentry and Software Carpentry Foundation, and supports the development of both initiatives. Currently, Aleksandra is collaborating on training with the ELIXIR project supporting the bioinformatics community. As a certified Software and Data Carpentry instructor Aleksandra has taught at a number of workshops, including Software Carpentry for Women in Science and Engineering, which she co-organised.
Jason Williams ( @JasonWilliamsNY) is the Lead of the iPlant Collaborative’s Education, Outreach, Training (EOT) group, based at Cold Spring Harbor Laboratory, where he has worked for over 10 years. He is also a Lead Instructor of “The Science Institute” at Yeshiva University High School for Girls, and the Treasurer of the Software Carpentry Foundation. His background is in molecular biology and bioinformatics. Diversity is a focus of Jason’s work at the DNA Learning Center and with iPlant, where he works to target outreach along the entire spectrum of underrepresented and underserved groups ranging from minorities in urban communities to first-generation college students at rural institutions.

In addition the BOSC 2015 co-chairs Nomi Harris and Peter Cock will be on hand, along with other Open Bioinformatics Foundation (OBF) Board Members and BOSC organising committee members, to comment on what BOSC and the OBF are trying to do to improve diversity in the open source bioinformatics community, and listen to suggestions.

P.S. Today is the deadline for discounted early registration, and the deadline to submit a late breaking lightning talk or poster abstract. See BOSC 2015 for more details.

Open Source, Open Door: increasing diversity in the bioinformatics open source community

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 02 Apr 2015 22:09:39 +0000

The Bioinformatics Open Source Conference (BOSC) has always been about community. Launched in 2000, BOSC aims to provide a forum for both bioinformatics developers and users to share ideas and code and learn about the latest developments in open source bioinformatics and open science.

Our goal this year is to welcome even greater participation, opening the door even wider to participants who have historically been underrepresented in the world of open source bioinformatics and, therefore, at BOSC. This includes (but is by no means limited to) women, people who aren’t white, older people, people from outside North America and Europe, and non-programmers.

During a Birds of a Feather (BoF) session held at BOSC 2014, we discussed ways to increase the diversity of BOSC attendees, and gathered many useful suggestions from the participants, some of which we have already acted upon.

One of the suggestions from the 2014 BoF was to add someone to the organizing committee to focus on outreach and community-building. In January 2015, we welcomed Dr. Sarah Hird as our new Outreach Coordinator. Sarah is currently a UC Davis Chancellor’s Postdoctoral Fellow with Jonathan Eisen in the UC Davis Genome Center, where her research interests lie at the intersection of phylogeography, bioinformatics and microbial diversity. Sarah is also known for her focus on promoting diversity in STEM. " I am personally and professionally interested in how we can make “the Academy" a more representative sample of the world around us," she says.

During the 2014 BoF, we were asked whether BOSC planned to adopt a Code of Conduct. We felt that this should be an ISCB-wide effort, not one that is limited to a single SIG. Our advocacy efforts with the ISCB were successful with a code of conduct published on the ISMB/ECCB 2015 website. We are very pleased that ISCB joins us in wanting to foster a collegial and productive environment for everyone who attends the conferences. The code of conduct will also be announced in the ISCB April Newsletter.

The high price of travel and registration can make it hard for some people to attend BOSC. We are trying to lower this barrier by offering free or half-price registration to a limited number of accepted speakers - please indicate in the Comments section of your abstract submission if you would like to apply for this. We also award Student Travel Fellowships to the authors of the three best student abstracts each year; these provide $250 to offset travel costs, as well as granting free registration to BOSC.

Every year, the agenda at BOSC includes a panel that gives all participants the opportunity to engage each other in discussion. This year, our panel discussion will focus on increasing diversity in our community and at our conferences. The panel will be chaired by Monica Munoz-Torres and will include panellists Holly Bik and Jason Williams (see bios below).

Dr. Monica Munoz-Torres (Twitter: @monimunozto) is the lead biocurator at Berkeley Bioinformatics Open-Source Projects (BBOP). She is part of the development teams for Web Apollo (a web-based annotation editor designed to support community-based curation of genomes) and the tools of the Gene Ontology (GO) Consortium. She co-leads the Community Curation group within the global initiative to sequence and annotate the genomes of 5,000 arthropods (i5K Initiative), and is a member of the Executive Committee of the International Society for Biocuration (ISB).
Dr Holly Bik (Twitter: @hollybik) is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes.
Jason Williams (Twitter: @JasonWilliamsNY) is the Lead of the iPlant Collaborative’s Education, Outreach, Training (EOT) group, based at Cold Spring Harbor Laboratory, where he has worked for over 10 years. He is also a Lead Instructor of “The Science Institute” at Yeshiva University High School for Girls, and the Treasurer of the Software Carpentry Foundation. His background is in molecular biology and bioinformatics.

We are looking for two more panellists, and have some ideas - but your suggestions are welcome! Please [email the BOSC committee](mailto:bosc@open-bio.org?subject=BOSC 2015 Panelists) or just tweet panellist ideas at @OBF_BOSC.

term paper writing service

Finally, please spread the word about BOSC! The deadline for submitting abstracts for regular-length talks is tomorrow (Friday, April 3 - update: extended to Tuesday, April 7 due to Easter/Passover weekend), but there will also be opportunities for last-minute lightning talks and posters.

BOSC 2015 Keynote Speakers

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 26 Mar 2015 16:05:48 +0000

Announcing the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2015:

Holly Bik

Dr Holly Bik is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. She obtained her Ph.D. in molecular phylogenetics at the University of Southampton, UK (working in conjunction with the Natural History Museum, London), followed by subsequent postdoctoral appointments at the Hubbard Center for Genome Studies at the University of New Hampshire and the UC Davis Genome Center.

Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes. Holly’s keynote talk topic is “Bioinformatics: Still a scary world for biologists”.

Many biological disciplines remain staunchly traditional, where high-throughput DNA sequencing and bioinformatics have not yet become widely adopted. In this talk, I’ll discuss the ongoing challenges and barriers facing biologists in the age of ‘Omics, based on my experiences in transitioning from nematode taxonomy to computational biology research.

Homepage: Holly Bik, Twitter: @hollybik

Ewan Birney

Dr Ewan Birney is Joint Associate Director of EMBL-EBI, as well as Interim Head of the Centre for Therapeutic Target Validation. Together with Dr Rolf Apweiler, he has strategic responsibility and oversight for bioinformatics services at EMBL-EBI.

Ewan played a vital role in annotating the genome sequences of the human, mouse, chicken and several other organisms; this work has had a profound impact on our understanding of genomic biology. He led the analysis group for the ENCODE project, which is defining functional elements in the human genome. He was also one of the leaders of the BioPerl project. Ewan’s main areas of research include functional genomics, assembly algorithms, statistical methods to analyse genomic information (in particular information associated with individual differences) and compression of sequence information.

He has received a number of prestigious awards including the 2003 Francis Crick Award from the Royal Society, the 2005 Overton Prize from the International Society for Computational Biology and the 2005 Benjamin Franklin Award for contributions in Open Source Bioinformatics. He was elected a Fellow of the Royal Society in 2014.

Ewan was a cofounder of the Open Bioinformatics Foundation, the organization that sponsors BOSC, and has been involved in BOSC since the first conference in 2000. He chaired the meeting in 2001, and gave one of the keynote talks in 2002. We are delighted to have him back as a keynote speaker for 2015.

Ewan’s talk topic will be announced soon.

Homepage: Ewan Birney, Twitter: @ewanbirney

The BOSC 2015 call for abstracts is currently open, and BOSC/ISMB/ECCB 2015 registration has also just opened. We hope to see you in Dublin!

BOSC 2015 call for Abstracts

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 05 Mar 2015 21:00:11 +0000

Call for Abstracts for the 16th Annual Bioinformatics Open Source Conference (BOSC 2015), a Special Interest Group (SIG) of ISMB/ECCB 2015.

Dates: 10-11 July, 2015
Location: Dublin, Ireland
Web site: /wiki/BOSC_2015
Email: bosc@open-bio.org
BOSC announcements mailing list
Twitter: @OBF_BOSC and @OBF_News

Important Dates:

March 24, 2015: Registration opens for ISMB and BOSC ( https://www.iscb.org/ismbeccb2015-registration)
April 3, 2015: Deadline for submitting BOSC abstracts
May 3, 2015: Notification of accepted talk abstracts emailed to authors
July 8-9, 2015: BOSC Codefest 2015, Dublin
July 10-11, 2015: BOSC 2015, Dublin
July 10-14, 2015: ISMB/ECCB 2015, Dublin

The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. We particularly wish to invite those who have not participated in previous BOSCs to join us this year!

Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics. BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.

We invite you to submit one-page abstracts for talks and posters. As mentioned, any topics relevant to open source bioinformatics and open science are welcome. Here are some potential session topics (but please don’t feel limited to these!):

Open Science and Reproducible Research
Standards and Interoperability
Data Science
Visualization
Translational Bioinformatics
Bioinformatics Open Source Libraries and Projects

If your company or organization is interested in being a sponsor for BOSC 2015, please contact us! Sponsors of BOSC 2014 included Google, Eagle Genomics, GigaScience, and Curoverse - we thank them for their support.

BOSC 2015 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Sarah Hird, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres.

BOSC welcomes Sarah Hird as Outreach Coordinator

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 05 Jan 2015 03:56:15 +0000

The BOSC 2015 Organizing Committee is pleased to welcome Sarah Hird as our new Outreach Coordinator. BOSC is eager to increase the participation of individuals and groups that have been historically underrepresented at our conferences, and Sarah will be spearheading this effort.

Sarah is currently a UC Davis Chancellor’s Postdoctoral Fellow with Jonathan Eisen in the UC Davis Genome Center, where her research interests lie at the intersection of phylogeography, bioinformatics and microbial diversity. She earned her PhD in biology and bioinformatics at LSU. Sarah is also known for her focus on promoting diversity in STEM. “I am personally and professionally interested in how we can make “the Academy” a more representative sample of the world around us,” she says.

Please join us in welcoming Sarah to the BOSC organizing committee, and stay tuned for more information about BOSC 2015 (which will take place July 10-11, 2015, in Dublin).

BOSC 2015 will be in Dublin with ISMB/ECCB 2015

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 18 Sep 2014 09:42:06 +0000

We have asked you, and you have spoken! 59 past and/or future BOSC attendees participated in our survey, answering questions about what they liked at BOSC 2014, what changes they’d like to see, and — most importantly — what they thought about the proposal to possibly hold BOSC 2015 in Norwich (UK) rather than as an ISMB/ECCB SIG in Dublin (Ireland)..

Under this plan, BOSC 2015 would have been shortly before ISMB/ECCB, but in Norwich. We would have been hosted by The Genome Analysis Centre (TGAC) just after and co-located with the Galaxy Community Conference 2015 (GCC 2015, hosted by The Sainsbury Laboratory). Although some survey participants indicated that they would be more likely to attend BOSC 2015 if it were co-located with GCC, the majority preferred BOSC to remain an ISMB SIG, so we will hold BOSC 2015 in Dublin right before ISMB/ECCB 2015.

Here is the summary of responses to the questions about the location of BOSC 2015:

Although the survey is now closed, we are always happy to hear your suggestions for BOSC 2015. (We are particularly interested in increasing diversity at BOSC, and welcome suggestions of people to invite.) You can reach us at bosc@open-bio.org

Nomi Harris and Peter Cock Co-Chairs, BOSC 2015

Catering at BOSC CodeFest 2014

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 02 Apr 2014 11:13:25 +0000

Bioinformatics Open Source Codefest, July 9 and 10th in Boston, now with sponsored food and drinks!

The OBF will be holding the fifth annual BOSC Codefest, an informal two day “hackathon” or “coding festival” preceding the Bioinformatics Open Source Conference (BOSC 2014) in Boston (USA).

This year, the BOSC Codefest 2014 is being hosted by hack/reduce (a wonderful hackerspace in Cambridge, Boston) and has also been kindly sponsored by Curoverse (the team behind the open source platform Arvados) and Harbinger Partners, Inc. Thanks to this sponsorship, this year the organisers will able to include catering for the participants - I’m expecting at least coffee and pizza, plus what ever caffeine rich drinks or local pastries are in fashion with the Boston programmers? I checked on wikipedia and Jolt Cola doesn’t exist in the USA any more… so I’m waiting to see what our local organisers Brad Chapman & Michael Heuer have planned.

If you are wondering what happens exactly at a CodeFest, I suggest Brad’s blog post from the BOSC Codefest 2013, or Möller et al (2013). Basically these meeting are a chance for developers of open source bioinformatics (not just the OBF’s Bio* projects) to get together and work on common interests. Things work best with some pre-meeting planning on the usual project development mailing lists or IRC, but are also a great way to meet other scientists and developers in person with more time to chat than during a conference coffee break.

Please note that while there is no registration fee for the BOSC Codefest 2014, please do fill in the registration form to help with the planning/catering.

We’re hoping all the Codefest participants will stay for the BOSC meeting itself, which requires formal paid registration as one of the big ISCB 2014 conference’s SIG satellite meetings. Note that we’re offering a BOSC fee waiver for student speakers, this year. If you are going to BOSC, please remember to submit your BOSC abstracts this week!

Peter

Free registration to student presenters at BOSC 2014

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 19 Mar 2014 18:21:22 +0000

To encourage more student presentations at the Bioinformatics Open Source Conference (BOSC), this year we’re waiving the registration fee for accepted student presenters. When you submit your abstract ( BOSC abstract call open until 4th April), you must tick the student box:

Student submissions must have a full-time student as the first named and presenting author, and be mostly written by students.

Please note that because BOSC registration is via the ISCB as one of the ISCM SIG meetings, eligible students must contact us before filling in their ISCB registration to ensure the BOSC SIG fee is waived.

Furthermore, as in previous years, BOSC Student Travel Awards sponsored by Eagle Genomics will be awarded to the top student presentations to help with your travel and accommodation costs.

Update (2 May 2014): We’ve just sent out the accepted talk invitations, and are offering a registration fee waiver to four student speakers.

BOSC 2014 call for abstracts

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 04 Mar 2014 18:18:57 +0000

Call for Abstracts for the 15th Annual Bioinformatics Open Source Conference (BOSC 2014), a Special Interest Group (SIG) of ISMB 2014.

Dates: July 11-12, 2014
Location: Boston, MA, USA
Web site: /wiki/BOSC_2014
Email: bosc@open-bio.org
BOSC announcements mailing list
Twitter: @OBF_BOSC and @OBF_News

Important Dates:

March 24, 2014: Registration opens for ISMB and BOSC
April 4, 2014: Deadline for submitting BOSC abstracts
May 1, 204: Notification of accepted talk abstracts emailed to authors
July 9-10, 2014: BOSC Codefest 2014, Boston
July 11-12, 2014: BOSC 2014, Boston
July 11-15, 2014: ISMB 2014, Boston

The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics.

BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.

We invite you to submit one-page abstracts for talks and posters. This year’s session topics are:

Open Science and Reproducible Research
Software Interoperability
Genome-scale Data and Beyond
Visualization
Translational Bioinformatics
Bioinformatics Open Source Libraries and Projects

Once again we thank Eagle Genomics for sponsoring the BOSC Student Travel Awards, and welcome the open access journal GigaScience as a new sponsor for BOSC 2014.

BOSC 2014 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Hans-Rudolf Hotz, Hilmar Lapp

BOSC 2014 Keynote Speakers

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 24 Dec 2013 05:34:18 +0000

Thanks to those who participated in the BOSC 2014 Keynote Competition! Our winner is Manuel Corpas, who correctly surmised Philip Bourne:

https://twitter.com/manuelcorpas/status/412520369044463616

(In fact, we had already confirmed Philip Bourne as our second keynote speaker before his new job at NIH was announced.) Congratulations, Manuel, on winning free admission to BOSC 2014!

Dr. Bourne’s keynote talk will be entitled “Biomedical Research as an Open Digital Enterprise”:

The biomedical research lifecycle is fast becoming completely digital and increasingly open to the point that publishing could simply become changing the access control on given research objects comprising ideas, hypotheses, data, software, results, conclusions, reviews, grants and so on. This offers immense opportunities for software developers to enable the enterprise. I will describe a vision for the digital enterprise and what the NIH and others are doing to support the notion with the intent to accelerate scientific discovery.

Our other keynote speaker at BOSC 2014, as already announced, will be Titus Brown, whose topic is “A History of Bioinformatics (in the Year 2039)”.

BOSC 2014 Keynote Competition

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 13 Dec 2013 12:24:53 +0000

We’re pleased to officially confirm that one of the two keynote speakers for the 15th annual Bioinformatics Open Source Conference ( BOSC 2014) will be C. Titus Brown, as he announced on Twitter recently:

Titus Brown (@ctitusbrown): Excited to be a keynote speaker at BOSC 2014! My title: “A History of Bioinformatics (in the year 2039)” - plenty of room for mischief ;) https://twitter.com/ctitusbrown/status/410934403565490176

In recognition of the growing use of Twitter and social media within science as a way of connecting across geographical divides, we’re announcing a Twitter competition to guess who is scheduled to give the second keynote at BOSC 2014 in Boston.

To enter, please tweet using hashtag #bosc2014 and include us via @OBF_BOSC, e.g.

I think @OBF_BOSC should invite “Professor X” to be a keynote speaker at #BOSC2014 because …

The first correct entry (within one week) will be awarded one complementary BOSC 2014 registration fee for themselves, or a nominated group member. This does not cover travel or accommodation, and there is no cash substitute if you cannot attend BOSC 2014. Members of the OBF board, BOSC organizing committee, and ISMB SIG committee are not eligible, nor are the keynote speakers themselves.

We intend to announce the mystery keynote speaker and any Twitter competition winner in one week’s time, but reserve the right to cut short, modify, or cancel the competition.

Our ulterior motive is to crowd source ideas for future keynote speakers in BOSC 2015, so some serious suggestions please ;)

Further details about BOSC 2014 will be posted here: /wiki/BOSC_2014

Thank you,

Peter Cock & Nomi Harris, BOSC 2014 co-chairs.

Biopython 1.62 released

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 28 Aug 2013 22:14:43 +0000

Source distributions and Windows installers for Biopython 1.62 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI).

Python support

This is our first release of Biopython which officially supports Python 3. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are not supported.

We still fully support Python 2.5, 2.6, and 2.7. Support under Jython is available for versions 2.5 and 2.7 and under PyPy for versions 1.9 and 2.0. However, unlike CPython, Jython and PyPy support is partial: NumPy and our C extensions are not covered.

Please note that this release marks our last official for support Python 2.5. Beginning from Biopython 1.63, the minimum supported Python version will be 2.6.

Highlights

The translation functions will give a warning on any partial codons (and this will probably become an error in a future release). If you know you are dealing with partial sequences, either pad with “N” to extend the sequence length to a multiple of three, or explicitly trim the sequence.
The handling of joins and related complex features in Genbank/EMBL files has been changed with the introduction of a CompoundLocation object. Previously a SeqFeature for something like a multi-exon CDS would have a child SeqFeature (under the sub_features attribute) for each exon. The sub_features property will still be populated for now, but is deprecated and will in future be removed. Please consult the examples in the help (docstrings) and Tutorial.
Thanks to the efforts of Ben Morris, the Phylo module now supports the file formats NeXML and CDAO. The Newick parser is also significantly faster, and can now optionally extract bootstrap values from the Newick comment field (like Molphy and Archaeopteryx do). Nate Sutton added a wrapper for FastTree to Bio.Phylo.Applications.
New module Bio.UniProt adds parsers for the GAF, GPA and GPI formats from UniProt-GOA.
The BioSQL module is now supported in Jython. MySQL and PostgreSQL databases can be used. The relevant JDBC driver should be available in the CLASSPATH.
Feature labels on circular GenomeDiagram figures now support the label_position argument (start, middle or end) in addition to the current default placement, and in a change to prior releases these labels are outside the features which is now consistent with the linear diagrams.
The code for parsing 3D structures in mmCIF files was updated to use the Python standard library’s shlex module instead of C code using flex.
The Bio.Sequencing.Applications module now includes a BWA command line wrapper.
Bio.motifs supports JASPAR format files with multiple position-frequence matrices.

Additionally there have been other minor bug fixes and more unit tests.

Contributors

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

Alexander Campbell (first contribution)
Andrea Rizzi (first contribution)
Anthony Mathelier (first contribution)
Ben Morris (first contribution)
Brad Chapman
Christian Brueffer
David Arenillas (first contribution)
David Martin (first contribution)
Eric Talevich
Iddo Friedberg
Jian-Long Huang (first contribution)
Joao Rodrigues
Kai Blin
Lenna Peterson
Michiel de Hoon
Matsuyuki Shirota (first contribution)
Nate Sutton (first contribution)
Peter Cock
Petra Kubincová (first contribution)
Phillip Garland
Saket Choudhary (first contribution)
Tiago Antao
Wibowo ‘Bow’ Arindrarto
Xabier Bello (first contribution)

BOSC 2013

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 17 Jul 2013 14:33:58 +0000

Hello from Berlin, where the pre-BOSC informal CodeFest 2013 meeting is already underway. We’re looking forward to seeing even more of you on Friday and Saturday for BOSC 2013.

BOSC 2013 will be the 14th annual Bioinformatics Open Source Conference, and is organised by the Open Bioinformatics Foundation (OBF). It is held as a Special Interest Group (SIG) meeting in conjunction with the ISMB conference, which itself is held jointly with the ECCB meeting every second year. This year the ISMB/ECCB 2013 is in Berlin, Germany.

You can follow BOSC on Twitter @OBF_BOSC, and we’ll be using the Twitter Hashtag #BOSC2013.

We also have a low-volume BOSC announcements mailing list, please sign up if you’d consider attending or submitting a talk or poster for next year - BOSC 2014 and the ISMB 2014 will be in Boston, USA in July 2014.

Call for abstracts for BOSC 2012

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 05 Mar 2012 19:54:28 +0000

Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012), a Special Interest Group (SIG) of ISMB 2012.

Dates: July 13-14, 2012 Location: Long Beach, California Web site: /wiki/BOSC_2012 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:

April 13, 2012: Deadline for submitting abstracts
May 7, 2012: Notification of accepted talk abstracts emailed to authors
July 11-12, 2012: Codefest 2012 programming session
July 13-14, 2012: BOSC 2012
July 15-17, 2012: ISMB 2012

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

We invite you to submit one-page abstracts for talks and posters. This year’s session topics are:

Cloud and Parallel Computing
Linked Data
Genome-scale Data Management
Data Visualization and Imaging
Translational Bioinformatics
Software Interoperability (possibly a joint session with BSI-SIG, the Bioinformatics Software Interoperability SIG)
Bioinformatics Open Source Project Updates
Interfacing with Industry (panel)

Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards. Each winner will be awarded $250 to defray the costs of travel to BOSC 2012.

For instructions on submitting your abstract, please visit /wiki/BOSC_2012#Submitting_Abstracts

BOSC 2012 Organizing Committee: Nomi Harris (chair), Jan Aerts, Brad Chapman, Peter Cock, Chris Fields, Erwin Frise, Peter Rice

Bioinformatics Open Source Conference (BOSC 2011) Call for Abstracts

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 04 Mar 2011 15:42:59 +0000

Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference ( BOSC 2011), an ISMB 2011 Special Interest Group (SIG).

Dates: July 15-16, 2011 Location: Vienna, Austria Web site: /wiki/BOSC_2011 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:

April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

We invite you to submit abstracts for talks and posters. Sessions include:

Approaches to parallel processing
Cloud-based approaches to improving software and data accessibility
The Semantic Web in open source bioinformatics
Data visualization
Tools for next-generation sequencing
Other Open Source software

In addition to the above sessions, there will be a panel discussion about “Meeting the challenges of inter-institutional collaboration”. We are also working to arrange a joint session with one of the other ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011.

For instructions on submitting your abstract, please visit /wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor

BOSC 2010 Proceedings published today in BMC Bioinformatics

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 21 Dec 2010 19:29:42 +0000

On behalf of the BOSC 2010 Organizing Committee, I am pleased to announce that the BOSC 2010 Proceedings has been published today in BMC Bioinformatics. Special thanks go to the abstract and proceedings reviewers who helped make this possible.

Reminder: BOSC Abstract Deadline April 15

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 07 Apr 2010 05:46:00 +0000

Just a friendly reminder that abstracts for BOSC 2010 are due next Thursday, April 15. See the BOSC web site at /wiki/BOSC_2010 for details. Submissions will only be accepted electronically at http://events.open-bio.org/BOSC2010/openconf.php.

Graduate students, don’t forget we are offering $250 student travel awards this year. Be sure to check the box indicating that you are a graduate student to be considered for the award.

We are also pleased to announce that Guy Coates, Group leader of the Informatics Systems Group at the Wellcome Trust Sanger Institute, and Ross Gardler, Vice President of the Apache Software Foundation, will be giving keynote presentations at BOSC. http://www.sanger.ac.uk/

On behalf of the BOSC 2010 organizing committee, I hope to see you there!

BOSC 2010 Call for Abstracts

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 03 Mar 2010 01:19:29 +0000

**Abstract submissions for the 11th Annual Bioinformatics Open Source Conference (BOSC 2010) are now open.**At-a-glance BOSC is an ISMB 2010 Special Interest Group (SIG) Date: July 9-10, 2010 Location: Boston, Massachusetts, USA BOSC 2010 web site: /wiki/BOSC_2010 Abstract submission via Open Conference System site: http://events.open-bio.org/BOSC2010/openconf.php E-mail: bosc@open-bio.org Bosc-announce list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates April 15: Abstract deadline May 5: Notification of accepted abstracts May 28: Early Registration Discount Cut-off date July 8-9: Codefest 2010 July 9-10: BOSC 2010 August 15: Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics

We have some exciting things planned this year, including:

Codefest 2010 programming session for the two days preceeding BOSC: See /wiki/Codefest_2010 for details.
OpenBio Solution Challenge: See session description below and /wiki/SolutionChallenge for details.
Student Travel Fellowships: Through generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce the competition for three Student Travel Awards for BOSC 2010. Each winner will be awarded $250 to defray the costs of travel to BOSC 2010. See /wiki/BOSC_2010#Student_Travel_Awards for details.
First-ever BOSC Proceedings will be published in the Open Access journal, BMC Bioinformatics. Manuscripts will be due after BOSC on August 15. See /wiki/BOSC_2010#First-ever_Published_BOSC_Proceedings for details.
Sessions on approaches to analyzing high-throughput ‘omics data, cloud-based approaches to improving software and data accessibility, the semantic web in open source bioinformatics, see below:

We invite abstracts for talks at the following sessions: OpenBio SolutionChallenge -- Bioinformatics library providers: please join us in a friendly competition to solve a shared biological problem, demonstrating the utility of your toolkit alongside other developers. Instead of the traditional Bio* updates that we’ve had at previous conferences, this year, we’re planning to organize these talks around a central theme: the OpenBio Solution Challenge. We start with a biological question of general interest, and the project talks will focus around how you would solve that problem using your toolkit and programming language. This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed). Specific challenges are being discussed on the SolutionChallenge page and through the various Bio* mailing lists. Alternately, each project could highlight a challenge that they particularly do well, focusing tutorial-style on how to solve a particular problem.

OpenBio solution challenge: Project updates at BOSC 2010

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 28 Jan 2010 20:45:59 +0000

The BOSC 2010 organizing committee is hard at work getting prepared for this July’s meeting in Boston:

/wiki/BOSC_2010

One of the items we’ve traditionally had at the conference is a project update from each of the OpenBio affiliated groups. This year, we’re thinking about organizing these talks around a central theme: the OpenBio solution challenge. We start with a biological question of general interest, and each of the project talks would focus around how you would solve that problem using your toolkit and programming language.

This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed).

For this to be successful, it of course requires interest and enthusiasm from y’all fine folks involved with the projects. Specifically:

Is there interest from your group in participating in the challenge? You’ll want at least a few people interesting in working on it, and someone to give a presentation at BOSC.
Do you have suggestions on a good theme or specific biological problem to tackle? We’ll hope to pick something in a sweet spot that is challenging enough to be of interest, yet reasonable for presentation and preparation.

Let’s discuss ideas and get this together. Since the schedule for BOSC is developing rapidly, please give us an idea if you’re interested by February 12th, and copy responses to the BOSC mailing list as a central place for discussion.

bosc@open-bio.org

BOSC 2010 Request for Input

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 19 Dec 2009 01:39:24 +0000

BOSC 2010 is currently in the planning stages. It will be held for 2 days in conjunction with the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010) in Boston, Massachusetts, USA. The dates of BOSC 2010 are July 9-10; the main ISMB Conference runs July 11-13, 2010. The BOSC 2010 web site can be accessed here: /wiki/BOSC_2010.

The BOSC organizing committee is soliciting input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community. You may send your suggestions to the bosc@open-bio.org e-mail address or add suggestions to the BOSC 2010 talk/discussion wiki page at: /wiki/Talk:BOSC_2010. Please respond to any or all of the questions below:

1. For the last several years BOSC has consisted mainly of one or two keynote presentations, other talks chosen from among the submitted abstracts organized into sessions by topic, updates from the Bio* projects, Lightning Talks, and informal Birds of a Feather sessions. Would you rather see BOSC continue in this fashion, or would you support changing the format to one or all of the following:

Tutorials where there were in depth demonstrations and code tutorials. This could be lead off by the OBF projects instead of the traditional update talks, but could feature any open source projects interested. These would be hands on sessions with real code examples, with a focus on teaching people how to leverage various code bases to make real life work easier. Would you be willing to organize/lead such a session for your project?
Discussion following the hands on tutorials, these would be interactive sessions focused around dealing with unsolved issues. The “speaker” would be responsible for setting up a set of discussion topics around an issue of interest, and then facilitating ideas and opinions from the attendees. The goals would be to talk through problems and gather a consensus about options for solving them. Would you be willing to organize/lead such a session for your project?
Mini-hackathon either before, during, or after the 2-day BOSC. The subject of the hackathon would need to be organized by the individual project leaders/teams. Some suggestions would be adding/extending support for next-gen sequencing; organizing bugs/tasks so that new beginners can start contributing to the project easily and working on some of those bugs/tasks; organizing some type of contest like the Genome Annotation Assessment Project (GASP) where solutions from different projects compete on arriving at some type of goal. Would you be willing to organize/lead this type of session?
Organizing/creating a LiveCD or Debian download of Bio* projects with documentation to support outreach to the larger bioinformatics community. Would you be willing to organize/lead this type of session?
What session topics would you like to see represented for traditional talks?
Who would you like to hear as a keynote speaker?

2. The BOSC 2010 organizing committee is in discussion with an open access journal to publish a formal Proceedings for BOSC. If you are planning on submitting an abstract for BOSC 2010, are you interested in submitting a more formal paper to the BOSC proceedings, given that as the author you would need to pay the page charges that could run between US$500-1000? We are likely to move ahead with plans to have a proceedings, but it would be helpful to know how many submissions to expect.

3. Call for volunteers. Organizing tutorial/hackathons and such will only be possible if individuals step forward to lead these sessions. Please let us know if you would be willing to serve in any capacity. We also need volunteers to review abstracts for the more “traditional” sessions, please let us know if you are willing to do this as well.

Timeline: We are planning on putting out the Call for Abstracts in mid-January. To be on track, we would like to receive your input by Friday, January 8. If you are willing to step forward to organize a tutorial/discussion/hackathon, you would need to commit by that time, although there would still be some more time to put the actual program together in the new year.

Thanks and Happy Holidays!

Kam Dahlquist Chair, BOSC 2010 on behalf of the BOSC 2010 Organizing committee: Brad Chapman, Michael Heur, Darin London, Anton Nekrutenko, Steffen Moeller, Jim Procter And the O|B|F Board: Chris Dagdigian, Nomi Harris, Hilmar Lapp, Jason Stajich

BioPerl interview in latest FLOSS Weekly

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 22 Nov 2009 20:27:50 +0000

Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly. The interview is now available as an MP3 on the FLOSS Weekly website; several streaming versions (including podcast) are also available.

BOSC Schedule Posted

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 02 Jun 2009 02:09:18 +0000

The BOSC 2009 schedule of speakers with links to abstracts has been posted at /wiki/BOSC_2009_Schedule.

BOSC Update: Ruttenberg, Hanmer confirmed as Keynotes, Early Registration Deadline Friday

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 14 May 2009 01:12:53 +0000

Alan Ruttenberg of Science Commons and Robert Hanmer of the Hillside Group have been confirmed as Keynote Speakers for BOSC 2009. For more information, see the BOSC 2009 web site at /wiki/BOSC_2009.

Abstract acceptances went out today–stay tuned for the schedule, which will be posted once the speakers have confirmed their invitations.

The early registration deadline for BOSC is Friday, May 15; don’t forget to take advantage of the discounted fee for early registrants at http://www.iscb.org/ismbeccb2009/registration.php.

Reminder: Abstracts for BOSC 2009 Due April 13

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 10 Apr 2009 20:41:27 +0000

This is a reminder from the BOSC 2009 Organizing committee that abstracts for BOSC are due on Monday, April 13.

BOSC 2009 Call for Abstracts

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 24 Feb 2009 22:09:24 +0000

Please forward as appropriate and forgive multiple postings.

Call for Abstracts for the 2009 Bioinformatics Open Source Conference (BOSC) 2009

An ISMB 2009 Special Interest Group (SIG) Date: June 27-28, 2009 Location: Stockholm, Sweden URL: /wiki/BOSC_2009 Abstract submission via EasyChair: https://www.easychair.org/login.cgi?conf=bosc2009

Important Dates Monday, April 13: Abstract deadline May 1, 2009: Notification of accepted abstracts May 15, 2009: Early Registration Discount Cut-off date June 27-28, 2009: BOSC 2009

Many open source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards. One of the hallmarks of BOSC is the coming together of the open source developer community in one location to meet face-to-face. This creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done and attendees can learn about new or on-going developments that they can directly apply to their own work.

This year’s conference will mark the 10th anniversary of BOSC. To celebrate the special occasion, the theme of this year’s conference is “Looking Back and Looking Ahead: Open Source Solutions to Grand Challenges in Bioinformatics.” We are inviting abstracts for two different types of talks:

1. Descriptions of a particular open source software implementation by a member of the development team, especially in the areas listed below.

2. Reviews of open source software that compares and contrasts different solutions to the same bioinformatics problem.

In addition, we are asking all speakers to come prepared to lead an informal tutorial on their software during a Birds of a Feather/hackathon session. This year’s topics include: Topics Design Patterns in Bioinformatics Regulatory Genomics Multicore and GPGPU computing Data & Analysis Management (shared session with DAM SIG) Computational Grids Visualization There will also be updates from O|B|F-sponsored projects, and as always, abstracts may be submitted for open source software that does not fit neatly into the above categories. Lightning Talks will also highlight very recent developments.

To contact the organizing committee, e-mail bosc at open-bio.org.

To sign up for BOSC-related announcements, subscribe to the Bosc-announce list ( http://lists.open-bio.org/mailman/listinfo/bosc-announce).

BOSC 2009 Organizing Committee Kam D. Dahlquist (Chair) Lonnie R. Welch (Co-chair) Hilmar Lapp Jens Lichtenberg Frank Drews Andrew Dalke Jim Procter Seán I. O’ Donoghue Anton Nekrutenko Steffen Moeller

BOSC 2009 accepted by ISMB

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 07 Jan 2009 17:07:10 +0000

Belated, and probably most of you knew already, but just in case you didn’t, the 2009 Bioinformatics Open Source Conference (BOSC) was accepted on Dec 16 as a Special Interest Group (SIG) meeting by the respective ISMB 2009 review committee. Special thanks and congratulations to Kam Dahlquist, who agreed again this year to chair the conference, and who pulled the proposal together.

You can follow the organization and the conference taking shape at the BOSC 2009 wiki page. Ideas, preliminary schedules, etc are discussed on the associated talk page. You are welcome and encouraged to join us there. The blurb for publicizing the event on the ISMB website is due on January 16, in a little more than 1 week. If you have ideas or would like to help, do let us know.

Julian Lombardi will present keynote at BOSC 2008

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 18 May 2008 19:23:50 +0000

The BOSC 2008 Organizing Committee is pleased to announce that Julian Lombardi will be giving the keynote address this year. Dr. Lombardi is one of the original architects of the open-source, peer-to-peer OpenCroquet platform for creating and deploying deeply collaborative multi-user online applications and virtual worlds.

For further information about Dr. Lombardi, see the Wikipedia entry about him, his blog, and the OpenCroquet website.

BOSC 2008 is on

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 18 Feb 2008 15:35:07 +0000

Our application to hold BOSC as a two-day SIG (Special Interest Group) meeting in conjunction with ISMB has been accepted for this year. BOSC will take place July 18 and 19 in Toronto, Canada.

For the first time this year, the second conference day will overlap with the ISMB tutorial day, in an attempt to make the overall stay shorter for those who want to attend both BOSC and ISMB. The other upside of this is that BOSC attendees who stay on for ISMB can reflect on the event at the ISMB Opening Reception, which will be held the same night as BOSC concludes.

In our outline we propose a more structured agenda with several sessions dedicated to specific challenging topics in our field, for example on currently intractable (or very hard) problems in bioinformatics, emerging technologies, best practices, and - of course - bioinformatics open source software. Over the next couple of weeks we’ll flesh those out as needed, and put up calls for submissions.

Hence, if you were thinking about submitting, don’t hold off preparing until the official call, and if you weren’t, think again. It’s going to be a really interesting conference. Also, if you have any suggestions for session topics, please come forward and email us as soon as possible at bosc@open-bio.org.

BOSC Schedule Posted

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 16 Jun 2005 23:52:45 +0000

The BOSC 2005 schedule has been posted. Lightning talks are still being accepted.

BOSC 2005

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 29 Jan 2005 16:48:50 +0000

BOSC 2005 website /bosc/

The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology.

see http://www.iscb.org/ismb2005 for more information.

Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2005, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community.

Slides of Bioperl-db / BioSQL talk at BOSC03

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 21 Sep 2003 09:36:00 +0000

I posted the slides for the Bioperl-db/BioSQL talk I gave at BOSC03.

-hilmar

BOSC'2003 Pictures are online

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 02 Jul 2003 04:59:11 +0000

Our “Bioinformatics Open Source Conference” was held in Brisbane, Australia in conjunction with the larger ISMB'2003 meeting. It was quite successful — 96 attendees, wireless internet, BOF rooms and 30+ presentations over 2 days.

Pictures are online here: http://gallery.open-bio.org/

BOSC finishes and I weep as I miss it already

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 28 Jun 2003 11:08:51 +0000

BOSC always comes and goes so fast. I am a melancholy kind of guy so whenever things finish up I get a little misty eyed with regrets at the things I could have done and the people I could have met. But it was all so great it makes me smile with the understanding of the entire world. Plus weeping really gets you the women – makes you look quite sensitive. And I am all about sensitivity. But before I got into this mindset, I tried to write down what happened. Read and feel my joy.

You may be wondering what Australia is like. So am I. So far I have been entirely in the service of you, the faithful reader of BOSC news, and have been basically a good boy attending conferences and generally getting my money’s worth. All this science. All in Australia.

But yes, in case you are wondering if I suddenly turned into an all-contributing hard-core science type who works day and night thinking only of how I can further increase the general scientific knowledge of the world, this is not at all true. So last night it was time to explore the wonderful world of Australian bars. And I’m happy to report on that; if I could remember any of it.

Okay, I can remember. I’m not all that bad, dontchaknow. My first impressions of this region of Australia basically center around two points – there are not a lot of bars around here, and damn these streets are complicated. Sadly, the first impression is likely due to the second – I am the kind of person that get readily lost. But no one cares – the point is that we ended up at the apparently only bar on this side of the river separating our conference site from the downtown casino part of Brisbane; South Brisbane versus the rest of Brisbane.

As an amateur sociologist, amongst other things, I am very interested in the people of Australia. Specifically, I was watching the flight information on the plane ride from Melbourne to Brisbane and noticed something very interesting and peculiar. The flight info basically said the same things – fasten your seatbelt, put on your oxygen mask before helping small children and invalids around you, blah blah blah. The interesting thing is that even though it was the exact same information, it was presented in an entirely different sort of fashion. The language and intonations of the talk was all in English, but it was Australian English, a factor of living in Australia and speaking with Australian people. Its more than just different phrases, but a completely different way of thinking about saying a sentence.

The search for understanding these differences of course proceeded directly to the bar. Understand the Australian animal in its native environment. Study the behavior and write it all down in the notebook. I forgot my notebook. Or if I had one it sunk to the bottom of the Brisbane river when I fell in. But I can remember what I learned and the key to it all is this – Australians love karaoke. We ended up in bar featuring karaoke that was so massive that we actually confused it as being two bars. I talked with several Australian women, on a purely professional basis of course, and asked extensively about my in-flight language realizations. I came to the conclusion that an Australian can’t say what it means to be Australian any more than I can say what it is like to be an American. You suck up the culture and people and just become what you become without thinking about it and then you are that region. In one day, or one week, or one month, I am never going to learn what it’s like to be Australian. So we all gave up on that quest, drank a lot of beer (mmm, good beer) and I sang karaoke for no apparent reason. And it sucked.

That last bit of philosophy and thinking was incredibly boring, but of course it is my mindset for the next few days in Australia. Experience it all, understand it all, wake up with no memories of the previous night next to eighteen Australian women on the roof of the conference center wondering what substance inspired you to get a tattoo of a kangaroo on your forehead. I like wallabies much better.

And there are talks going on. I am diligent. This is what I heard. It may not necessarily be what was actually said, but all one can report on is their perception of reality. Before I degenerate into cheesy Matrix-philosophy pretending that I actually know something about philosophical thinking further then watching Kevin Spacey play a philosophy professor in a movie on the plane, here’s how the talks have been going:

You’re my PAL. Heh. Heh. – Matthew Goode

Let’s say you have to do phylogenies. Lots of us do. I can faithfully say as a current study of phylogenetic techniques that these analyses might be the single most complicated thing on this planet. One consequence of all this is that with all the assumptions and differences in the variety of techniques you normally want to try multiple analyses on your data. My normal thinking is – do a lot of trees in various ways. If you can get yourself the same basic tree using a variety of acceptable methods, then you can probably get yourself to trust it. So the thing you would like to be able to do is write code that will run all of these various trees using different methods and assumptions, let it go all night, wake up in the morning and then evaluate it. If you program in Java, you are lucky enough to have this fine project to help you with this goal. This code looks incredible – it has all your favorite algorithms and substitution models and all those good things. Beautiful. My highest recommendation. Four stars. I recommend the oyster platter with sea clams in mint garlic sauce. Tasty.

Generic Model Organisms and their Database – Suzanna Lewis

Continuing on a food theme (damn, when is lunch?), let’s say you take a dash of collaboration, a pinch of model organisms (geez, these cheesy recipe metaphors are really painfully bad. I will stop now), and you mix it all up (oh yeah, I was supposed to stop that. I promise now. Promise.) with some folks who know how to code and you get out a model organism database. The history of these types of databases is that each organism had a central type of database that a research organization worked on. Each organism had it’s own schemas and tools and people working on it. The more organisms that came about, the more this development philosophy led into duplication of tools. Additionally, some databases had nicer tools for certain things, depending on the expertise of the people in that group, and other organism databases wanted to use it. Well thanks to the genius of many great people in the open-source biology world, it was decided to build a generic model organism database with shared tools. Every lab donated certain tools, they all began to work together, and the beauty and elegance and greatness (man, I am feeling really happy-happy this early morning; everyone is beautiful and happy and time to go frolic in the grass with bunnies and sunflowers and, stay on task, stay on task) became GMOD. This set of tools has great things for literature curation, gene expression data, genome organization, laboratory notebooks, genome analysis – basically everything you’d like to have for your organism. So, yeah, I’ve got this whole plan for job searching – find a job working on an organism that needs a database and get the job setting up the database. Use GMOD, forget to mention that you just used all this free open source, code, and then take six months off traveling around the world on a sailboat you built yourself when you are “working” on developing this database. I think I’m gonna sail my boat to Puerto Rico.

Biopython – me

This was the worst talk I’ve ever seen. This speaker is complete bollocks. I would have walked out if I wasn’t up there giving the talk.

Lightning Talks – lots of people

Come on these go every five minutes. The only good way to describe them is with stream of consciousness. Plus I’ve been reading lots of Joyce, so what are you gonna do. Spreadsheets. Those are all about biologists. We love spreadsheets. Well not me, but let me tell you that the folks who write Excel should hire several people in my lab as stress testers for new version of Excel. They wouldn’t even have to pay them. But the point is that getting your data and programs to be easily integrable with spreadsheets is incredibly smart.

Java beans. Web Services. These are very good things and putting them together is even better. This is the kind of thing that could make you famously famous. Like the famous Amos. That is my favorite episode of Taxi ever, if you haven’t seen it. If you believe, they put a man on the moon.

Lightning talks are flying by and where am I where is the pointer not in my pocket maybe up on the stage I couldn’t have lost it could I have that would be terrible. Three lightning talks in a row. That is serious. I get lost with a single talk to give. Of course, my brain is small. Buzzwords are really in the house right now. After the beans, after the java. Now XML. UML. JML, HML, RNA, DNA, WWW, WWF, RDF. Networks. All those terms and good words about Biopython. Associate in your mind – Biopython, buzzword, Biopython, buzzword, Biopython, buzzword. You know you want to. Hold on a second, I am writing a blog. I am writing a story, and the talk is about weblogs. Cosmic occurrence. Integrated with this kind of ridiculous rambling (well, he might have better rambling then I can manage) are PubMed entries. So you are actually bringing in science with your rambling and potentially contributing to a quality discussion about research articles. The only bad thing is that words like BioPHP pop up. What happened to Biopython. Dueling it out PHP versus Python. Whoah, this is really degenerating. I need a better filter on my brain.

Microarray data from all over. Philosphically, all these organisms must fit together somehow, especially in the wonderful land of Louisiana where they’re eating cajun food. Somehow all of the microarrays come together in my head. Normalization. C++. BASE. Microarray databases. Work-flow for open source microarray analysis. Honestly, I wish I was getting into the world of microarrays at the current time – exploring these types of open-source projects and all the active development in the area really makes me incredibly excited and interested. Which shows you exactly the kind of dork I am.

Population genetics. Wow. Not seen very often in the ol’ bioinformatics circles. Very nice to see, I know several people in my lab who would be salivating right now. I am also salivating along with them as it’s written in Python. PyPop. Nice. It uses dataflows and goes back and forth with Excel. Once again, we know what it’s like to work with laboratory biologists completely in love with Excel. Here’s the URL for those of you who would be searching just like me: http://allele5.biol.berkeley.edu/pypop/

The really nice thing about BOSC this year is that there is lots of room for people to make contributions “on-the-fly.” A really nice example of this type of interactive talk is from Andrew, who is talking about his experiences contributing to BioPerl right now. Honestly, this is really one of the great things about BOSC in my mind – getting people interested in and contributing to projects. I am back into my the world is beautiful and lets frolic with bunnies and bikini babes mindset.

The other great thing about BOSC is exemplified in this next talk (and for me in the PyPop talk) – learning about software that might do something you need to know. Right now we are looking at pretty pictures of sequences and picking out problems with sequences; very nice visualization tools for looking at tons of sequences that come off a sequencer (quality values, sequence features). This is incredibly useful for finding problems with the sequencer, with the assembly, with the quality of sequences.

Two messages for five minutes. I have to disagree with Richard, who doesn’t feel that crops are sexy. I find Sorghum incredibly sexy, but purely in a platonic sort of way. Again – learning about useful tools. Do you need to track genealogies and matings for your crosses in the field? Talk with Richard, he has got your software.

Social policy bonds is what we are hearing about right now. The basic question is whether companies or governments (closed versus open, basically) are better at producing useful things for society. This is economics, and honestly I don’t know anything about economics other than a single (but enlightening) agricultural economics class I took back in my senior year to fulfill some graduation requirements (but also ‘cause I was interested, of course). However, stretching your mind is extremely important to continue to keep yourself an intelligent contributing member of society (or in my case, to pretend). The idea is to fund open-source by putting a “reward” on getting something done, and then paying the reward to the first group or person who accomplishes it. This gets at the question of who is most efficient at producing a useful software product, and the benefit is in supporting software “freelancers” as opposed to building research institutes or the like to produce the things you would like. My immediate concerns would be – who determines what makes a “good” software product that does something. This could build a niche for software junk-bond type traders who could churn out patched together code that did something but wasn’t extensible or potentially good for everyone. Interesting ideas, all the way.

Sadly, the evil that is computer battery time is now eating away at my ability to record further events. Surely this will bring cheers and tears of happiness from those folks who were wondering exactly when I would stop all this damn rambling. Well now is the time as the battery dies and the lack of appropriate power converters leaves me with no other choices but declare myself finished for the day. Plus my fingers hurt.

They let me into Australia, and this is what I saw

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 28 Jun 2003 09:26:53 +0000

If you are not lucky enough to be here in wonderfully beautiful Brisbane with beaches next to the river and where every man and woman is a perfect physical specimen, then you can read all about BOSC colored through my mind. Enjoy.

Where the hell am I? I distinctly heard someone refer to me as mate and I was supposed to be heading to Australia, so I’m thinking that’s where I might be. After three thousand straight hours of airports and planes and ticket counters where bored airline workers are informing you that you won’t reach your destination until three days after your expected date and offer you a 10 dollar food and beverage coupons for your trouble, it’s hard to grasp reality. And yes, of course I spent that 10 dollars on beer. What the hell else would I want to buy in the airport? Okay, Bloody Mary’s, but I only had 10 dollars so you gotta make it stretch at those airline prices.

But it’s okay. Now it’s another morning, another day. Well, maybe it’s a new day. Or maybe it’s the last day. Or damn, it could be two days ahead or three days behind or Christmas or next year’s New Year’s Eve wooo everyone let’s celebrate the beginning of a new millennium. Woo! Man, I am totally messed up.

So let me tell you something you should not do. You should not travel across the United States and then across the world (up and down) in a mad marathon trip that takes approximately 48 hours of flight delays and being left over in airports and sitting on plains with old ladies next to you telling you their life stories and, man, you would have thought she’d have noticed I fell asleep a half hour ago. Another Fosters please, kind flight attendant. But, yes, you should not make this kind of trip, then go straight to a conference, try and run a little meeting of Biopython, take a quick shower, eat a Kabob, start drinking tasty Australia brews named VB interspersed with Tequila shots, sing a karaoke song in the worst possible drunken manner at the best Friday night Karaoke in all of Brisbane according to native Brisbaneans I chatted with, then wander home completely lost throughout half of Brisbane without a map or any idea where you are going being assaulted by random threatening Brisbaneans who happen to up in the middle of the night and then stumbling across people smoking hookah’s right in the middle of the sidewalk whoah where was that bar I gotta get back there. Do not do this. I did this. It was a mistake. I am in Australia. And I am completely mad.

It is with this state of mind that I bring you a report for Australia on BOSC. Good god, this is not an official report sponsored by any reasonable person. What is it then? It’s the kind of rambling I can manage and it’s how BOSC looks through my eyes and do not look too carefully or scrutinize too closely lest you feel it is your civic duty to have me locked up immediately as a threat to myself and others. Come on, friends, I am completely harmless. And this is what I’ve seen so far in the land down under at the number one meeting in the entire world of open-source biology folks.

Python and Systems Biology – Michiel de Hoon

Cool graphics with python. So let’s say we’ve got one hundred million expression data and we want to make a gene regulatory network from them. To put it simply, you have information about how genes express and would like to tie them together in an understandable way. This is the wide and wonderful world of Systems Biology. And that’s where we are today. This involves delving into the head-splitting mania that is differential equations, and I’m taking it for granted that there are some pretty smart mathematically inclined folks are doing things correctly. You can too, as they are all implemented for your use in Python. As always, open-source is helping you not think; more beer time. I can steal that phrase this year since Jason isn’t here this year. Ha. Back to the talk – another thing you might want to do with your gene expression data is try and predict the regulatory transcription factors causing the expression patterns. I’m certainly fond of the belief that cis and trans factors affecting genes are nearly as important as the gene and protein sequences; so it fills the dorky scientific part of me with delight to think about understanding and combining these types of factors into analyses. And all in Python. Always Python. Sweet. Of course, also sweet open-source since you can get the code and documentation and tutorials about how to get started programming with Python. We want to help you help yourself.

Eukaryotic Linear Motifs and Disorder – Rune Linding

This one day I’m walking along, minding my own business, whistling gently the tune to my favorite Frank Sinatra song, and I run into this protein. Bam, right outta nowhere. Some of the time you meet a new protein and it’s wearing a Hello My Name Is (my name is, my name is) tag and you are all set and you can give it a heide-ho and be on your way. But most of the time you meet this protein and have zero idea what exactly it is called, or what it does. There are lots of ways to learn how exactly to meet this protein, but what we are talking about here is learning about the protein by learning it’s peptide motifs. So yeah, peptide motifs are these short linear stretches of protein sequence which are conserved. They often serve as binding sites for other proteins. So, an alternative method to learn about proteins is to discover these regions within your unknown protein, and use these regions to make predictions about the function of your protein. That’s the idea, as my fuzzy brain can understand it. In addition to this approach, you can also use a more standard approach to look for functional sites in the proteins. But I dig the disordered small linear motifs so I rambled on about that the most. Sue me. There is a nice database to search and classify proteins using these methods, which is what this talk is all about. As with all good things it’s developed in Python using Biopython. Bonus.

Sort of like close to Lectin Domains – Alex Zelensky

This domain completely rules. It has more then 2000 references in GenPept and tons of ligands and groups and types all over vertebrates. So, we have got to sort this thing out. I completely sympathize with this type of analysis as a common question a nice laboratory scientist might come up with it – hey, this domain seems really cool, can I look at how it works over the world of all the sequences. You think – no worries, I’ll download a couple of these bad boys from NCBI, do a little phylogenetic tree (using of course the most appropriate method for my question (scientific-type insertion sponsored by the Foundation to Impress Brad’s PhD committee and let him graduate and pass all his exams)) and then go to lunch and slug back a couple of martinis. Of course, when you actually get into it you find that this family you just happened to be interested in spans every single organism ever sequenced and you realize that your martini plans with famous supermodels might have to be put on hold for a year and a half. So this is exactly the problem we are getting into here and the solution in this case, which makes me really hope that next time I am interested in a family of proteins I will be interested in this domain, was to develop an on-line database of these motifs completely sorted out. Beautiful, MySQL, BioPerl. Life is good and I’m gonna make that lunch date; give Claudia a call to let her know.

Nice popular terms like Web Services – Martin Senger

If you ever accidentally forget to uncheck one of those “send me as many mails as possible” boxes while filling out a form to download Java from the good folks at Sun, then you will be like me and find your work mailbox completely filled every day with magazines of complete rubbish called things like “System Administrator’s Weekly.” These magazines suck hard. They are killing so many trees. To the person out there that is sending me these magazines – please stop, I never read them. I don’t even look at them. I just let them pile up until they reach a level so high that it is declared a national hazard and I have to throw them away. My point, however, is that if you glance at the cover of any of these millions of magazines you will see the words Web Services. You will see these words over and over and over and over again. We love Web Services. It will save the world. So what exactly is it. XML, SOAP, web protocols. Sending data between distributed places using standard interoperable protocols and specifications. This will likely not go away anytime soon, so it’s a good thing to read at least a page about it so if someone mentions it – say, between body shots on a stripper at a local sleazy dive bar – you will be able to make a reasonable comment about it. Either “web services’ rulz” or “web services’ suck” normally works. Choose your side. But, I’m distracted. The point is that if you need to get data in the future, you will likely find that more and more of it will be available through web services. This is the case in bioinformatics, and the EBI and EMBL folks are jumping on the bandwagon. An excellent example is OpenBQS – in short terms you can get all of MEDLINE through web services. Sweet. I just want to end this with one point – Web Services are like high school sex. I had trouble concentrating on the rest of the talk once I got that thought in my head. I blame it all on the cheerleaders packing out my Memphis to LAX flight of hell.

Bosc on Open Bioinformatics Foundation

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Join us at ISMB CollaborationFest 2025!

BOSC 2025 potential keynote speakers–community comment period open

Announcing BOSC 2025; seeking keynote speaker nominations

We invite you to join us for BOSC 2025, a vibrant gathering at the forefront of open-source bioinformatics and open science!

Exciting news for 2025:

BOSC 2024 Videos Now Available

My Amazing BOSC 2024 Experience

Join us for CoFest 2024!

BOSC 2024 Review Committee

Gemma Turon's ISCBAcademy talk available on video

Early Poster Acceptance Round 2024

FAQ

ISCBacademy: Gemma Turon on open source AI/ML for (antimicrobial) drug discovery

Gemma Turon, PhD (CEO and co-founder at Ersilia Open Source Initiative) will present on March 5

Abstract

About the speaker

ISCBacademy

Community comment period open for potential BOSC 2024 keynotes

Nominate a keynote speaker for BOSC!

BOSC CollaborationFest 2023 Report

Some advances made during CoFest 2023

New features added to iCn3D protein viewer

Proposal

What was done

Updating the BLAST book

Proposal

What was done

Future work

Progress on various Biopython projects

Proposal

What was done

Future work

Question to CoFest group

MultiK parallelization using Future

Proposal

What was done

Future work

Make installation of Bionano tools easier

Proposal

What was done

Future work

Applications of open source LLMs in bioinformatics

Proposal

What was done

Future work

FAIR Biomedical Research Software (FAIR-BioRS)

Proposal

What was done

Future work

Question to CoFest group

Next release of Common Workflow Language

Proposal

What was done

Future work

Questions to CoFest group

SPARQL WR RO-Crate queries

What was done

Future work

MultiK parallelization using `Future`

WfExS-backend changes to support `envvars` and get conformant to Workflow Run RO-Crate 0.2

Call for OBF Travel Fellowship is Open until 1 December 2019