Conferences 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.

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!

Jacqueline Wahura: experience at the Royal Entomological Society Conference 2024

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 07 Jan 2025 15:12:20 +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. Jacqueline Wahura Waweru, a PhD researcher at the University of Cape Town and International Center of Insect Physiology and Ecology, was awarded an OBF Event Fellowship to attend the annual Royal Entomological Society Conference (Ento24).

I was privileged to virtually attend the annual Royal Entomological Society conference Ento24 ( Ento24: In-person - Royal Entomological Society), which took place on 10th to 12th September at the University of Liverpool, UK. The theme of the conference was insect science. Diverse speakers spanning various sub-themes, including pest and natural enemies, host microbiome interactions, genetics and genomics, vector surveillance and control, among others were present. This being the first broad range insect conference that I have ever attended, the diversity in the range of sub-themes covered at the conference made me fully appreciate the diversity in research and interests in the various insect species being presented. Each speaker was eligible to give a 15-minute presentation on their work.

The conference started with a keynote talk on Conservation Biology by Prof Michael Samways from Stellenbosch University, who is the author of the recently published “Conservation of Dragonflies”. This talk was very insightful in highlighting the challenges in protecting species from extinction. In addition, he highlighted some of the drivers of insect species extinction and the challenge that has on the ecosystem. With the threat that climate change presents, and the effect of human activities on the ecosystem, insect species must be protected to protect biodiversity and the gains that come with having insects in the environment, such as offering pollination services to plants used for human food.

During the pests and natural enemies session, I was excited to hear a diverse range of strategies being employed to control pests and natural enemies including the use of insect endosymbionts. It was exciting to hear of symbiosis research in insects like aphids, given that symbiosis is a theme on which my current research focuses, albeit in a different insect model, the mosquito. In addition, there were talks on controlling the Fall armyworm insect, which is a major pest in maize, through intercropping and push pull technology.

It was during the host microbiome interaction session that I was privileged to do my presentation titled “An influential insider: Microsporidia MB influences the gut microbiota composition in Anopheles arabiensis mosquitoes” ( RES_annual_conference_JWahura). Microsporidia MB is an insect endosymbiont in Anopheles arabiensis mosquitoes that was shown to impair the transmission of Plasmodium falciparum. In my talk, I highlighted my key findings that Microsporidia MB influenced the gut microbiota in infected mosquitoes to favor microbes with the Plasmodium transmission blocking phenotype. I outlined the steps followed in my methods and provided a GitHub link to the audience detailing the steps I followed in analyzing the gut microbiota data. It was interesting to see how my research, which is still in its infancy, stirred interest in the audience, and I received feedback on considerations I ought to take in my analysis pipeline as well as research gaps to consider filling.

Other interesting talks during the host microbiome interaction session included those of the effect of different environmental variables on the gut microbiota of mosquitoes, the effect of endosymbionts in aphids on the host microbiome and the protective effect of microbiomes in insects such as ants on fruits such as apples.

The second day of the conference started with a keynote talk on tsetse fly ecology and control by Prof Steve Torr from Liverpool School of Tropical Medicine. During this talk, we were brought to speed on the history of the tsetse fly and the burden of the disease associated with it. In addition, he highlighted all the control strategies that have been developed to reduce the burden associated with the disease and the outlook of gaps to be addressed in the future.

The genetics and genomics session was highly exciting to me as it aligns with my interests in bioinformatics. Various interesting talks on topics such as reproductive manipulation of insects for massive field releases, understanding the genetic drivers of polyphagy in plant pests and talks on genome assemblies formed the basis of this session. The range of talks during this session provided insight into the breadth of genomics research and the scale of adoption of open science practices in insect science. Additionally, there was a strong highlight on the application of insect endosymbionts such as Wolbachia in managing key vectors, including Anopheles gambiae and Aedes aegypti, during the vector surveillance session.

The last keynote talk on the last day was on “Co-evolution in social parasites and their hosts” by Prof Suzanne Foltzik from Johannes Gutenberg, University of Mainz. She did an excellent talk spanning genomics, microbiomes and proteomics and showcased the progress they have made in understanding the co-evolution of parasites and their host ants and bees.

This conference was one of a kind to me in helping me gain a broad perspective on insects and the dynamic range of ongoing research on various insect models. I was also able to gain new insights on alternative niches I could explore in my work by attending this conference. Although I was attending the conference virtually, I managed to get the emails of some attendees with whom I was interested in having follow up discussions on potential avenues of collaboration. It was also exciting to see how different scientists and students are embracing open science globally and also how they are contributing to developing open-source tools.

I am sincerely thankful to the Open Bioinformatics Foundation (OBF) for supporting my attendance at the Royal Entomological Society’s Ento24 conference and for allowing me to contribute to open science by sharing my approaches to malaria transmission blocking using insect endosymbionts.

My Journey at the nf-core Hackathon and Nextflow Summit 2023: Coding and Community

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 17 Dec 2023 16:00:38 +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. Raquel Manzano Garcia, a PhD researcher at the University of Cambridge, was awarded an OBF Event Fellowship to attend the Nextflow Summit 2023 .

This October, I had the incredible opportunity to attend the Nextflow Summit 2023 in Barcelona, thanks to the support of a generous travel grant from the Open Bioinformatics Foundation (OBF) and my supervisor Prof. Carlos Caldas. The eent wasn’t just a conference; it was a confluence of ideas, coding, and camaraderie, set against the vibrant backdrop of one of Spain’s most iconic cities.

One of the most memorable aspects for me was the transition from digital interactions to real, meaningful connections. Meeting individuals I had previously only connected with online, such as my nf-core mentor, Maxime Garcia, was an incredible experience. The chance to collaborate in person, beyond the confines of a shared screen, was both enriching and inspiring. It brought a fresh and exciting dimension to our ongoing work.

The hackathon wasn’t just about coding; it was about building connections. I found myself surrounded by beautiful minds. The experience of learning new tricks and tips in such a collaborative setting has prompted me to reflect on my career trajectory, reaffirming my desire to thrive in similar environments. I am immensely thankful for the individuals I encountered – their patience, kindness, and enjoyable approach to addressing every question, discussion or concern were truly remarkable. Among them were professionals from my own area, with whom I’ve not only reconnected since the event but also started making plans for potential collaborations.

Additionally, I got the opportunity to meet Geraldine Van der Auwera, someone whose work I’ve followed and admired for quite some time. Her work has always amazed me, and meeting her in person was another highlight. This experience was enriched when I was invited to do an interview for the Nextflow podcast channel, an unexpected but thrilling event as it was a first for both of us.

I also had the chance to present my work at the Nextflow Summit in a talk. The interaction with the audience during my presentation reinforced the sense of collaboration and community, making it clear that my coding efforts were part of a larger, shared journey. It’s these moments of exchange and learning that represent the spirit of the Nextflow Summit.

Left: hackathon buzz; right: me presenting my talk at the Nextflow summit

Raquel’s presentation at the Nextflow Summit.

But it wasn’t all work! The summit ensured our schedules were packed with fascinating talks and social events. Making paella, going for runs, and attending a fancy party at the Barcelona port with Seqera’s new sponsored team were just a few highlights. These experiences were fun and engaging, truly enjoyable events. Plus Barcelona, with its incredible beauty, was the perfect host. A walk – and a run – along the beach was a nostalgic reminder of my coastal hometown (Cadiz, Spain), bringing a piece of my heart into this global gathering.

Top: Morning run along the beach; bottom left Shoko dinner party; bottom right: Social event in La Patente - cooking traditional paella.

In conclusion, the nf-core Hackathon and Nextflow Summit 2023 were more than just gatherings; they were vibrant showcases of innovation, collaboration, and diverse cultures. With the support of the OBF travel grant and my supervisor, I’ve come back not only re-energized about my work but also enriched with valuable new professional connections.

Participants at the nf-core hackathon

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

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.

Microbiome (k)nights

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 29 Dec 2022 20:21:04 +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. Luise Rauer, a PhD student at the Technical University of Munich, was awarded an OBF Event Fellowship to participate virtually in the 9th International Human Microbiome Consortium (IHMC) conference in November 2022.

What do a total lunar eclipse and the 9th International Human Microbiome Consortium (IHMC) conference have in common? While they are both exciting and rare events that started in Kobe, Japan, on 8th November 2022, they also happened in the very early morning for any spectator from Europe. With the IHMC conference starting at 1 a.m. for me as a virtual participant based in Central Europe, my very unique preparation for this conference included changing my sleeping rhythm to become a nighthawk for 3 days and nights. But it was worth it!

Lunar eclipse during the IHMC conference in Kobe, Japan. Copyright: IHMC2022Kobe on Twitter: https://t.co/fcZmwRyDXr / Twitter

IHMC conference venue in Kobe, Japan. Copyright: IHMC2022Kobe on Twitter: https://t.co/gyksCdOLuK / Twitter

The great selection of talks at the IHMC conference showed that microbiome research is really starting to fulfill its expectations. Kjersti Aagaard summarized a decade of her research on preterm birth in Malawi, which is prevented by supporting beneficial bacteria in the mouth microbiome with a specific chewing gum at the other end of the body. Similarly, Eran Segal reported successful stool transplants in atopic dermatitis – or in simple words, receiving other people’s poop treats your skin disease. Isn’t that amazing?

While we learned that stool transplants are working in relieving some diseases, it is still unclear which bacteria are actually doing the job. An alternative idea – and probably a more appealing solution to patients – is using defined bacterial communities without the attached dark matter, as presented by Bernat Olle. The prospect of treating bacterial infections with pro biotics ( = living bacteria) instead of anti biotics ( = killing bacteria) is the way of positive thinking that I like.

As a methodology enthusiast, I particularly enjoyed the talks by Ami Bhatt, promoting absolute abundance data and investigating how sample storage affects microbiome results, and by Jun Terauchi, presenting recent harmonization efforts in the microbiome field. In the same vein, I presented my two posters on methodological challenges in microbiome research, and how to tackle them using open-source software for quality control and the power of FAIR data and research. Therefore, one of my personal highlights was the keynote presentation by Rob Knight, impressively summarizing his long-standing contribution to the field, starting from early methodological work on diversity measures to the more recent development of open science data platforms.

Rob Knight’s keynote presentation at the IHMC conference in Kobe, Japan. Copyright: IHMC2022Kobe on Twitter: https://t.co/0nJwbV4rg5 / Twitter

While microbiome researchers have been caring a lot about microbial diversity ever since, geographic and ethnic diversity of the sampled humans have only started to be considered, as illustrated earlier in 2022. But science is moving forward: Projects like the Microbiota Vault aim to collect microorganisms across human cultures for sustainable microbiome health, data sharing practices are increasingly enforced by scientific journals, and hybrid events like the IHMC conference allow a wider inclusion of researchers in the scientific exchange through remote participation. While I really enjoyed following the talks from the distance, it would have been great to be able to exchange directly with other remote and onsite participants. Can the just announced next IHMC conference 2024 in Rome further foster interaction between all attendants, e.g. by providing digital sessions or hybrid interaction spaces?

To sum it up, the IHMC conference did not only provide me with an exciting overview on new microbiome research around the globe, but also illustrated the importance of fair, inclusive, open science to me once more. Starting at a small scale, I want to contribute to this development in microbiome research by further providing open-source code on my Github account and by promoting open science practices in my work environment. Therefore, I highly appreciate the work of the OBF, and would like to thank them again for awarding me with the OBF Event Fellowship for attending the IHMC conference.

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!

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.

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!

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!

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.

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.

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

Travel award recipients for April 2018

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 25 May 2018 14:54:46 +0000

We had another great round of applications for the OBF Travel Fellowship this spring. After reviewing the applications, the OBF Board selected three recipients, who have all accepted the award.

Congratulations to our spring 2018 recipients:

Anisha Keshavan – attended the eLife Innovation Sprint. Anisha is a postdoctoral fellow at the University of Washington, where she develops open source code, including citizen scientist platforms for image quality classification and image segmentation ( update - see blog post).
Farah Zaib Khan – attending GCCBOSC2018 including the CollaborationFest. Farah is a Common Workflow Language contributor based at the University of Melbourne. She has recently been working on a project to record the provenance of CWL workflows, and first attended BOSC in 2017 ( update - see blog post).
Tendai Mutangadura – attending GCCBOSC2018 including the CollaborationFest. Tendai is a first-time BOSC attendee who works at the University of Missouri and focuses on studying disease-causing mutations in canine genomics ( update - see blog post).

Watch this space for blog posts from each of the awardees ( update - links added above).

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.The program is aimed at increasing diverse participation at such events. See the OBF travel award page for details and how to apply.

Saving science from itself: A review of the 2018 eLife Innovation Sprint

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 22 May 2018 12:54:41 +0000

This is a guest blog post from Anisha Keshavan, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the 2018 eLife Innovation Sprint in Cambridge, May 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. The current call closes 15 August 2018, you might want to apply? It is hard for me to put into words the thrill, excitement, and inspiration I’m feeling after attending the 2 day eLife Innovation sprint on May 10th and 11th. The #eLifeSprint ( https://elifesciences.org/events/c40798c3/elife-innovation-sprint-2018) in Cambridge, UK, brought together software developers, researchers, designers, and anyone who was passionate about leveraging web technology to advance open scientific communication. The goal: to save science from itself!

What do I even mean by this? Well, let me explain how the process unfolds:

Get some background knowledge on your topic of interest, read a bunch of publications and about all the experiments and theories up to this point in time #readallthepubs
Think of a new scientific hypothesis or theory, design an experiment to test it
Write up exactly what you did in your experiment, the results, and your interpretation #reproduceit
Show your write up to your peers and have them review it – it’s their job to make sure what you did was legit, and that your results and interpretation makes sense #sanitycheck
Share it with the scientific community and world, which adds to the growing pile of theories/evidence/background in 1. #sharetheknowledge

Sounds great. Why do we need to save science from itself?

#readallthepubs: Turns out, scientists are publishing SO MUCH that its nearly impossible to read and comprehend all the scientific literature out on the web. This is also called research debt (and here’s a great article: https://distill.pub/2017/research-debt/ )

#reproduceit: You’d think computers would have made our lives easier because we can automate data analyses, but actually reproducing an analysis is really difficult. Describing what the analysis code does in the methods section of a paper just doesn’t cut it. And if another scientist can’t reproduce an experiment, can we trust the original experiment’s outcome?

#sanitycheck: Reviewing a paper well is a lot of work! Peer reviewers do this for free and anonymously, which sucks because they never get recognized for the work they put in. Understandably, its not a high priority to review papers in a timely manner, and this means that important research findings don’t get published for a long time.#sharetheknowledge: Now that a scientist has read all the background on their topic of interest, designed and ran a reproducible experiment, and revised their manuscript based on peer review, they submit their article to a journal so that other scientists all over the world can read it. Usually, they pay the journal to publish their paper, and then other scientists also pay the journal to read the paper (Yes, these journals make BANK $$$). If you and your institution can’t pay all the fees, that’s a bummer. In fact, its a bummer for all of science! Progress is majorly hindered when bright, intelligent scientists with something to contribute to a field don’t have access to vital information because they can’t pay publishers. For example, a Liberian physician doesn’t have access to Ebola research articles because each article costs half a weeks salary. Information needs to be open to everyone, regardless of how much money you have.

Ok, so clearly science needs a major course correction. Enter: the 2018 eLife innovation sprint! In the following sections I’ll list the project prototypes and links from the sprint that aim to correct one or more of the the four topics above.

#readallthepubs

https://appstract.pub :My team! We built a citizen science game to collect annotations on publications, so that we can run meta-analyses to summarize a large set of publications. You can compete with friends on the leaderboard, win badges, and contribute to science!WikiCiteViz: A project to visualize citations, so you can see how a study has influenced other studies in the field.Zotero Insights: When you read papers, you can take notes in Zotero on a PDF. This project extracts all your notes (or annotations) and puts it into a machine-readable format, and creates reports and analyses of your notes: a way to find more relevant papers to read using citation data, and finds papers you may have missed.Abstract Babel: what it sounds like! Translate abstracts to different languages . I don’t speak any other languages, but they say the translations are solid!

Funda: a project roadmap for teaching web literacy in South Africa.

#reproduceit

New technology has made our science experiments a little more complicated. We’re collecting a ton of data, and we write a lot of custom programs to crunch the numbers and make inferences. It turns out that sometimes what works on your computer won’t work on someone else’s! It can take a lot of CS skills to get the same analysis running on your computer, and that really slows us down. The following tools can help address this:Reproducible computational research:a case study that shows reproducible computational neuroscience research using Popper and Sumatra .Project Trackbook:an open lab notebook that “gives researchers an interface to securely share and version control files in a decentralized network”.Jupyter + Stencila: combines some great tools: the Stencila editor, the Jupyter notebook, and mybinder, to create “interactive, reproducible, and transparent” scientific articles!

#sanitycheck

Project Octopus: This was probably the biggest group at the sprint, and covers both the #sanitycheck and #sharetheknowledge. On the octopus platform, you’ll be able to review other scientist’s work, and get credit for doing so! You should also checkout the blog on their website, which does a great job explaining in depth the problems we face in science, and how octopus can help.PREreview: " Putting the ‘peer’ back into peer review!" Many scientists have started to upload their manuscripts to preprint servers, so that scientists can access the information before the lengthy peer-review and publication process. And this is really great for authors! For example, here is a preprint on how preprints that are posted before conference submission garner more citations than those posted after. PREreview is a platform for the “collaborative writing of preprint reviews” :) I found a very useful blog post on their site on guidelines for writing a preprint review.

#sharetheknowledge

Project Octopus: On the octopus platform, all published work will be open to everython, and as a scientist, you’ll be able to “publish your hypotheses, methods, results and analyses in Octopus as you produce them, in whatever language you are most comfortable in”.Plaudit: It would be great if the value of the paper was not dependent on journal status, but instead on the quality of the work! Plaudit lets you publicly endorse an article, so that scientists don’t have to worry about whether your article is published in a name brand journal, and it incentivizes open publishing and publishing preprints.

Conclusions

Sometimes I feel really pessimistic about science, because of how inefficient and unfair it can be. But all the amazing participants at the eLifeSprint showed me that 1) SO many people care about these issues, 2) people have brilliant ideas and prototypes to address these issues, and 3) how many tools already exist, that I just didn’t know about until I attended the sprint (I was excited to learn about the amazing openaccessbutton.org API). Overall I left feeling very optimistic about the future of science! Thanks to Naomi Penfold and eLife for organizing this amazing event, and especially, thanks to OBF for the travel award so that I could attend!

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.

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.

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).

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.

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 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 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

BOSC 2014 video recording

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 19 Jun 2014 15:56:18 +0000

We’re pleased to publicly announce that we aim to video record all the talks at BOSC 2014, and the panel discussion, to be made freely available online after the conference. This is on an opt-out basis, and thus far none of our speakers have declined to be filmed. Last year we managed to record many of the talks - including both keynotes, which you can watch via the YouTube links on the BOSC 2013 Schedule. This year we are hiring a professional from Next Day Video ( @NextDayVideo on Twitter).

This is thanks to very generous support from Google’s Open Source Programs Office (who also run the amazing Google Summer of Code program which the OBF and its member projects have regularly taken part in), a new sponsor for BOSC this year.

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.