General on Open Bioinformatics Foundation

BOSC CollaborationFest 2023 Report

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

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

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

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

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

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

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

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

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

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

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

Some advances made during CoFest 2023

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

New features added to iCn3D protein viewer

Proposal

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

What was done

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

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

The BLAST book from 2003 (cover).

Updating the BLAST book

Proposal

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

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

What was done

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

Future work

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

Progress on various Biopython projects

Proposal

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

What was done

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

Future work

Try to get the converted Tutorial to build without errors.

Question to CoFest group

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

MultiK parallelization using `Future`

Proposal

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

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

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

What was done

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

Future work

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

Make installation of Bionano tools easier

Proposal

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

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

What was done

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

Future work

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

Applications of open source LLMs in bioinformatics

Proposal

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

Sharing resources and ideas:

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

What was done

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

Future work

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

FAIR Biomedical Research Software (FAIR-BioRS)

Proposal

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

What was done

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

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

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

Future work

Outreach/communication effort.

Question to CoFest group

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

Next release of Common Workflow Language

Proposal

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

What was done

All done!

See:

Future work

Get these changes reviewed & merged.

Questions to CoFest group

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

SPARQL WR RO-Crate queries

What was done

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

Future work

Add more queries to the list.

Question to CoFest group

How to use SPARQL queries as unit tests?

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

What was done

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

Our sponsors

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

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

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

Our suppliers

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

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

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

Coffee break

Happy participants at lunch

BOSC 2023 Report

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

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

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

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

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

Lunch at CoFest 2023

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

BOSC 2023 keynote speakers Sara El-Gebali and Joseph Yracheta

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

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

BOSC 2023 participants

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

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

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

Julie McMurry and her dog at the GigaScience party

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

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

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

OBF mailing lists migrating to paid hosting, likely Mailchimp

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 22 Mar 2023 16:07:27 +0000

We’re sharing some important news with you regarding our mailing lists. From early on, we’ve maintained a self-hosted Mailman server for any OBF project that needs a mailing list, including our member roster list. After careful consideration, we have decided we need a solution that keeps track more reliably with current and emerging spam-fighting technologies and standards, and that simultaneously requires much less administration time and know-how. Specifically, we are planning to migrate the lists to paid hosting, possibly Mailchimp.

As an open-source community, we understand the importance of using open solutions whenever possible. However, in this case, we feel that switching to a paid provider is the right call for our organization. Mailchimp will offer us a simpler solution with features that should significantly improve the overall user experience for our members. Additionally, it will be easier for us to maintain and manage the mailing lists, which will free up resources for other important initiatives.

We understand that open-source solutions are important to many of our members, but having a stable, reliable, user-friendly, and cost-effective mailing list is essential to our community’s success. If you have personal experience with another mailing list provider that you believe would provide similar or better functionality than Mailchimp, and that is more open, we’d love to hear about it – please contact us by Monday 3 April 2023. You can submit your suggestions by leaving comments in this GitHub issue, or contact us in the OBF Slack.

OBF Public Board Meeting, 2022-10-21

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 29 Sep 2022 17:33:38 +0000

Date, Time, and How to Join

Date and time: 2022-10-21, 15:00 UTC (8am PT / 11am ET / 4pm UK)

Agenda

Board Officer Elections

Chris Fields wishes to step down as Secretary, and Nomi Harris is standing for election to this role
This will be an electronic ballot of the current board members

Elections to the Board

Iddo Friedberg, running for Board member at-large ( statement of interest)
This will be an electronic ballot of the current board members

Bylaw Changes

We periodically review our bylaws
Changes must formally approved by the Board at a public board meeting
We plan minor changes to avoid gendered language, including subsuming the Secretary role (with historical gendered associations) into a Vice President role.
Proposed changes expressed as a Pull Request

Minutes

After the meeting, the meeting minutes will be made available in the obf-docs GitHub repository.

OBF Community Support Sponsorship

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 11 May 2021 17:08:35 +0000

The following outlines a potential new grant programme, subject to approval by the OBF membership in a formal vote, which the OBF board would hope to launch this year.

Motivation

In 2016, the OBF introduced a “Travel Fellowship” to help individuals attend meetings, aiming to improve diversity in the bioinformatics community. Awardees were reimbursed (with receipts) after the event in which they participated, with a standard cap of USD $1000. The Travel Fellowship was later renamed the “Event Fellowship” reflecting that with the COVID-19 pandemic (and hopefully longer-term changes in scientific conferences to promote the participation of diverse members in online events and reduce carbon emissions), attending events no longer automatically means travelling in person.

This fellowship and some of the applications to it have drawn our attention to the fact that for similar amounts of money, we may be able to help grassroots projects running event(s) in their own communities. It would be practical if we do not have to handle itemised receipts for reimbursement, as that would be a significant time overhead for volunteer board members. Instead, the proposal is to follow the existing model of sponsoring conferences whereby the organisers of the event OBF has agreed to support to invoice us an agreed amount (e.g. USD $1000) before the event, and in return our logo appears on their event webpages and materials, acknowledging our support. Where appropriate, applicants will be encouraged to become OBF Affiliate Projects.

This mechanism will require the event organisers to have some sort of bank account or fiscal sponsor (e.g. a university staff member’s budget, a local hackerspace) where we can transfer the funds.

The scope explicitly excludes well-established organisations, which are able to solicit donations and sponsorships on their own. Since some of the OBF’s funds are donated to us by other organisations, we can hopefully be a useful intermediary between our supporters and smaller efforts globally.

Scope

Single events like a scientific meeting, small conference, training workshops, hackathon, or time-limited series like monthly seminars. An organisation can receive only one financial award per calendar year, to ensure that we can offer this support to the wider community.

Essential:

Strong bioinformatics component
Strong Open Source / Open Science component
Code of Conduct

Desirable:

Applying for OBF affiliate membership (need indicative time scale). If the group is already an affiliate member, rather than using this scheme, please email the board directly to discuss direct funding.
The event that is not yet well-established or well-funded
Promotes diversity of bioinformatics participants
Organisers largely based in countries on the World Bank’s low or lower-middle-income list
Meeting materials will be shared under an open licence (e.g. talk slides/videos under CC-BY)

What is not in the scope:

Well established groups able to attract their own donors and sponsors directly (e.g. ISCB, The Carpentries)

Budget

An initial commitment of $10,000 over two years as an evaluation period, with an individual grant award cap of USD $1000 per event or $2000 for an event series.

Logo and text

We would need a standard logo/image banner, URL, and perhaps text for the event to use.

Argument For

With this scheme, OBF will be able to offer benefits to community projects that are aligned with OBF’s mission but are working on a low budget or without any organisational support. This will be an opportunity to reach the demographic and communities that are not yet served by OBF but that promote Open Source and Open Science practices. Furthermore, by encouraging new projects to become affiliated members of OBF, we will enhance the representation of diverse bioinformatics projects through the OBF platform. As a volunteer organisation that holds funds earned by volunteer labour (in particular via conference fees and Google Summer of Code), it helps to reassure OBF volunteers that funds earned through their efforts are being put to good use empowering communities that have aligned goals.

Argument Against

This proposal is a deliberate expansion on where the OBF spends its income, the vast majority of which is earned through the volunteer labour of OBF community members, including those helping to organize BOSC and serving as mentors and administrators in the OBF’s Google Summer of Code participation. The OBF’s assets and income are finite, and thus funds given to projects, events, or initiatives outside of the OBF umbrella are no longer available to spend on OBF members or membership projects. In other words, for the funds committed to this program, the assumption is that frequently more meritorious recipients and/or causes can be found outside of the OBF umbrella, in the scope of this program, than within OBF’s umbrella, in the full scope of OBF’s mission. There’s little evidence supporting this assumption, and until there is, income earned through OBF volunteer labour should be disbursed within the OBF community (which, as it includes BOSC and its attendees, is already broadly defined).

Process

What happens next? This post outlines our vision; next, we will ask the OBF membership if they approve of the idea in principle. We invite feedback via this GitHub issue or emails to the board by Friday 4th June 2021. If the membership approves, the exact policy wording will be drafted as another OBF policy document on GitHub for the board to approve.

Seeking community volunteers: nomination open for OBF board election 2021

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 15 Feb 2021 19:02:32 +0000

TL;DR: Nominate candidates or yourself for the OBF board via this form or work with OBF in other volunteer capacities.

Nominations are welcome for the OBF Board election

OBF is committed to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The roles and functions of OBF have evolved over the last 20 years, and currently include:

- hosting and sponsoring the annual events, Bioinformatics Open Source Conference - running open source events like CodeFests and Google Summer of Code (GSoC) - offering Event fellowships to promote diversity of underrepresented community members at open source events - onboarding and supporting OBF member projects by providing financial management support (e.g., reimbursements and payments and advertising) - maintaining OBF website, social media and newsletter for information dissemination - advocating through policy and public statements

OBF board members are elected through public nomination and voting. As board member Yo Yehudi (see this post) reaches the end of her term, we are reflecting on the need to recruit new and more diverse board members.

In particular, we would like to invite members from low-tech/low-income communities or historically marginalised groups to bring new perspectives to the OBF community and highlight new areas of interest. Elected members of the OBF Board will be instrumental in steering OBF’s work to address urgent challenges and needs in open source bioinformatics communities that we might not have yet recognized.

If the OBF’s goals and values resonate with you, we encourage you to nominate yourself or someone else (please check with them first!) who would be a good addition to the OBF board. Please fill out this form by 1 April 2021: https://forms.gle/PJZLoPXGqKQsEYGJA.

An election for new board members will be held at the next public board meeting (around May or June 2021 - exact data will be announced soon).

Working with OBF in other volunteer capacity

In addition to the projects mentioned earlier, we are grateful to the members of the OBF community who participate in other community initiatives including (but not limited to) organising BOSC annually, handling GSoC mentorship activities and building capacity (skill development and training) and advocacy around open source in bioinformatics.

These tasks could not have been accomplished without the support of our community members. If you would like to be involved in OBF but don’t want to nominate yourself for a position on the Board, we would be delighted talk to you about how you could get involved with these or other projects:

- Curate and edit our quarterly (approximately) newsletter, time commitment approximately 4 hours per issue - Help maintain and update our website: https://www.open-bio.org (WordPress, HTML, CSS skills) - Help manage our social channels (such as Twitter) - Become a GSoC mentor or organisation admin - Volunteer at the Bioinformatics Open Source Conference

We appreciate that many of these roles may be new to you and we would offer mentorship and support if it is your first time occupying this type of position - please don’t feel that inexperience should stop you from applying!

OBF also offers support for individuals and groups to promote open source practices and build bioinformatics skills. Here are a few opportunities that you can benefit from:

- Apply for the OBF Event fellowship, 2 deadlines on 1 April and 1 October 2021 - Become an OBF member to participate in the community - Apply to become an affiliate project by discussing with the board ( see currently affiliated projects) - Apply for the OBF Grassroots Event Sponsorship (will be announced soon)

We would also love to hear your ideas for how you could help boost OBF’s commitments to:

- representing interests of bioinformatics and open source communities from developing countries - onboarding member projects from low and middle-income backgrounds - supporting individuals and communities who are contributing to policy development - boosting grassroots projects that can benefit from OBF’s support - spreading awareness of OBF Event Fellowship and affiliation programs

Sound interesting? If so, please get in touch with the board by emailing board@open-bio.org. If you want more information, or want to talk to one of us about being on the board or in the OBF community in general, see the OBF Board page for contact information.

Goodbye mediawiki, hello new website!

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 08 Apr 2019 12:15:44 +0000

Above: the old BOSC page. Below: the new one.

If you’ve been around the OBF and BOSC community, you’re probably familiar with our slightly rusty old site, which ran on MediaWiki, the same open source software that runs Wikipedia. While they’re both awesome tools, we decided it was time for a refresh.

Over the last few months, our Outreachy Intern Deepashree Deshmukh designed and implemented the new OBF website(with supervision by OBF Board member Yo Yehudi). The goal was an attractive and easily-updatable site that can function as a community-oriented hub. Did we accomplish that? Your feedback on the new site is welcome!

What’s going to happen to the old OBF and BOSC websites?

The two old sites - the old wiki / main site at /wiki and the blog at http://news.obf.org - will stick around for a while, but they won’t be updated any more. One of our goals was to make sure not to break any of our old links - some of them have been around for years. You’ll probably notice a banner at the top of the old pages, pointing towards the new site. Longer term, we’re hoping to redirect all our old URLs directly to their equivalents on the new website.

What to do if you spot any bugs or strange things

We’ve spent a lot of time testing, updating content, tweaking things, and squashing bugs - but no site is ever perfect so it’s possible (probable?!) we’ve missed things. If you spot broken links, layout problems, browser compatibility issues, or anything else, please let us know. If you have a GitHub account, you can log an issue directly, or if it’s easier drop by our gitter homepage chat and let us know there. You’re also welcome to pick the issue up if you know how to fix it!

Acknowledgements

As well as the fantastic hands-on work from Deepashree, we’d like to thank Yo Yehudi for her excellent mentorship of our first OBF intern, Nomi Harris for updating the content and reporting bugs, Hilmar Lapp for setting up a staging server and migrating content to the live site, and the rest of the OBF board and BOSC committee for proofreading and bug reports. A lot of people put time and effort info this and we couldn’t have done it without you!

Next OBF Travel Fellowship application deadline is Dec 15!

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 08 Dec 2017 00:25:15 +0000

The Open Bioinformatics Foundation travel fellowship program was launched in 2016 to help increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. There are four application deadlines per year; the next will be December 15, 2017. If you are hoping to attend an open source / open science bioinformatics even and travel costs are a barrier, we encourage you to apply for one of our $1000 travel fellowships. More information, including a link to the application form, can be found at https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md.

OBF visioning 2017

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 14 Nov 2017 17:08:43 +0000

TL;DR: The OBF isn’t doing enough in public policy and advocacy around Open Science, and we are looking to recruit a new board member who is interested in this role. Is that you? If yes, then contact us.

At our October meeting, the OBF board took some time to think broadly about the OBF, current and future. We tried to answer the questions: What do we say we do? What do we actually do? What more do we wish we could do? We re-read our mission statement and list of public activities from the OBF main page, listed the current efforts of the board members and affiliates, and assessed how our actual work aligned with the stated goals of the organization. This was motivated by having board members who are new-ish to the OBF, as well as upcoming board elections.

Our general mission is fairly broad (“promoting the practice and philosophy of Open Source software development and Open Science within the biological research community”). We aim to do this through running / sponsoring BOSC and other open source events (codefests and Google Summer of Code); running a travel fellowship program; managing servers, mailing lists, domain names and other assets for our member projects; and by advocacy through policy and public statements.

With BOSC being our flagship event, it is not surprising that about 50% of our board time is spent on organizing this meeting, with our remaining effort about equally focused on the travel fellowship, server / domain management, and financials.

What more could we be doing? OBF could help facilitate other events, as we do for Google Summer of Code (GSoC). In this model, the board does not directly run the event, but instead provides support with financial management (e.g., reimbursements and payments) and advertising, while the hands-on organization is done by non-board members. In the case of GSoC, Kai Bin has been the OBF GSoC administrator for the past couple of years (thanks, Kai!). So, even though the board members don’t have bandwidth to organize other events, we could certainly help in a ‘producer’ role.

The big area where we aren’t doing enough is advocacy and communication. There is huge interest in Open Science, reproducibility, software sustainability and other similar topics, but the OBF is surprisingly silent. This doesn’t reflect a lack of interest (or opinion!) among the board members, but rather the difficulty in carving out time from other OBF jobs.

So, we are looking to recruit a new board member who is interested in policy and advocacy around Open Science. Does that sound like you? If you want to put your name forward, please email the board. The election will be held at the upcoming public board meeting in January. If you want more information, or want to contact one of us to talk about being on the board, see the OBF Board page.

Mailing list outage, and public board meeting update

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 12 Nov 2017 09:50:20 +0000

This time of year we’d normally be having a public board meeting as part of our commitment to communication with our member projects and the wider OBF community. As per our bylaws we notify the community at least 10 days in advance, and we’d also handle election of new board members and leadership changes where appropriate. For a couple of reasons, we’re going to postpone that until early 2018.

Our mailing list server (which hosts many of our member project lists) has been overwhelmed in the past few days, leading to delayed or blocked communication not just to our members but for our member projects who rely on it. We’re looking into options for solving this problem, which might include migrating to a hosted solution.

This comes at the same time that the OBF board has been taking a look at how best to direct the organisation as we move forward. We’d like to have that conversation with our members after we’ve crystallised our thoughts a bit, and we’re still in the process of doing that.

As we’re sorting this out, we decided to push the public meeting back to early 2018 so everyone involved can get the most out of it. We hope you understand, and we’re looking forward to hearing from as many of you as we can at that meeting.

Biopython on Podcast.init

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 05 Sep 2017 16:17:08 +0000

Podcast.__init__ describes itself as “The Podcast About Python and the People Who Make It Great”, and the most recent episode is " Biopython with Peter Cock, Wibowo Arindrarto, and Tiago Antão (Episode 125)".

Listening to the finished podcast, interviewer Tobias Macey did a great job. There are things I would have liked to have said - but it turned out pretty well. I hope you’ll agree:

Its worth looking back over the podcast archives, here are a few that caught my eye:

BOSC CodeFest 2016

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

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

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

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

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

BOSC 2016 Keynote Speakers

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

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

Jennifer Gardy

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

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

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

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

Homepage: Jennifer Gardy, Twitter: @JenniferGardy

Steven Salzberg

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

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

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

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

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

Homepage: Steven Salzberg, Twitter: @StevenSalzberg1

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

BOSC 2015 Keynote Speakers

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 26 Mar 2015 16:05:48 +0000

Announcing the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2015:

Holly Bik

Dr Holly Bik is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. She obtained her Ph.D. in molecular phylogenetics at the University of Southampton, UK (working in conjunction with the Natural History Museum, London), followed by subsequent postdoctoral appointments at the Hubbard Center for Genome Studies at the University of New Hampshire and the UC Davis Genome Center.

Her research uses high-throughput environmental sequencing approaches (rRNA surveys, metagenomics) to explore biodiversity and biogeographic patterns in microbial eukaryote assemblages, with an emphasis on nematodes in marine sediments. Through active collaborations with computer scientists and participation in software development projects, her long-term research aims to address existing bottlenecks encountered in –Omic analyses focused on microbial eukaryotes. Holly’s keynote talk topic is “Bioinformatics: Still a scary world for biologists”.

Many biological disciplines remain staunchly traditional, where high-throughput DNA sequencing and bioinformatics have not yet become widely adopted. In this talk, I’ll discuss the ongoing challenges and barriers facing biologists in the age of ‘Omics, based on my experiences in transitioning from nematode taxonomy to computational biology research.

Homepage: Holly Bik, Twitter: @hollybik

Ewan Birney

Dr Ewan Birney is Joint Associate Director of EMBL-EBI, as well as Interim Head of the Centre for Therapeutic Target Validation. Together with Dr Rolf Apweiler, he has strategic responsibility and oversight for bioinformatics services at EMBL-EBI.

Ewan played a vital role in annotating the genome sequences of the human, mouse, chicken and several other organisms; this work has had a profound impact on our understanding of genomic biology. He led the analysis group for the ENCODE project, which is defining functional elements in the human genome. He was also one of the leaders of the BioPerl project. Ewan’s main areas of research include functional genomics, assembly algorithms, statistical methods to analyse genomic information (in particular information associated with individual differences) and compression of sequence information.

He has received a number of prestigious awards including the 2003 Francis Crick Award from the Royal Society, the 2005 Overton Prize from the International Society for Computational Biology and the 2005 Benjamin Franklin Award for contributions in Open Source Bioinformatics. He was elected a Fellow of the Royal Society in 2014.

Ewan was a cofounder of the Open Bioinformatics Foundation, the organization that sponsors BOSC, and has been involved in BOSC since the first conference in 2000. He chaired the meeting in 2001, and gave one of the keynote talks in 2002. We are delighted to have him back as a keynote speaker for 2015.

Ewan’s talk topic will be announced soon.

Homepage: Ewan Birney, Twitter: @ewanbirney

The BOSC 2015 call for abstracts is currently open, and BOSC/ISMB/ECCB 2015 registration has also just opened. We hope to see you in Dublin!

BOSC 2015 call for Abstracts

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 05 Mar 2015 21:00:11 +0000

Call for Abstracts for the 16th Annual Bioinformatics Open Source Conference (BOSC 2015), a Special Interest Group (SIG) of ISMB/ECCB 2015.

Dates: 10-11 July, 2015
Location: Dublin, Ireland
Web site: /wiki/BOSC_2015
Email: bosc@open-bio.org
BOSC announcements mailing list
Twitter: @OBF_BOSC and @OBF_News

Important Dates:

March 24, 2015: Registration opens for ISMB and BOSC ( https://www.iscb.org/ismbeccb2015-registration)
April 3, 2015: Deadline for submitting BOSC abstracts
May 3, 2015: Notification of accepted talk abstracts emailed to authors
July 8-9, 2015: BOSC Codefest 2015, Dublin
July 10-11, 2015: BOSC 2015, Dublin
July 10-14, 2015: ISMB/ECCB 2015, Dublin

The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. We particularly wish to invite those who have not participated in previous BOSCs to join us this year!

Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics. BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.

We invite you to submit one-page abstracts for talks and posters. As mentioned, any topics relevant to open source bioinformatics and open science are welcome. Here are some potential session topics (but please don’t feel limited to these!):

Open Science and Reproducible Research
Standards and Interoperability
Data Science
Visualization
Translational Bioinformatics
Bioinformatics Open Source Libraries and Projects

If your company or organization is interested in being a sponsor for BOSC 2015, please contact us! Sponsors of BOSC 2014 included Google, Eagle Genomics, GigaScience, and Curoverse - we thank them for their support.

BOSC 2015 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Sarah Hird, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres.

Sadly OBF not accepted for GSoC 2015

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 03 Mar 2015 13:30:35 +0000

Last year’s Google Summer of Code 2014 was very productive for the OBF with six students working on Bio* and related bioinformatics projects. We applied to be part of GSoC 2015, but unfortunately this year were not accepted.

Google’s program is enormously popular, and over-subscribed, meaning Google has had to rotate organisation membership. The OBF is grateful to have been accepted in 2010, 2011, 2012 and 2014. This year any participation will be down to individual projects to find a willing umbrella group from the organisations accepted for GSoC 2015. For example, a Biopython project was included under NESCent for GSoC 2013.

Other organizations with bioinformatics as keyword are Ruby Science Foundation, Department of Biomedical Informatics, Stony Brook University, OncoBlocks, University of Nebraska - Helikar Lab. Other organizations related to sciences are ASCEND , BRL-CAD, Debian Project, HPCC Systems®, International Neuroinformatics Coordinating Facility , lmonade: scientific software distribution, OSGeo - Open Source Geospatial F oundation, The Concord Consortium, The Visualization Toolkit. Languages: Python, Scala, Apache Foundation. Last but not least : Global Alliance for Genomics & Health.

On behalf of the OBF, we would like to thank our volunteer GSoC Administrators, Raoul Bonnal and Francesco Strozzi, for organising our application - and all our potential mentors across the Bio* projects who put forward potential project suggestions.

Catering at BOSC CodeFest 2014

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 02 Apr 2014 11:13:25 +0000

Bioinformatics Open Source Codefest, July 9 and 10th in Boston, now with sponsored food and drinks!

The OBF will be holding the fifth annual BOSC Codefest, an informal two day “hackathon” or “coding festival” preceding the Bioinformatics Open Source Conference (BOSC 2014) in Boston (USA).

This year, the BOSC Codefest 2014 is being hosted by hack/reduce (a wonderful hackerspace in Cambridge, Boston) and has also been kindly sponsored by Curoverse (the team behind the open source platform Arvados) and Harbinger Partners, Inc. Thanks to this sponsorship, this year the organisers will able to include catering for the participants - I’m expecting at least coffee and pizza, plus what ever caffeine rich drinks or local pastries are in fashion with the Boston programmers? I checked on wikipedia and Jolt Cola doesn’t exist in the USA any more… so I’m waiting to see what our local organisers Brad Chapman & Michael Heuer have planned.

If you are wondering what happens exactly at a CodeFest, I suggest Brad’s blog post from the BOSC Codefest 2013, or Möller et al (2013). Basically these meeting are a chance for developers of open source bioinformatics (not just the OBF’s Bio* projects) to get together and work on common interests. Things work best with some pre-meeting planning on the usual project development mailing lists or IRC, but are also a great way to meet other scientists and developers in person with more time to chat than during a conference coffee break.

Please note that while there is no registration fee for the BOSC Codefest 2014, please do fill in the registration form to help with the planning/catering.

We’re hoping all the Codefest participants will stay for the BOSC meeting itself, which requires formal paid registration as one of the big ISCB 2014 conference’s SIG satellite meetings. Note that we’re offering a BOSC fee waiver for student speakers, this year. If you are going to BOSC, please remember to submit your BOSC abstracts this week!

Peter

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.

OBF Board meeting 13 Nov

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 06 Nov 2012 15:58:44 +0000

The Open Bioinformatics Foundation (OBF) will be holding a public Board of Directors meeting on Tuesday, 13 Nov, 2012, at 11.30am EST (8.30am PST, 17:30 CET, 16:30 UTC/GMT).

The meeting will be held online or over conference call. We will post details about how to dial in or connect closer to the date ( here).

On the agenda Richard Holland and Chris Fields are running for election to the Board, and some other items primarily up for discussion, including how to keep our membership roll up-to-date and increasing with the least barriers. We will post a more detailed agenda in advance of the meeting ( here).

OBF members should have already received notice of this meeting via the OBF member’s mailing list.

OBF is now an SPI-associated project

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 12 Oct 2012 19:01:49 +0000

I am very pleased to announce that the Open Bioinformatics Foundation (O|B|F) is now a Software in the Public Interest (SPI) associated project, rather than its own not-for-profit incorporation.

An electronic vote of O|B|F members on whether or not to provisionally approve the invitation from SPI closed yesterday at 19:00 UTC. We had a participation of 39 out of 105 eligible, or 37%, which is far above the quorum of 10%. The tally is 38 for provisionally accepting and 1 against. The tally can be seen (and audited) here: https://vote.heliosvoting.org/helios/e/OBFjoiningSPI

The SPI Board vote on resolution 2012-09-28.jb.1 (“Open Bioinformatics Foundation as associated project”) resulted in 8 yes, 0 no, 0 abstain. Given the result of our election, I accepted the invitation right away.

Thanks to everyone who voted. On behalf of the Board, I am thrilled about the turnout!

This terminates O|B|F’s status as its own corporation, which over the years has been more trouble than gain. As an SPI-associated project, we can now accept donations that are 501(c)3 tax-exempt in the US, aside from other benefits. In the coming weeks and months we will be articulating what kind of objectives, platforms, and activities we can or should pursue, given our new status. I’ll communicate separately about that once it gets off the ground.

Finally, please join me in thanking Josh Berkus (SPI & PostgreSQL) for shepherding our joining SPI all the way through. And please also join me in saying hi to the SPI community - as I have done earlier I’d like to encourage everyone to consider joining the SPI as well. It’s a friendly community, and I like to think we can enrich it.

This is a historic day for our organization. Have a drink tonight :-)

Cheers,

-hilmar

Note: This post is based on an email sent yesterday to the OBF member’s mailing list.

OBF Annual Meeting 2011

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 28 Oct 2011 20:54:15 +0000

The annual Board of Directors Meeting of the Open Bioinformatics Foundation will take place on November 8, 2011. As in previous years, it will be held by conference call, estimated to be about 2 hrs long.

The meeting will on Tuesday 8 November 2011, at 11am EST, 8am PST, 16:00 UTC/GMT, 17:00 CET, or Wednesday 9 November 1am JST. Note for translating into other time zones that by then both Europe and the US have gone off DST.

Note that this meeting, like all O|B|F Board meetings, is public; every member may call in at their leisure. Please see the agenda of the meeting (including dial-in information), see also the current board.

BioPerl 1.6.9 released

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 14 Apr 2011 20:03:27 +0000

BioPerl 1.6.9 is now available in CPAN. In this release:

Refactored Bio::Species/Bio::Tree
New SeqIO modules (gbxml, msout, mbsout)
Updates for perl 5.12
Bio::Assembly support for SAM/BAM, Newbler, ace output
Bio::DB::SeqFeature updates
PAML updated to work with v. 4.4d
lots of various bug fixes, around 50

Just to note, this is the first release after we reworked the Build.PL system, so we will probably hit a few speed bumps along the way. This is in effort to simplify the process for further work this summer on modularizing BioPerl, but it also makes new releases much easier to make. In particular, this has only been tested on Ubuntu Linux and Mac OS X (no Windows testing has occurred yet). Please post if there are any problems.

Enjoy!

Biopython 1.54 released

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 20 May 2010 19:04:27 +0000

The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of bug fixes.

This is the first stable release to feature the new Bio.Phylo module which can be used to read, write and take data from phylogenetic trees in Newick, Nexus and PhyloXML formats. The module is the result of Eric Talevich’s Google Summer of Code project which was supported by The National Evolutionary Synthesis Center (NESCent).

Biopython now supports the reading, writing and indexing of Standard Flowgram Format (SFF) files produced in 454 sequencing. Jose Blanca (the brains behind the widely used sff_extract tool) provided code to handle SFF files and Peter Cock has integrated that code with Bio.SeqIO. Adding SFF support to SeqIO makes it possible to convert these files to the FASTQ, FASTA and QUAL formats (as trimmed or untrimmed reads).

As well as adding features the new release tweaks and extends some of the core modules:

Both Bio.SeqIO and Bio.AlignIO will accept filenames as well as handles, as detailed here.
The multiple sequence alignment object that underlies Bio.AlignIO has been improved.
Bio.SeqIO can read and write EMBL nucleotide files.
The dictionary-like objects returned by Bio.SeqIO.index() have a new method " get_raw" that gets unparsed data from a file as a string, as detailed here.
Bio.Entrez includes some more DTD files, in particular eLink_090910.dtd, used by our NCBI Entrez Utilities XML parser.

Binaries and source files for Biopython 1.54 are available from the downloads page. The documentation has been updated to include the changes made since our last release.

A big thanks to every one who tested our beta release or submitted bugs since Biopython 1.53. And an especially big thanks to everyone who contributed to this release, including five first time contributors:

Anne Pajon (first contribution)
Brad Chapman
Christian Zmasek
Diana Jaunzeikare (first contribution)
Eric Talevich
Jose Blanca (first contribution)
Kevin Jacobs (first contribution)
Leighton Pritchard
Michiel de Hoon
Peter Cock
Thomas Holder (first contribution)

BioPerl has moved to GitHub

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 14 May 2010 04:18:33 +0000

BioPerl has migrated to git and GitHub! We have also set up a mirror set of several key repositories at the great public git hosting site repo.or.cz.

If you are a current BioPerl developer (had a previous account for direct access to our prior Subversion repository), please sign up for a GitHub account and let us know your user ID. Also, add the extra email (where ‘DEVNAME’ is your original Subversion account ID). This should map any previous commits from the older Subversion and CVS repository to your new GitHub account.

The following are ways everyone can download the latest code.

Using git

Note you can replace ‘bioperl-live.git’ with any of the repository names (bioperl-db, bioperl-run, etc). For BioPerl developers (GitHub collaborators) you have a choice of SSH or HTTP:

 git clone git@github.com:bioperl/bioperl-live.git

 git clone https://bioperl@github.com/bioperl/bioperl-live.git

The open read-only link (for everyone):

 git clone git://github.com/bioperl/bioperl-live.git

or using the mirror site:

 git clone git://repo.or.cz/bioperl-live.git

Using SVN (read-only)

We will also support read-only access to GitHub with Subversion. We may allow write support at some later point. To use svn:

 svn checkout http://svn.github.com/bioperl/bioperl-live.git

Direct downloads

Tagged releases can be found here:

http://github.com/bioperl/bioperl-live/downloads

The latest source code here:

http://github.com/bioperl/bioperl-live/archives/master

Forking BioPerl and Pull Requests

We intend on using git and GitHub to their fullest. With that in mind, we encourage users to fork BioPerl code, make changes, commit them to your forked repository, and submit pull requests.

Documentation

We’re also in the process of updating our local developer documents for help with those who haven’t used git before. In particular, we have a Using Git page, and have added RSS feeds for our repository commits.

Enjoy!

chris

Update: SVN version fixed, thanks to DaveMessina++ for pointing it out.

Reminder: BOSC Abstract Deadline April 15

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 07 Apr 2010 05:46:00 +0000

Just a friendly reminder that abstracts for BOSC 2010 are due next Thursday, April 15. See the BOSC web site at /wiki/BOSC_2010 for details. Submissions will only be accepted electronically at http://events.open-bio.org/BOSC2010/openconf.php.

Graduate students, don’t forget we are offering $250 student travel awards this year. Be sure to check the box indicating that you are a graduate student to be considered for the award.

We are also pleased to announce that Guy Coates, Group leader of the Informatics Systems Group at the Wellcome Trust Sanger Institute, and Ross Gardler, Vice President of the Apache Software Foundation, will be giving keynote presentations at BOSC. http://www.sanger.ac.uk/

On behalf of the BOSC 2010 organizing committee, I hope to see you there!

BOSC 2010 Request for Input

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 19 Dec 2009 01:39:24 +0000

BOSC 2010 is currently in the planning stages. It will be held for 2 days in conjunction with the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010) in Boston, Massachusetts, USA. The dates of BOSC 2010 are July 9-10; the main ISMB Conference runs July 11-13, 2010. The BOSC 2010 web site can be accessed here: /wiki/BOSC_2010.

The BOSC organizing committee is soliciting input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community. You may send your suggestions to the bosc@open-bio.org e-mail address or add suggestions to the BOSC 2010 talk/discussion wiki page at: /wiki/Talk:BOSC_2010. Please respond to any or all of the questions below:

1. For the last several years BOSC has consisted mainly of one or two keynote presentations, other talks chosen from among the submitted abstracts organized into sessions by topic, updates from the Bio* projects, Lightning Talks, and informal Birds of a Feather sessions. Would you rather see BOSC continue in this fashion, or would you support changing the format to one or all of the following:

Tutorials where there were in depth demonstrations and code tutorials. This could be lead off by the OBF projects instead of the traditional update talks, but could feature any open source projects interested. These would be hands on sessions with real code examples, with a focus on teaching people how to leverage various code bases to make real life work easier. Would you be willing to organize/lead such a session for your project?
Discussion following the hands on tutorials, these would be interactive sessions focused around dealing with unsolved issues. The “speaker” would be responsible for setting up a set of discussion topics around an issue of interest, and then facilitating ideas and opinions from the attendees. The goals would be to talk through problems and gather a consensus about options for solving them. Would you be willing to organize/lead such a session for your project?
Mini-hackathon either before, during, or after the 2-day BOSC. The subject of the hackathon would need to be organized by the individual project leaders/teams. Some suggestions would be adding/extending support for next-gen sequencing; organizing bugs/tasks so that new beginners can start contributing to the project easily and working on some of those bugs/tasks; organizing some type of contest like the Genome Annotation Assessment Project (GASP) where solutions from different projects compete on arriving at some type of goal. Would you be willing to organize/lead this type of session?
Organizing/creating a LiveCD or Debian download of Bio* projects with documentation to support outreach to the larger bioinformatics community. Would you be willing to organize/lead this type of session?
What session topics would you like to see represented for traditional talks?
Who would you like to hear as a keynote speaker?

2. The BOSC 2010 organizing committee is in discussion with an open access journal to publish a formal Proceedings for BOSC. If you are planning on submitting an abstract for BOSC 2010, are you interested in submitting a more formal paper to the BOSC proceedings, given that as the author you would need to pay the page charges that could run between US$500-1000? We are likely to move ahead with plans to have a proceedings, but it would be helpful to know how many submissions to expect.

3. Call for volunteers. Organizing tutorial/hackathons and such will only be possible if individuals step forward to lead these sessions. Please let us know if you would be willing to serve in any capacity. We also need volunteers to review abstracts for the more “traditional” sessions, please let us know if you are willing to do this as well.

Timeline: We are planning on putting out the Call for Abstracts in mid-January. To be on track, we would like to receive your input by Friday, January 8. If you are willing to step forward to organize a tutorial/discussion/hackathon, you would need to commit by that time, although there would still be some more time to put the actual program together in the new year.

Thanks and Happy Holidays!

Kam Dahlquist Chair, BOSC 2010 on behalf of the BOSC 2010 Organizing committee: Brad Chapman, Michael Heur, Darin London, Anton Nekrutenko, Steffen Moeller, Jim Procter And the O|B|F Board: Chris Dagdigian, Nomi Harris, Hilmar Lapp, Jason Stajich

Sanger FASTQ format and the Solexa/Illumina variants

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 17 Dec 2009 16:28:55 +0000

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects:

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants Peter J. A. Cock ( Biopython), Christopher J. Fields ( BioPerl), Naohisa Goto ( BioRuby), Michael L. Heuer ( BioJava) and Peter M. Rice ( EMBOSS). Nucleic Acids Research, doi:10.1093/nar/gkp1137

This will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them.

BioPerl interview in latest FLOSS Weekly

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 22 Nov 2009 20:27:50 +0000

Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly. The interview is now available as an MP3 on the FLOSS Weekly website; several streaming versions (including podcast) are also available.

BioPerl 1.6.1 released

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 29 Sep 2009 17:55:27 +0000

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here:

Via CPAN:

http://search.cpan.org/~cjfields/BioPerl-1.6.1/

Via the BioPerl website:

http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip

The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes available).

Tons of bug fixes and changes have been incorporated into this release. For a more complete change list please see the ‘Changes’ file included with the distribution.

A few highlights:

FASTQ parsing and interconversion of the three FASTQ variants (Sanger, Illumina, Solexa) now works (a concerted OBF effort!)
Significant refactoring of Bio::Restriction methods
Complete refactoring of Bio::Search-related tiling code, including HOWTO documentation
GBrowse-related fixes:
- berkeleydb database now autoindexes wig files and locks correctly
- add Pg, SQLite, and faster BerkeleyDB implementations
Infernal 1.0 output is now parsed
New SearchIO-based parser for gmap -f9 output
BLAST XML parsing essentially complete
Installation via CPANPLUS should now work
For those using Strawberry Perl on Windows, the latest build is expected to pass all tests.
‘raw’ sequence format now parsed by line or optionally as a single sequence
SCF parsing/writing now round-trips
Demo code for using RPS-BLAST and Bio::Tools::Run::RemoteBlast
Bio::Tools::SeqPattern now has a backtranslate() method
Bio::Tree::Statistics now has methods to calculate Fitch-based score, internal trait values, statratio(), sum of leaf distances
Scripts
- update to bp_seqfeature_load for SQLite
- hivq.pl - commmand-line interface to Bio::DB::HIV
- fastam9_to_table - fix for MPI output
- gccalc - total stats
- einfo - simple script to find up-to-date NCBI databases, list field and link values for a specific database

We will shortly release updates for BioPerl-db, BioPerl-run, and BioPerl-network. Enjoy!

chris

BOSC Update: Ruttenberg, Hanmer confirmed as Keynotes, Early Registration Deadline Friday

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 14 May 2009 01:12:53 +0000

Alan Ruttenberg of Science Commons and Robert Hanmer of the Hillside Group have been confirmed as Keynote Speakers for BOSC 2009. For more information, see the BOSC 2009 web site at /wiki/BOSC_2009.

Abstract acceptances went out today–stay tuned for the schedule, which will be posted once the speakers have confirmed their invitations.

The early registration deadline for BOSC is Friday, May 15; don’t forget to take advantage of the discounted fee for early registrants at http://www.iscb.org/ismbeccb2009/registration.php.

Biopython on twitter

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 27 Mar 2009 11:19:56 +0000

Just to let you all know, Biopython is now on twitter. And in case you missed the OBF announcement last month, so is the O|B|F News feed (and BioPerl). You are welcome to follow us (all) on twitter.

I’d also like to remind people there are news feeds for the Biopython news posts (as RDF, RSS, RSS2, or Atom format). We’re planning to have these automatically echoed onto twitter in future… (update) …and that seems to be working now :)

Google Summer of Code: Project ideas page

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 10 Mar 2009 05:56:04 +0000

A wiki page for collecting ideas, possible projects, prerequisites, possible solution approaches, mentors, other people or channels to contact for more information or to bounce ideas off of, etc. has been setup:

http://open-bio.org/wiki/Google_Summer_Code_2009

BOSC 2009 Call for Abstracts

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 24 Feb 2009 22:09:24 +0000

Please forward as appropriate and forgive multiple postings.

Call for Abstracts for the 2009 Bioinformatics Open Source Conference (BOSC) 2009

An ISMB 2009 Special Interest Group (SIG) Date: June 27-28, 2009 Location: Stockholm, Sweden URL: /wiki/BOSC_2009 Abstract submission via EasyChair: https://www.easychair.org/login.cgi?conf=bosc2009

Important Dates Monday, April 13: Abstract deadline May 1, 2009: Notification of accepted abstracts May 15, 2009: Early Registration Discount Cut-off date June 27-28, 2009: BOSC 2009

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

Many open source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards. One of the hallmarks of BOSC is the coming together of the open source developer community in one location to meet face-to-face. This creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done and attendees can learn about new or on-going developments that they can directly apply to their own work.

This year’s conference will mark the 10th anniversary of BOSC. To celebrate the special occasion, the theme of this year’s conference is “Looking Back and Looking Ahead: Open Source Solutions to Grand Challenges in Bioinformatics.” We are inviting abstracts for two different types of talks:

1. Descriptions of a particular open source software implementation by a member of the development team, especially in the areas listed below.

2. Reviews of open source software that compares and contrasts different solutions to the same bioinformatics problem.

In addition, we are asking all speakers to come prepared to lead an informal tutorial on their software during a Birds of a Feather/hackathon session. This year’s topics include: Topics Design Patterns in Bioinformatics Regulatory Genomics Multicore and GPGPU computing Data & Analysis Management (shared session with DAM SIG) Computational Grids Visualization There will also be updates from O|B|F-sponsored projects, and as always, abstracts may be submitted for open source software that does not fit neatly into the above categories. Lightning Talks will also highlight very recent developments.

To contact the organizing committee, e-mail bosc at open-bio.org.

To sign up for BOSC-related announcements, subscribe to the Bosc-announce list ( http://lists.open-bio.org/mailman/listinfo/bosc-announce).

BOSC 2009 Organizing Committee Kam D. Dahlquist (Chair) Lonnie R. Welch (Co-chair) Hilmar Lapp Jens Lichtenberg Frank Drews Andrew Dalke Jim Procter Seán I. O’ Donoghue Anton Nekrutenko Steffen Moeller

Google Summer of Code: Call for Bio* Volunteers

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 13 Feb 2009 21:01:36 +0000

Google is committed to run the Summer of Code program again this year. It will be for the 5th time.

In broad strokes, the program funds what you might call remote summer internships for students to contribute to an open-source software project. Projects (or umbrella organizations) wishing to participate in the program apply during the organization application period (March 9-13 in 2009). Those accepted into the program provide project ideas and supply mentors that guide the work on those. Students apply to a project within the program with specific project ideas, based on those suggested or based on their own idea, get ranked by the mentors of the project, and those accepted into the program get paired up with mentors. Projects are chiefly about programming, the coding period is 3 months (Jun-Aug), and there is no travel required by either student or mentor. The program is global; other than the US trade restrictions that Google is under, there are no restrictions as to where student or mentor reside. The main motivations behind the program are to recruit new contributors to open-source projects, and to produce more open-source code. See the program FAQs for more information.

I’ve had the honor of being part of the program for the last two years, administering NESCent’s participation as an organization in 2007 and 2008 and in 2007 mentoring a student. I have to say I find it the most awesome open-source program since sliced bread (or the invention of BLAST if that means more to you). Despite that and sadly enough, there has been a dearth of participating bioinformatics projects (though some notable ones, such as CytoScape have participated).

There have been two Bio* Summer of Code projects under the NESCent umbrella, one in 2007 and one in 2008. I would be willing to volunteer to take the lead on and administer a full-blown participation of O|B|F as a Bio* umbrella organization, provided 1) at least one Bio* person volunteers to serve as backup administrator, and 2) enough Bio* contributors volunteer to serve as prospective mentors. (Note that if we apply as an organization, there is no guarantee that we would be accepted. In fact, in the past up to 2/3 of applying organizations have been rejected.)

Mentoring involves participating in creating the page of project ideas (I’d provide template and guidance), corresponding with applicants who have questions, participating in student application ranking, and for primary mentors (those directly assigned to a student) based on empirical evidence at least 5hrs/week of time spent with the student to help him/her get over obstacles or avoid wrong paths.

I think almost all mentors would concur that the experience was very gratifying, but as a mentor you will be spending a non-negligible amount of time with the student. I think it is the student-mentor pairing and interaction, not the stipend, that in the end makes the participation for students uniquely productive in terms of learning, and different from simply contributing to the project of choice (which they could always do).

For a personal impression for how the program is from a mentor perspective, I’ll let Chris Fields speak who was the mentor for the 2008 phyloXML in BioPerl project. From a student’s perspective, I’ll leave it to the 2007 Biojava student Bohyun Lee (blee34-at-mail.gatech.edu) and the 2008 BioPerl student Mira Han (mirhan-at-indiana.edu) to comment (if they are still on the list).

So if you think this is a good idea for Bio* to be part of, if you would like to help in some way, if you can see yourself as a mentor, or if you are a lurking would-be student, please let yourself be heard. Email either to the developer list of your Bio* project or to me.

Hello, (twitter) world

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 11 Feb 2009 21:27:09 +0000

O|B|F News feed is now available in Twitter! You are welcome to follow us.

Cheers, The O|B|F Admins.

OBF Conference Call Board Meeting

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 18 Nov 2008 19:46:32 +0000

The OBF Conference call is scheduled for 12:30PM to 2PM PST on Wednesday Nov 19, 2008. Members of the Open Bioinformatics Foundation and those interested in the decisions are invited to listen in and participate. A brief agenda is available here.

Please email Hilmar Lapp at hlapp _AT_ gmx.net for call in number and codes if you wish to participate or listen to the discussion. Those official members should have gotten an email via the OBF members email list.

CVS server move

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 25 Mar 2006 17:10:39 +0000

The CVS repository is migrating from ‘pub’ to a new host called ‘dev’ and requires us to re-issue accounts. This will be a good opportunity to verify email addresses and remove unused accounts.

You should have received an email from Chris D requesting specific information and you will get a new password in the response. If not you will need to send a note to the helpdesk at support_AT_open-bio.org. The changover will happen around March 25th.

Gallery updated

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 18 Feb 2006 18:23:36 +0000

The BOSC 2002 pictures have been migrated to the O|B|F gallery site hackathon2002.

Thanks to Nat Torkington and his continual hosting of the original site.

O|B|F Board of Directors Meeting

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 24 Jun 2005 17:58:57 +0000

The 2005 Board of Directors meeting for the Open Bioinformatics Foundation was held on Thursday, June 24th 2005 in Detroit, MI USA at the site of the BOSC2005 meeting.

This was a major meeting and represents the first attempt to build a governance platform for the organization as well as set up the mechanism for building a voting membership. The O|B|F members will be able to direct the operation of the organization and will also be able to join the Board.

Other major news from the meeting: - Ewan Birney steps down as president; joins Board as at-large member - Jason Stajich joins board and is elected President - Hilmar Lapp is elected to a new position of ‘Parlimentarian’ - Determined efforts to build a voting membership body

Links to meeting minutes and Election Bylaws follow are below …

The new Election bylaws adopted by the Board can be found here: Download file

Meeting minutes are still being approved; when they are ready this article will be edited and a download link will be inserted here.

site updated prior to server move

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 24 Jun 2005 14:25:53 +0000

The backend MovableType software powering this site was upgraded and the backend storage was switched from berkelyDB to SQL. These preparations are being done to ease the transition of http://news.open-bio.org to a new server. The primary purpose of this news entry is to confirm that the posting system still works after the upgrade!

BioKnoppix

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 19 Feb 2004 02:33:56 +0000

BioKnoppix is a new live CD linux, based on KNOPPIX, with EMBOSS 2.8.0, jemboss, artemis, clustalx, Cn3D, ImageJ, BioPython, Rasmol, Bioperl, Bioconductor. It being made available by The University of Puerto Rico High Performance Computing facility (HPCf) and the Puerto Rico Biomedical Research Infrastructure Network (BRIN-PR). Great stuff!

Server downtime announcement

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 30 Aug 2003 21:07:42 +0000

Hi Everyone,

Apologies for the mass cross-posting but this email is about server and IP changes that will affect all of our projects and servers.

Simply put – Wyeth, the company that provides us with our hosting and wonderful T3 connection to the internet is cutting their internet connection circuits over from one ISP to a different Tier 1 internet backbone.

Technically the changeover will be swift as the circuit and new routers/firewalls are already in place. Should be a matter of bringing down the old gear and lighting up the new stuff.

The backbone change will have a significant affect on us though – all of our server IP addresses will change.

The change is scheduled for the evening (EST/EDT timezone) of September 2nd 2003. I’ll be onsite at Wyeth in the datacenter as the change occurs so that I can bring down our servers and plug in the new IP addresses.

The really nice thing is that all of our primary and secondary DNS nameservers are hosted at places other than Wyeth. This means that we can almost instantly be pushing out the new correct IP addresses for all of our open-bio.org, biojava.org etc. domain names.

If I can get my act together during the day on Tuesday I’ll start seeding our DNS servers with shorter TTL values which will speed up the spread of the new information.

For people with ‘fresh’ DNS data our servers will appear back on the internet within 30 minutes or so. For people behind nameserver caches that do not refresh all that often please expect our servers to “vanish” from the internet for a period of about 8-24 hours while the new information propagates out through the internet.

Regards, Chris open-bio.org

BioPython 1.2.0 released

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 28 Jul 2003 02:33:36 +0000

Available now at http://biopython.org/download/

Changes include: added Andrew Dalke’s EUtils library added Michiel de Hoon’s gene expression analysis package updates to setup code, now smarter about dependencies updates to test suite, now smarter about code that is imported Michael Hoffman’s fixes to DocSQL syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible updates in NCBIStandalone, short query error Sebastian Bassi submitted code to calculate LCC complexity Greg Kettler’s NCBIStandalone fix for long query lengths slew of miscellaneous fixes from George Paci miscellaneous cleanups and updates from Andreas Kuntzagk Peter Bienstman’s fixes to Genbank code – now parses whole database Kayte Lindner’s LocusLink package miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman miscellaneous BLAST fixes and updates Iddo added new code to parse BLAST table output format Karl Diedrich’s patch to read T_Coffee files Larry Heisler’s fix for primer3 output Bio.Medline now uses proper iterator objects copen now handles SIGTERM correctly small bugfixes and updates in Thomas Hamelryck’s PDB package bugfixes and updates to SeqIO.FASTA reader updates to Registry system, conforms to 2003 hackathon OBDA spec Yu Huang patch to support tblastn in wublast expression

BOSC'2003 Pictures are online

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 02 Jul 2003 04:59:11 +0000

Our “Bioinformatics Open Source Conference” was held in Brisbane, Australia in conjunction with the larger ISMB'2003 meeting. It was quite successful — 96 attendees, wireless internet, BOF rooms and 30+ presentations over 2 days.

Pictures are online here: http://gallery.open-bio.org/

Foundation views wrongly characterized in Genome Technology

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 25 Mar 2003 05:56:07 +0000

In the March 2003 issue of Genome Technology, “Opposite Strand” contributor Gerald Barnett’s insightful article on “free choice for open source” is blighted by a gross misattribution. He writes that Open Bioinformatics Foundation has proposed that “all federally funded bioinformatics software should be released as open source.” In fact, the O|B|F has explicitly rejected this extreme and inflexible view, as specified in our January 2002 statement on public funding & open source, which states:

“The Open Bioinformatics Foundation believes that scientific software developed with public support should be distributed under terms analogous to those applied to biological materials. In common with treatment of reagents under the UBMTA and good practice, we believe that the essential source code necessary for reproducing published results should be made readily available for non-commercial research use.

“While acknowledging that open source licenses may not be optimal in every instance, we believe that development and release of software under open source licenses is often beneficial and efficient in creating valuable scientific software, and in encouraging its widespread use and most successful exploitation.

“We view researchers as the individuals most capable of determining if their software will be developed and exploited in an optimal manner under an open source license, and we therefore encourage institutions to delegate to their scientists the opportunity to select non-restrictive and open source licenses for their software.”

We believe that Gerald has confused the Open Bioinformatics Foundation (http://open-bio.org) with the efforts of a similar sounding group located at http://www.openinformatics.org/

The O|B|F Board is preparing a response that will be sent to the magazine.

New mailing list Bioped-l

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 17 Mar 2003 16:26:59 +0000

A new mailing list has been created for discussion of software system for genotypes, pedigrees, and linkage data at /mailman/listinfo/bioped-l

This is intended to build off the initial work done in Perl for bioperl-pedigree but is applicable to all who want to contribute to the design or implementation in any language. Database persistence and pedigree rendering are initial areas that will be addressed.

NCICB reviews two LSID Resolution proposals

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 16 Mar 2003 07:47:28 +0000

Members of the caCORE team at the NCICB have been discussing if and how best to use LSIDs. Attached is an analysis of the two LSID Resolution proposals. The document also includes brief descriptions of two use cases that seem appropriate to us. We would be very interested in any responses to this analysis.

The document is also available at: ftp://ftp1.nci.nih.gov/pub/cacore/caBIO/lsid/lsid_memo.doc

Joshua Phillips SAIC Advanced Information Technology Center, Annapolis, MD NCI Center for Bioinformatics, Gaithersburg, MD Phone: (301) 402-7087

2003 Singapore Hackathon

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 20 Feb 2003 04:36:24 +0000

About 30 open source informatics developers are hacking away in Singapore now working on various efforts. The main website is at http://hackathon.open-bio.org and contains links to the Blog site and the picture gallery.

Chris breaks dev.open-bio.org

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 17 Feb 2003 07:02:56 +0000

Urgent notice –> Primary CVS server has been relocated to pub.open-bio.org

“dev.open-bio.org” – our primary developer server is down in Boston with a corrupt password file. Chris blames the Solaris audit subsystem for not liking root commands issued via SSH connections :)

We have moved the CVS repositories to a Linux box called “pub.open-bio.org”. Developer accounts have been created but with different passwords. Email the OBF Sysadmin team at root-l@open-bio.org to get your new password.

Note: This news affects developers only (ie people who have write/commit access to one or more codebase repositories). Our Anonymous CVS server ( cvs.open-bio.org) is unaffected.

2002 Bioinformatics Open Source Conference

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 15 Aug 2002 22:23:50 +0000

Site URL is: http://open-bio.org/bosc2002 and the pictures from the event are available at http://gallery.open-bio.org/gallery/bosc2001

July 2002 O|B|F Newsletter

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 01 Jul 2002 22:13:52 +0000

Available online at http://open-bio.org/newsletters/2002-08-newsletter.html

O|B|F Statement on Public Funding & Open Source

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 01 Jan 2002 23:41:43 +0000

Preliminary Policy Statement on Public Funding and Open Source

The Open Bioinformatics Foundation believes that scientific software developed with public support should be distributed under terms analogous to those applied to biological materials. In common with treatment of reagents under the UBMTA and good practice, we believe that the essential source code necessary for reproducing published results should be made readily available for non-commercial research use.

While acknowledging that open source licenses may not be optimal in every instance, we believe that development and release of software under open source licenses is often beneficial and efficient in creating valuable scientific software, and in encouraging its widespread use and most successful exploitation.

We view researchers as the individuals most capable of determining if their software will be developed and exploited in an optimal manner under an open source license, and we therefore encourage institutions to delegate to their scientists the opportunity to select non-restrictive and open source licenses for their software.

The Open Bioinformatics Foundation is a 501(c)(3) non-profit (pending) organization dedicated to supporting the development, distribution, and understanding of collaborative software in computational biology and bioinformatics. Dating from 1994 and incorporated in 2001, the Foundation sponsors the annual Biological Open Source Conference, software development workshops, and provides umbrella support to the Bioperl, Biopython, BioJava, and other open source bioinformatics development efforts. More than 1000 individuals have signed on to Foundation lists or attended its conferences. Also referred to as open-bio and O|B|F, the Open Bioinformatics Foundation has no affiliation with the similarly named groups at openinformatics.org or bioinformatics.org. The Foundation’s website is at http://open-bio.org/

October 2001 O|B|F Newsletter

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 01 Oct 2001 22:11:13 +0000

Available online at http://open-bio.org/pipermail/open-bioinformatics-foundation/2001-October/000001.html

2001 Bioinformatics Open Source Converence

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 15 Jun 2001 22:22:10 +0000

Site URL is: http://open-bio.org/bosc2001 and the pictures from the event are available at http://gallery.open-bio.org/gallery/bosc2001

General on Open Bioinformatics Foundation

BOSC CollaborationFest 2023 Report

Some advances made during CoFest 2023

New features added to iCn3D protein viewer

Proposal

What was done

Updating the BLAST book

Proposal

What was done

Future work

Progress on various Biopython projects

Proposal

What was done

Future work

Question to CoFest group

MultiK parallelization using Future

Proposal

What was done

Future work

Make installation of Bionano tools easier

Proposal

What was done

Future work

Applications of open source LLMs in bioinformatics

Proposal

What was done

Future work

FAIR Biomedical Research Software (FAIR-BioRS)

Proposal

What was done

Future work

Question to CoFest group

Next release of Common Workflow Language

Proposal

What was done

Future work

Questions to CoFest group

SPARQL WR RO-Crate queries

What was done

Future work

Question to CoFest group

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

What was done

Our sponsors

Our suppliers

BOSC 2023 Report

OBF mailing lists migrating to paid hosting, likely Mailchimp

OBF Public Board Meeting, 2022-10-21

Date, Time, and How to Join

Agenda

Board Officer Elections

Elections to the Board

Bylaw Changes

Minutes

OBF Community Support Sponsorship

Motivation

Scope

Budget

Logo and text

Argument For

Argument Against

Process

Seeking community volunteers: nomination open for OBF board election 2021

Goodbye mediawiki, hello new website!

Next OBF Travel Fellowship application deadline is Dec 15!

OBF visioning 2017

Mailing list outage, and public board meeting update

Biopython on Podcast.__init__

BOSC CodeFest 2016

BOSC 2016 Keynote Speakers

Jennifer Gardy

Steven Salzberg

BOSC 2015 Keynote Speakers

Holly Bik

Ewan Birney

BOSC 2015 call for Abstracts

Sadly OBF not accepted for GSoC 2015

Catering at BOSC CodeFest 2014

BOSC 2014 Keynote Speakers

BOSC 2014 Keynote Competition

MultiK parallelization using `Future`

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

Biopython on Podcast.init