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Chris Mungall (Lawrence Berkeley National Laboratory)

 Keynote talk for joint BOSC/BOKR session (title TBA)

Dr. Chris Mungall is a Senior Scientist at the Berkeley Lab, where he heads the Biosystems Data Science department.

BOSC 2025 Keynotes

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

Announcing BOSC 2025; seeking keynote speaker nominations

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community.

Jacqueline Wahura: experience at the Royal Entomological Society Conference 2024

Erin (Rin) Krichilsky: Leveraging Open Data to Address the Bee Biodiversity Crisis

The


 Open Bioinformatics Foundation (OBF) Event Fellowship program


 aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community.

Jacob González Isa: Bioinformatics, Spain and I

Starting in July 2019, OBF Board public meeting minutes can be found in our GitHub repository.

Meeting minutes after 2019

Zehra Köksal: My unforgettable experience presenting accessible software to 1000 forensic experts

The talk videos from BOSC 2024 are now available on YouTube. They are also linked from the BOSC talk schedule (scroll down to “Talks”).  Stay tuned - our full report on BOSC 2024 will be published soon!

BOSC 2024 Videos Now Available

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

BOSC 2024 Review Committee

Mélanie Courtot (Ontario Institute for Cancer Research)

 The Data Shows We Need Better Data

Big data, AI, LLMs… do they live up to the hype? In a bright and hopeful future, AI accelerates progress, revolutionizes healthcare, alerts us to health risks, and creates fresh career paths. Yet, in a bleaker outlook, it obliterates jobs, fosters rampant misinformation and increases inequity.

BOSC 2024 Keynotes

As of November 21, 2023, the Open Bioinformatics Foundation and BOSC will no longer post on Twitter/X. Although in the past it was a useful social medium, it is no longer compatible with our values, as expressed in the OBF Code of Conduct:  We are committed to creating a friendly and respectful place for learning, sharing and contributing. All participants in our events and communications are expected to show respect and courtesy to others.

OBF and BOSC leaving Twitter/X

In conjunction with our annual meeting, BOSC, the OBF runs a collaborative event (formerly called CodeFest, short for coding festival, and now called CollaborationFest, or CoFest for short). At these events, participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases.

OBF/BOSC CollaborationFest 2024

We are pleased to announce that BOSC and the newly-renamed Bio-Ontologies and Knowledge Representation (BOKR) will join forces for a day at ISMB/ECCB 2025!

BOSC and BOKR to join forces at ISMB/ECCB 2025

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Masturina Binti Md Mansor, a PhD student at the Universiti Putra Malaysia, was awarded an OBF Event Fellowship to attend Asia &amp;

Masturina Binti Md Mansor: My experience at the first APBJC2024 in Naha city, Okinawa, Japan

The call for applications for the OBF Event Fellowship 2024,

 round 2

, is now open.

 The deadline for this round is 1 August 2024.

Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

Call for the second round of OBF Event Fellowship 2024 &amp; overview of the last round of 2023.

A PhD student’s perspective on attending the 17th Annual International Biocuration Conference in Faridabad, India


 
 The
 


 
 Open Bioinformatics Foundation (OBF) Event Fellowship program
 


 
 aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community.

Open Data, Open Doors

Abstract submission for BOSC 2024 is now open! Since some people can’t get conference travel approval from their institution until they get confirmation that their abstract has been accepted for a presentation, we started offering

 Early Poster Acceptance

last year, and we are continuing the experiment this year.

Early Poster Acceptance Round 2024

We are seeking a diverse list of potential BOSC keynote speakers. We invite you, our community, to nominate people you think would be appropriate (and at least somewhat likely to accept the invitation – for example, it is extremely unlikely that we would get a ‘yes’ from a recent Nobel Laureate). Please submit your nominations here (as many as you like;

Nominate a keynote speaker for BOSC!

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

BOSC 2025 potential keynote speakers–community comment period open

The call for applications for

 round 3

of the OBF Event Fellowship for 2024 is now open.

 The deadline for this round is 1 December 2024.

You can submit your application through this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

Call for the third 2024 round of the OBF Event Fellowship &amp; overview of the second round.

The call for applications for

 round 1

of the OBF Event Fellowship for 2025 is now open.

 The deadline for this round is 1 April 2025.

You can submit your application through this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

Call for the first 2025 round of the OBF Event Fellowship &amp; overview of the last round of 2024

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Li Chuin Chong, a PhD student at the TWINCORE Centre for Experimental and Clinical Infection Research GmbH &amp;

Exploring Open Science in Computational Virology: Li Chuin Chong's Journey at ECCB2024

The call for applications for the OBF Event Fellowship 2024, round 1, is now open.

 The deadline for this round is 1 April 2024.

Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

Call for the first round of OBF Event Fellowship 2024 &amp; overview of the last round of 2023

Dear Biopythoneers,  Our first release of 2024 is now out, sooner than planned as this is purely to revert the removal of the .strand, .ref, and .ref_db attributes of the SeqFeature which was done in Biopython 1.82 without a deprecation period. They are again aliases for .location.strand etc, but now trigger deprecation warnings. See our deprecation policy. We apologize for any inconvenience, and thank you to those reporting this.

Biopython 1.83 released

This year will mark the 15th edition of the BOSC-associated CollaborationFest, or CoFest for short. At these events, participants work together on code, documentation, training materials, use cases, and analyses. CoFest 2024 will take place on July 17-18, right after ISMB and BOSC 2024. This will be a hybrid event, hosted at UQAM | Université du Québec à Montréal and online.

Join us for CoFest 2024!

The
 


 
 Open Bioinformatics Foundation (OBF) Event Fellowship program
 


 
 aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community.

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

Yvonne Walburga: Journeys across oceans

Gemma Turon, PhD (CEO and co-founder at Ersilia Open Source Initiative) will present on March 5 BOSC and the OBF will host an ISCBacademy webinar on

 March 5, 2024, at 8am PST (16:00 UTC).

Gemma Turon (see bio below) will speak about “Ersilia, open source AI/ML for (antimicrobial) drug discovery”. Abstract The Ersilia Open-Source Initiative is a non-profit organisation whose mission is to equip laboratories, clinics and

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

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

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

ISCBacademy is a series of free webinars sponsored by the International Society for Computational Biology. They are open to all, including those who are not ISCB members.

ISCBacademy webinar Oct 3

Diversity, inclusion and accessibility (also known as Diversity, Equity and Inclusion, DEI) are a major part of OBF and BOSC’s mission and core values. Below are some of the ways we have worked to promote DEI at OBF, BOSC, ISMB (the host conference for BOSC) and in the broader open bioinformatics community.

How we support diversity, inclusion and accessibility

Daniela Senra: My Experience at the Human Cell Atlas General Meeting 2023

The call for applications for the OBF Event Fellowship 2023, round 2, is now open. The deadline for this round is

 1 August 2023

. Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

Call for the second round of OBF Event Fellowship 2023 and the first 2023 round overview.

BOSC 2023 Keynotes Sara El-Gebali (SciLifeLab-DataCentre-Sweden)

 A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration

_Join us in humanity’s quest for knowledge and understanding, on a transformative odyssey of scientific progress, fueled by the power of open collaboration.

BOSC 2023 Keynotes

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.

OBF mailing lists migrating to paid hosting, likely Mailchimp

Ruth Nanjala: My experience attending and participating at the ICHG 2023 conference hosted in the Mother City

The call for applications for the OBF Event Fellowship 2023, round 1, is now open.

 The deadline for this round is 1 April 2023.

Applications should be submitted via this Google Form.

Call for applications for the first round of OBF Event Fellowship 2023 &amp; overview of the second 2022 round

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

Comment period on potential BOSC 2023 keynote speakers is now open

The call for applications for the OBF Event Fellowship 2022, round 2 is now open.

 The deadline for this round is 1 October 2022.

Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling the form – make a copy of this template.

Call for the second round of OBF Event Fellowship 2022 &amp; overview from the first round

The OBF Community Support Sponsorship scheme aims to sponsor small open-source-focused events like a scientific meeting, small conference, training workshop, hackathon, or time-limited series like monthly seminars. See details in this post. One application was funded under this program to prototype the workflow, with OBF offering financial support for a seminar series hosted by the Bioinformatics Hub Kenya.

OBF Community Support Sponsorship scheme funds first pilot project

’ello Co-Fest Friends! After failing to find a good spot for an in-person CoFest, we decided to have the CoFest remotely! I was really excited to meet you all at this event (and have you all meet each other) in the real world, but we’ll have to settle for doing that at BOSC (for those who are there).  By all means, don’t let this stop your in-person innovations! Want to meet up and work at a café? Do it! Hotel room? It’s your room!

Post-BOSC CoFest will be online

BOSC 2022 schedule at a glance (Scroll down to see the full lists of talks and posters.) BOSC 2022 Talk Schedule

 Coming soon!

For testing only: BOSC 2022 Schedule (duplicate)

BOSC 2022 Keynotes Melissa Haendel (University of Colorado Anschutz Medical Campus) Joint keynote, BOSC and Bio-Ontologies

 The open data highway: turbo-boosting translational traffic with ontologies


 Addressing complex scientific challenges requires a roadmap of data from diverse sources, organisms, contexts, formats, and granularities.

BOSC 2022 Keynotes

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to support and encourage diverse participation at events focusing on open source bioinformatics software development and open science practices in the biological research community. Each year we open two calls for applications, deadlines for which are 1 April and 1 October.

Round-Ups from 2021 OBF Fellowship Awardees

Announcement drafted by Malvika Sharan, Caleb Kibet and Hilya Zahroh, with the OBF Board’s input.

The call for applications for the OBF Event Fellowship 2022, round 1 is now open.

 The deadline for this round is 1 April 2022.

Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling the form – make a copy of this template.

Call for applications for OBF Event Fellowship, Round 1 of 2022

We are delighted to announce that Caleb Kibet and Hilyatuz Zahroh, two members who recently joined the OBF board, will be joining Malvika Sharan as the co-chairs of the OBF Event Fellowship program. Inviting contributions from the OBF board members, as well as bringing insights from their lived experiences, Caleb, Hilya and Malvika will re-evaluate how we can manage the OBF Event fellowship more effectively going forward.

Updates from the OBF Event Fellowship Chairs

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Tanakamol Mahawan, a PhD student at the Institute of Systems, Molecular and Integrative Biology , University of Liverpool, was awarded an OBF Event Fellowship to attend Asia &amp;

Discovering Okinawa at APBJC 2024: Tanakamol Mahawan's First Conference Back in Asia

BOSC 2025, the 26th annual Bioinformatics Open Source Conference, will take place July 21-22, 2025 in Liverpool, UK (as part of ISMB/ECCB 2025)

. BOSC covers all aspects of open source bioinformatics and open science. Abstract submission is open!

BOSC 2025

With a little help from your friends! -Learning bioinformatics online.

Open source and open minds - a memorable experience: TBNSS 2024

BOSC 2025 Abstract Submission BOSC 2025, the 26th annual Bioinformatics Open Source Conference, will take place July 21-22, 2025 in Liverpool, UK (as part of ISMB/ECCB 2025). BOSC covers all aspects of open source bioinformatics and open science.

 Abstract submission is now open!

We welcome submission of your 1-2 page abstract for consideration as a talk or poster.

Submit to BOSC 2025

We recognize that the high price of travel and registration can make it hard for some people to attend BOSC/ISMB. Below are some ways to apply for financial assistance to present your work at BOSC 2025. OBF Event Fellowships   The Open Bioinformatics Foundation (OBF)’s Event Fellowships are aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities.

Financial support options for attending BOSC 2025

CollaborationFest 2025 will be a two-day collaborative work event at which participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. Bring your own project ideas or come ready to collaborate with others on their projects! BOSC has held CollaborationFests (aka CoFests) every year before or after ISMB since 2010.

Join us at ISMB CollaborationFest 2025!

Over the past few weeks, we have been working behind the scenes to migrate our website, resulting in the page that you currently have in front of you! Our pages are now generated by the

 Go

-based, open source static site generator

 Hugo

, and are stored on GitHub.

Welcome to the new OBF website!

BOSC 2022   BOSC 2022 was held July 13-14, 2022, as part of the hybrid ISMB 2022 (in person in Madison, Wisconsin, USA and online).  A joint BOSC/ Bio-Ontologies session included keynote speaker Melissa Haendel. Jason Williams’s talk was a joint BOSC/Education COSI keynote. The program closed with a panel about Building and Sustaining Inclusive Open Science Communities.

BOSC 2022

The OBF held a public Board meeting on September 21, 2021, via Zoom. During the meeting, one Board member, Bastian Greshake Tzovaras, whose term expired, was elected to another term as Board member-at-large, and two new Board members were elected: Hilyatuz Zahroh and Caleb Kibet. Additionally, two proposals were presented (see below). The meeting minutes will be made available in the obf-docs GitHub repository.

Two new members elected to OBF Board

The deadline for applying for an OBF Event Fellowship has just been extended to

 October 4, 2021

! The OBF Event Fellowship program is aimed at increasing diverse participation at events relating to open source bioinformatics. You can read blog posts by previous Event Fellowship recipients. See more details on our webpage, and submit your application at

 https://forms.gle/7ocmgvypiFHeFNfy7

!

Event Fellowship deadline extended to October 4, 2021

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

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

The call for application for the second round of this year’s Open Bioinformatics Foundation (OBF) Event Fellowship is open. Please submit your application before

 October 1, 2021

(save a calendar reminder). Just announced: deadline extended to October 4, 2021!

Call for application for the OBF Event Fellowship - second round 2021

This post is guest-posted by Federica Trevisan, an OBF GSoC student with the Wellcome Trust.

Working on a data science project with the Open Bioinformatics Foundation, WellcomeML - Part one

OBF students and mentors at an OBF kickoff call  Every year the OBF applies to participate as a mentoring organisation for Google Summer of Code, a paid work experience program where students get the chance to do paid work on an open source project and open source organisations host the students to work on their projects.

Eight incredible GSoC students for the OBF this year ☀️

Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of shared interest. BoFs at ISMB/ECCB 2021 will take place each day of the meeting except the last day, at the same time as the poster session (not ideal, we know–but there are only so many viable hours in the day), from 15:20-16:20 UTC.

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

ISMB CollaborationFest 2025 will be a collaborative work event at which participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you. Bring your own project ideas or come ready to collaborate with others on their projects!

ISMB CollaborationFest 2025

Thanks to funding from our sponsors, we are opening a special call for applications to the BOSC-OBF Event Support Fund.

BOSC-OBF 2021 Event Support Fund

Biopython 1.79 has been released and is available from our website and PyPI. This is the final release supporting Python version 3.6. It also supports Python versions 3.7, 3.8, and 3.9, as well as PyPy 3.6.1 v7.1.1.  The major changes in this version are listed below:  - The Seq and MutableSeq classes in Bio.Seq now inherit from the same base class, ensuring their mutual consistency.

Biopython 1.79 released!

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

Join us at BOSC 2021!

It’s Google Summer of Code (GSoC) application time again - I’ll be leading the OBF GSoC application and org admin process this year alongside Sarthak Sehgal, Michael Crusoe, and Kai Blin.

Google Summer of Code 2021 - we need your project ideas!

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

 Jason Williams

( @JasonWilliamsNY) is a new member of the BOSC Organizing Committee, though he’s been a BOSC participant and an abstract reviewer for years.

Introducing the BOSC 2021 Organizing Committee!

The call for applications for the OBF Event Fellowship 2021, round 1 is now open.

 The deadline for this round is 1 April 2021.

Applications should be submitted via this Google Form. We invite applications from candidates who are seeking financial support to attend or host virtual events in 2021.

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

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

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

About three years ago I nervously responded to a blog post from the OBF looking for board member applications from people who were interested in leading open science related initiatives. This went as well as I possibly could have hoped - both myself and the other applicant, Bastian Greshake Tzovaras, officially joined the board in March of 2018 for a three-year term.

Would you like to make a difference in grassroots open bioinformatics?

The OBF has two sets of domain names available for adoption by a non-profit or open source project: biows.org, biows.com, biows.net and biocpp.org, biocpp.com, biocpp.net  These domains were registered and donated to us with bio-web-services (biows) and bio-c-plus-plus (BioC++ or BioCPP) in mind, but we’ve failed to find a good home for them.

Domain names available for adoption

OBF was accepted as a mentoring organisation for Google Summer of Code this year. It was another good year for OBF, with Kai Blin, Michael R. Crusoe, Sarthak Sehgal, and Yo Yehudi as administrators.

Google Summer of Code 2020 Wrap Up

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community.

H3ABionet’s Introduction to Bioinformatics Training (IBT) 2020: a report of the first iteration hosted in Cameroon

Biopython 1.78 has been released and is available from our website and PyPI. The main change is that Bio.Alphabet is no longer used. In some cases you will now have to specify expected letters, molecule type (DNA, RNA, protein), or gap character explicitly. Please consult the updated Tutorial and API documentation for guidance. This simplification has sped up many Seq object methods.

Biopython 1.78 released

We are glad to announce that the call for applications for the OBF Event Fellowship is now open.

 The deadline for this round is 1 October 2020.

Applications should be submitted via this Google Form.

Call for applications for OBF Event Fellowship, Round 2 of 2020

Getting introduced to Bioinformatics and Open Science through BCC 2020

A Software Engineer's Experience at BCC 2020

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

BCC2020 pre-conference open house

(This is the schedule for 2020. The 2021 schedule is here.)  BCC2020 overview (complete BCC2020 schedule here)        BOSC 2020 Talk Schedule   Below are the talks accepted to BOSC 2020 from submitted abstracts. The full schedule of BOSC and Galaxy talks (in both hemispheres) is available on the sched page.

BOSC 2020 schedule

Biopython 1.77 has been released and is available from our website and PyPI. This is the first release since we dropped support for Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing.

Biopython 1.77 released

The Open Bioinformatics Foundation (OBF) sponsors a Travel Fellowship program aimed at increasing diverse participation at events promoting Open Source bioinformatics software development and open science in the biological research community. Michael Thompson’s participation at the

Galaxy Admin Training 2020

 workshop in Barcelona was supported by this fellowship.

Galaxy Admin 2020 and beyond (guest post by OBF Travel Award recipient Michael Thompson)

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

BCC2020 (inc. BOSC 2020) abstracts due this week

CollaborationFest 2019   In conjunction with our annual meeting BOSC, the OBF runs a collaborative event (formerly called CodeFest, short for coding festival, and now called CollaborationFest, or CoFest for short). At these events, participants work together to contribute to bioinformatics software, documentation, training materials, and use cases.

BOSC 2019 CollaborationFest (for reference)

In light of the current outbreak, we urge everyone to avoid travelling if possible, in order to slow the rate at which the virus spreads to vulnerable people. You may have read that the BCC (BOSC+Galaxy) committee is delaying registration whilst considering the best options.

OBF travel fellowships update in light of the Coronavirus (COVID-19) ﻿

The 2020 Bioinformatics Community Conference (BCC2020), which brings together the BOSC and Galaxy communities, will take place online–more info here. The online meeting will still be held July 18-21. Registration will open in a few weeks, and fees will be lower than for an in-person meeting. Abstract submission will open soon and will close April 30th. We will follow the usual submission and review processes.

BOSC 2020 will be online

We are currently accepting applications for the

 first application round for the OBF Travel Fellowship 2020

. This fellowship aims to promote the conference/event participation of attendees who advocate and present their work related to open-source bioinformatics software development and open science in the biological research community.

OBF Travel Fellowship 2020: Round 1 and BCC 2020

Google Summer of Code 2022 Project Ideas   Shortcut to project ideas: Configurable feature visualization to improve the user experience and performance of the feature viewer Space- and time-efficient data format for mass spectrometry data (OpenMS) Efficient data layout for mass spectrometry data (OpenMS) GPU support for Toil-CWL-Runner (UCSC/CWL Project) Improving automated wrapping of C++ code in Python (OpenMS/autowrap) Migration of Journal

Project Ideas

Two awardees were chosen during the latest round of the OBF Travel Fellowship program, which closed on December 1, 2019. The program, which started in 2018, provides some travel funding to selected applicants who, by attending events in open source / open science, will help to promote diversity in the community.

OBF Travel Fellowship awards for December 2019

Biopython 1.76 has been released and is available from our website and PyPI. Coming relatively soon after our last release, the timing is linked to the official end of life for Python 2, and a focus hereafter on Python 3. We intend this to be our final release supporting Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing.

Biopython 1.76 released

Among the core values shared across the OBF community are inclusiveness and welcoming newcomers to contribute, without discrimination.

Creating an OBF-wide Code of Conduct

This post is co-authored by Bérénice Batut, Malvika Sharan, Emmy Tsang, and Yo Yehudi.

In 2016, Mozilla launched a program to help grow the skills of people interested in working openly and empower a generation of open-inspired leaders. The program has been through several stages of evolution, from early Working Open Workshops, and eventually to regular twice-yearly cohorts, mentoring project leads from all around the globe.

Supercharge your open project with leadership training

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

Computational biology without borders

Dear Biopythoneers,  Biopython 1.75 has been released and is available from our website and PyPI. This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and is expected to work on the soon to be released Python 3.8. It has also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0. Note we intend to drop Python 2.7 support in early 2020.

Biopython 1.75 released

A record number of people applied for the latest round of the OBF Travel Fellowship, which closed on August 15, 2019. Out of this great set of applicants, we offered travel awards to three who epitomize the goal of the awards: to promote diversity in the world of open source bioinformatics / open science.

OBF Travel Fellowship: August 2019 awards

Thanks to OBF support with a travel grant, I was able to attend the first European CarpentryConnect event in Manchester CCMcr19 organized by The Software Sustainability Institute. Colourful Manchester days post Pride weekend

 The Carpentries is a global community with a mission to teach

essential data and foundational computational skills to researchers for conducting efficient, open, and reproducible research.

Dos and Don’ts for computational training

At the OBF’s July 2019 public Board meeting (held at BOSC 2019), Malvika Sharan was unanimously elected as a new at-large Board member. Malvika, who earned a PhD in bioinformatics at the University of Würzburg, is a community outreach coordinator at the European Molecular Biology Laboratory (EMBL), Heidelberg. She is passionate about promoting the inclusion of historically underrepresented groups in bioinformatics and STEM in general.

Malvika Sharan elected to OBF Board

Dear Biopythoneers,  Biopython 1.74 has been released and is available from our website and PyPI. This release of Biopython supports Python 2.7, 3.4, 3.5, 3.6 and 3.7. However, it will be the last release to support Python 3.4 which is now at end-of-life.

Biopython 1.74 released

As Europe experienced a record-breaking heat wave, BOSC 2019 attendees stayed cool in the Basel Congress Center (and many took breaks by floating down the Rhine). This was the 20th annual BOSC. In 2018, BOSC partnered with the Galaxy Community Conference in GCCBOSC2018;

Meeting report: BOSC 2019, the 20th Annual BOSC

We are pleased to announce the April 2019 OBF Travel Fellowship recipients. The OBF Travel Fellowship program, established in 2016, aims to increase diverse participation at events related to open source bioinformatics.

Travel Award Recipients For April 2019

BOSC 2019 Schedule (2020 schedule is coming soon!)  Schedule at a glance     Download the program without the abstracts [PDF, 15 pages]  Download the complete program including abstracts [PDF, 147 pages] Note to speakers   Please copy your slides to the podium computer during the break before your session. Also, we encourage presenters to upload their slides to the BOSC F1000 collection.

BOSC 2019 Schedule (for reference)

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

2002 Bioinformatics Open Source Conference

August 2, 2002   Edmonton, Alberta, Canada Call to order   Board members present: Hilmar, Chris, Ewan, Steven, Andrew Recognition of observers (about 21)   This meeting was open to the the public. I don’t know all of the people who commented, hence the question marks.

Minutes of 2002 BOSC Meeting

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

July 2002 O|B|F Newsletter

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.

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2002 Bioinformatics Open Source Conference

Minutes of 2002 BOSC Meeting

July 2002 O|B|F Newsletter

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

October 2001 O|B|F Newsletter

2001 Bioinformatics Open Source Converence