Open Bioinformatics Foundation

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

Posted on February 19, 2021 | malvikasharan

The call for applications for the OBF Event Fellowship 2021, round 1 is now open. The deadline for this round is 1 April 2021. Applications should be submitted via this Google Form. We invite applications from candidates who are seeking financial support to attend or host virtual events in 2021. The selected awardees can use the OBF Event Fellowship to cover conference registration fees and potentially additional expenses associated with attending or hosting the event, such as small hardware (microphone, speaker, webcam), childcare for the duration of the event and high-speed internet. [Read More]

Seeking community volunteers: nomination open for OBF board election 2021

Posted on February 15, 2021 | malvikasharan

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 [Read More]

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

Posted on February 13, 2021 | yo

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. The OBF typically works as an umbrella organisation for other sub-projects - if you have an open + bio related code project that you think could use a student intern this year, please read on. TL;DR: Please send ideas for half-sized projects (1. [Read More]

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

Posted on February 12, 2021 | yo

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. Over the last (nearly) three years, I’ve learned a lot and have participated in many OBF activities I can be proud of. [Read More]

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

Posted on February 12, 2021 | nlharris

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. [Read More]

Domain names available for adoption

Posted on January 28, 2021 | peterc

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. Please note that this is like adopting a free puppy - we’ll transfer them at no cost, but domain names come with annual renewal charges which the recipient organisation would be responsible for paying. [Read More]

MetaDocencia: Teaching to Teach (Bioinformatics and more) Online in Spanish

Posted on January 13, 2021 | lacion

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. Dr. Laura Ación , a researcher at the Instituto de Cálculo, University of Buenos Aires, Argentina . She is also one of the co-founders of MetaDocencia , which she could partly support with the OBF Event fellowship granted to her in the December 2019 application round. [Read More]

Google Summer of Code 2020 Wrap Up

Posted on November 4, 2020 | sarthaksehgal

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. We hosted eight students all of which successfully completed their work: Srijan Verma (mentors: Dmitry Petrov, Dymitr Nowicki, Vlada Tyshchenko, Anton Kulaga) - Healthcare-Researcher-Connector (HRC): A Federated Learning package for bridging the gap between Healthcare providers and researchers Himanshi Mathur (mentors: Jun Aruga, Evan Nemerson, Michael R. [Read More]

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

Posted on September 24, 2020 | armando_djiyou

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. Armando Blondel DJIYOU DJEUDA, a researcher from University of Douala, Cameroon, set up and host H3ABioNet‘s Introduction to Bioinformatics course (IBT), supported by this fellowship granted to him in application round 1 of 2020. Due to the rich biodiversity of sub-Saharan African countries, bioinformatics and data management are crucial in helping to advance biomedical research. [Read More]

Biopython 1.78 released

Posted on September 4, 2020 | chebizarro

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. See https://biopython.org/wiki/Alphabet for more information. Bio.SeqIO.parse() is faster with “fastq” format due to small improvements in the Bio. [Read More]