Obf

The OBF is committed to providing a harassment-free and respectful environment for all members of our community. To ensure that we are clearly describing norms, rules, and recommended practices for all our participants and members, we have provided a first draft of the OBF Code of Conduct and shared it recently in our newsletter.

You can find the draft together with our request for comments on this pull request (see a preview here). If you have not already, please take a few minutes to add your comments in this pull request by June 4th, 2021.

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.

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

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. We launched a new community-designed OBF logo (special thanks to Aleix Lafita-Masip and all the others who contributed!), I mentored the fabulous Deepashree Deshmukh, an Outreachy intern, to migrate the OBF website from its old mediawiki-based format onto a shiny new Wordpress site, I joined the OBF GSoC org admin team alongside Sarthak Sehgal, and we launched an OBF newsletter. We’re still working on preparing an OBF Code of Conduct, which hopefully will be launched soon.

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:

1. 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
2. Himanshi Mathur (mentors: Jun Aruga, Evan Nemerson, Michael R. Crusoe) - Implementation of SVML in SIMDe ( final report, other blogs, SIMD Everywhere)
3. Boshen Yan (mentors: Amal Thomas, Marius Beek, Saket) - Implementing user-friendly search features in PysraDB ( final report, weekly writeup, work summary)
4. Shekhar Shukla (mentors: Oliver Alka, Hannes Röst, Timo Sachsenberg) - OpenMS R Package ( final report, blogs, OpenMS)
5. Francesco Porto (mentors: George Githinji, Erik Garrison, Pjotr Prins) - Parallel Graph Traversal for Variation Graphs
6. Eliza Martin (mentors: Dymitr Nowicki, Vlada Tyshchenko, Anton Kulaga) - Protein sequence and structural analysis CWL pipeline for comparative biology
7. Hidayat Ullah Khan (mentors: Jun Aruga, Evan Nemerson, Michael R. Crusoe) - SIMDe: Add implementations of ISA extensions (SSE4.2 and AVX512) and NEON implementations of SSE4.1,SSE4.2,SSE3,SSSE3 ISA extension ( final report, mentee blogposts, SIMD Everywhere)
8. T. Waschischeck (mentors: Chris Bielow, Julianus Pfeuffer) - Using DeNovo Sequencing to Predict Protein Database Suitability ( final report, student blog, OpenMS)

This year, OBF received 5000 USD from Google for being a mentoring organisation. The funds from GSoC go into the general OBF Fund that is primarily used to sponsor OBF Event Fellowships which is a program aimed at increasing diverse participation at events promoting open science practices such as resource development and dissemination in the bioinformatics and biological research community.

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.

Renaming from “OBF Travel Fellowship” to “OBF Event Fellowship”

One of the goals of the OBF fellowship is to increase the participation of members from traditionally underrepresented groups at events or communities that promote Open Source software development and/or open science practices in the biological sciences. Since so many scientific meetings have been or are now run online, and we wish to explicitly support remote participation for this year, we are renaming ‘OBF Travel Fellowship’ to ‘OBF Event Fellowship’.

on behalf of the OBF Board members

We are delighted to announce that four awardees have been selected to receive the OBF travel fellowship for 2020 round 1, to support their participation in virtual events.

The OBF travel fellowship is now offered 2 times a year to multiple awardees towards supporting their participation in scientific workshops, conference and training events. The selection of individuals is made based on their applications, which state how their participation in the chosen event helps them promote open science practices in bioinformatics and/or enhance representation of minority groups in their communities.

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

During the public OBF Board Meeting held on December 17, 2019, elections were held for five Board members whose terms were about to expire. All five stood for re-election to the Board, though with some changes of officers:

• Hilmar Lapp: stepped down after 8 years as President of the Board; elected to At-Large seat.
• Peter Cock: elected as President of the Board.
• Heather Wiencko: elected as Treasurer, replacing previous Treasurer Peter Cock.
• Chris Fields: re-elected as Secretary.
• Nomi Harris: re-elected as At-Large Board member.

In accordance with the OBF Bylaws, the newly elected Board members and officers will serve a three-year term.

Among the core values shared across the OBF community are inclusiveness and welcoming newcomers to contribute, without discrimination. Every year at BOSC, when we ask who is at BOSC for the first time, about half of the audience’s hands go up. To signify the importance of this, both to existing and prospective community members, BOSC successfully advocated several years ago for ISMB to adopt a Code of Conduct by ISMB (which applies to BOSC when it is held as part of ISMB).