Community

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’.

BCC2020 (the collaborative BOSC + GCC meeting) was held online, with over 800 people registered for some part of the meeting. We used Remo.co as the technology platform, along with Discord for chat. Read about why we chose those, how it worked out, and our tips for others who are organizing virtual conferences here.

“Table view” in Remo during BCC2020

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

Because Remo is not familiar to most BCC participants, we are holding two open houses, one in each hemisphere, the day before BCC training starts. These walk-throughs will introduce participants to Remo’s features and demonstrate how to navigate between sessions, poster/demos, BoFs, training and everything else.

We’re old hands at organizing in-person BOSC s (some of us were involved in planning the very first BOSC, in 2000), but this is the first time we’re attempting an online conference, and we want your help to make BCC2020 a rewarding experience for all.

We know many of you have attended other virtual conferences recently, and we’re interested in hearing what worked well and what didn’t. In particular, we are trying to figure out how to make virtual posters work, and how to run Q&A (with audio, or just typed? live, right after the talks, or asynchronous?). We’re also interested in ideas for adding fun social elements to what could otherwise be a pretty dull extended videoconference.

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 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.

Some of the recent round of the OBF Travel Fellowships will be supporting BCC2020 attendees with video conferencing costs (headsets, web-cameras, etc), full announcement coming soon.

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. Find more information here.

I had the opportunity to visit the Barcelona Supercomputing Center (B.S.C) in Spain from 2nd - 6th March 2020 to participate in the Galaxy Admin Training 2020, organized by Galaxy Europe and in partnership with B.S.C, Elixir, and de.NBI.

The Open Bioinformatics Foundation was shocked and saddened to learn that our colleague and collaborator James Taylor, a professor of biology and computer science at Johns Hopkins University, died on April 2, 2020. James was one of the creators and PIs of the Galaxy Project, which is among the most widely used platforms in open bioinformatics. The Galaxy community has created a tribute page for James.

We have close ties to James and the Galaxy project via our flagship conference. BOSC, which was first held in partnership with the Galaxy Community Conference (GCC) in 2018, will again be co-hosted with GCC at the online Bioinformatics Community Conference (BCC2020) this July.

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.

We are discussing how to arrange the schedule to allow for participation across the globe. We welcome your input on how to make our first Virtual Bioinformatics Community Conference a success.