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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.

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.

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.

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.

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.

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. While many African countries are emerging in those specific fields, Cameroon and Central African countries in general, are still lagging behind. Based on this observation, in 2019, we created Bioinformatics and Biostatistics Hub (B2Hub) at the Biotechnology Center of the University of Yaounde I. Our aim through this platform is to promote bioinformatics and biostatistics among graduate students and young researchers from Central Africa.

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.SeqIO.QualityIO module.

Online. By at least a factor of two.

Our recent article entitled Lessons learnt from organizing a virtual conference discusses some of our technology choices and how we leveraged them to put on a successful online meeting. That article touches briefly on some of the challenges we faced, but it doesn’t fully convey how much work it was–both in advance and during the event.

Before we go any further, who are you? This post was written by Nomi Harris, the long-time (co-)chair of BOSC, and the co-chair (along with Dave Clements) of BCC2020 (the Bioinformatics Community Conference, a collaboration between the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference (GCC)). The perspective expressed in this post is mine alone, and does not necessarily reflect the views of others on the BCC2020 organizing committee. Also, although BCC2020 was an equal partnership between BOSC and GCC and the planning was done jointly (except for abstract reviews), my perspective is naturally BOSC-centric.

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. Pengfei Fan, a researcher from Queen Mary University of London, was supported to participate in CLEO 2020 by this fellowship granted to him in the application round-1 of 2020. Find more information here.

During the last two decades, we are witnessing a fascinating growth of computational imaging (CI) methods, e.g. tomography, compressive sensing and 3D/super-resolved/lensless microscopy, and artificial intelligence (AI) algorithms, mainly machine learning and deep learning, both from the theoretical (mathematical) and practical (experimental) point of view. New computational capabilities in terms of, e.g., big data, large scale optimisation, neural networks and highly parallel computing, are facilitating further improvements in numerically enhanced imaging surpassing the limitations imposed by ‘classical’ all-optical information processing systems. It is joyful to observe how CI and AI merge to innovatively address challenging tasks fuelled by wide-spreading applications in 3D imaging, biomedicine, microscopy and general physics of light propagation in scattering media, to name just a few. When designing a computational imaging technique, one needs to originally link the applicable data acquisition scheme with the capable image reconstruction algorithm, often aided by learning-based frameworks employed not only for image classification and interpretation but also for image formation and final outcome restoration. As the AI stimulatory development continues to flourish, open-source tools and software, especially deep learning framework and platform, have become a key ingredient of modern science. Hundreds of software packages, libraries, and applications have become essential tools.

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’.