Open Bioinformatics Foundation (OBF)

Promoting practice & philosophy of OSS & Open Science in biological research.

Technologies
python, javascript, c/c++
Topics
bioinformatics, computational biology
Promoting practice & philosophy of OSS & Open Science in biological research.

The Open Bioinformatics Foundation (OBF) is a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.

Our main activities are:

  • Running and supporting the BOSC conferences.
  • Organizing and supporting developer-centric "Hackathon" events.
  • Participating in the Google Summer of Code program on behalf of our member projects as an umbrella mentoring organization.
  • Managing servers, colocation facilities, bank account, domain names, and other assets for the benefit of our member projects.
  • Public opinion and policy statements about matters related to Open Source and Open Science in bioinformatics.

The Foundation does not participate directly in the development or structure of the open source work, but as the members of the foundation are drawn from our projects' developer communities, there is clear commonality of direction and purpose.

The OBF is governed by a Board of Directors. Our bylaws lay out how the Board is elected, holds public meetings, and conducts its business, as well as the scope and role of our membership. OBF is an associated project with Software In The Public Interest, Inc., a fiscal sponsorship organization, and through SPI we can accept tax-exempt charitable donations.

The OBF is open to anyone who is interested in promoting open source bioinformatics / open science. Please see the Membership page for more information.

2020 Program

Successful Projects

Contributor
Himanshi Mathur
Mentor
Jun Aruga, Evan Nemerson, Michael R Crusoe
Organization
Open Bioinformatics Foundation (OBF)
Implementation of SVML in SIMDe
This project will be aimed to create an API-compatible open-source implementation of Intel's proprietary SVML which would be portable to other...
Contributor
Shekhar Shukla
Mentor
oliveralka, Hannes Rost, Timo Sachsenberg
Organization
Open Bioinformatics Foundation (OBF)
OpenMS R-Package
OpenMS, an open-source C++ library for the analysis of mass spectrometric data exposes a large part of its functionality to the Python community via...
Contributor
Francesco Porto
Mentor
George Githinji, Erik Garrison, Pjotr Prins
Organization
Open Bioinformatics Foundation (OBF)
Parallel Graph Traversal for Variation Graphs
Traditionally, Bioinformatics has focused its efforts on the study of single genomes, each representing an individual of a certain species. In more...
Contributor
Boshen Yan
Mentor
Amal Thomas, Marius van den Beek, Saket
Organization
Open Bioinformatics Foundation (OBF)
Implementing user-friendly search features
Pysradb provides a convenient method to retrieve information from NCBI’s SRA database. Currently, pysradb is transitioning to phase out its...
Contributor
Srijan Verma
Mentor
Dmitry Petrov, Dymitr Nowicki, Vlada Tyshchenko, Anton Kulaga
Organization
Open Bioinformatics Foundation (OBF)
Healthcare-Researcher-Connector (HRC): A Federated Learning package for bridging the gap between Healthcare providers and researchers
Nowadays, sharing and use of human biomedical data is heavily restricted and regulated by multiple laws. Such data-sharing restrictions allow keeping...
Contributor
Hidayat Ullah Khan
Mentor
Jun Aruga, Evan Nemerson, Michael R Crusoe
Organization
Open Bioinformatics Foundation (OBF)
SIMDe : Add implementations of ISA extensions (SSE4.2 and AVX512) and NEON implementations of SSE4.1,SSE4.2,SSE3,SSSE3 ISA extension
The project deals with writing portable implementations for SIMD ISA extensions SSE4.2 and AVX-512 functions and NEON implementations for...
Contributor
Eliza Martin
Mentor
Dymitr Nowicki, Vlada Tyshchenko, Anton Kulaga
Organization
Open Bioinformatics Foundation (OBF)
Protein sequence and structural analysis CWL pipeline for comparative biology
While there are a multitude of open source ML methods for prediction of various structural or biological related attributes, there are no open source...
Contributor
T. Waschischeck
Mentor
Chris Bielow, Julianus Pfeuffer
Organization
Open Bioinformatics Foundation (OBF)
Using DeNovo Sequencing to Predict Protein Database Suitability
When using mass spectrometry to analyze protein samples it is key to use the appropriate protein database. Most of the time a sample from only one...