Open Bioinformatics Foundation

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

Technologies
python, c/c++, java, perl, c++
Topics
bioinformatics
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.

2017 Program

Successful Projects

Contributor
Manvendra Singh
Mentor
Anton Khodak, Michael Crusoe, Janneke van der Zwaan
Organization
Open Bioinformatics Foundation
Adding Python 3 compatibility and improving mypy support for cwltool
The goal of this proposal is to enhance support and usability of cwltool by: Adding Python 3 compatibility to CWL Tool, Schema Salad and CWL Test...
Contributor
Nikos Patikas
Mentor
oliveralka, Artem Tarasov, timosachsenberg, Julianus Pfeuffer
Organization
Open Bioinformatics Foundation
Implement algorithms for the generation of high-resolution isotope patterns
In mass spectrometry the isotope pattern of an unknown molecule consists a powerful analytical tool to identify its molecular formula. Modern...
Contributor
Mariana Nave
Mentor
Marc Chevrette, Dr. Kai Blin
Organization
Open Bioinformatics Foundation
antiSMASH Migration to Template System
antiSMASH, a python-based tool to mine micro-organisms genomes, currently uses pyQuery to generate static HTML pages. Consequently, several...
Contributor
Dimitris Pliakos
Mentor
Jaime Huerta Cepas, Renato Alves, François Serra, Łukasz Roguski
Organization
Open Bioinformatics Foundation
ETE/Tree matcher
TreeMatcher is a subproject of ETE3. Target of TreeMatcher is to perform search on phylogenetic trees using tree patterns that allows relax...
Contributor
Christian Fischer
Mentor
Pjotr Prins-1
Organization
Open Bioinformatics Foundation
GeneNetwork Genome Browser
Modify GeneNetwork to embed the BioDalliance genome browser in it. BioDalliance (henceforth BD) would be integrated into GeneNetwork (henceforth GN);...
Contributor
Kapil kumar
Mentor
Anton Khodak, Michael Crusoe, Janneke van der Zwaan
Organization
Open Bioinformatics Foundation
Common Workflow Language reference implementation modernization- Making cwltool and schema-salad, Microsoft Windows compatible and providing complete Python 3 support for cwltool and schema-salad
Cwltool is a reference implementation of the Common Workflow Language. It provides comprehensive validation of CWL files and include tools related to...
Contributor
Tiago Jesus
Mentor
Bruno Vieira, Julian Mazzitelli
Organization
Open Bioinformatics Foundation
Bionode-Watermill - A Streaming Workflow Engine for Bioinformatics
This project started in last GSoC but is still missing core functionality