Open Bioinformatics Foundation
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.
Open Bioinformatics Foundation 2017 Projects
Adding Python 3 compatibility and improving mypy support for cwltoolThe 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...
antiSMASH Migration to Template SystemantiSMASH, a python-based tool to mine micro-organisms genomes, currently uses pyQuery to generate static HTML pages. Consequently, several...
Bionode-Watermill - A Streaming Workflow Engine for BioinformaticsThis project started in last GSoC but is still missing core functionality
Common Workflow Language reference implementation modernization- Making cwltool and schema-salad, Microsoft Windows compatible and providing complete Python 3 support for cwltool and schema-saladCwltool is a reference implementation of the Common Workflow Language. It provides comprehensive validation of CWL files and include tools related to...
ETE/Tree matcherTreeMatcher is a subproject of ETE3. Target of TreeMatcher is to perform search on phylogenetic trees using tree patterns that allows relax...
GeneNetwork Genome BrowserModify GeneNetwork to embed the BioDalliance genome browser in it. BioDalliance (henceforth BD) would be integrated into GeneNetwork (henceforth GN);...
Implement algorithms for the generation of high-resolution isotope patternsIn mass spectrometry the isotope pattern of an unknown molecule consists a powerful analytical tool to identify its molecular formula. Modern...