Google’s Summer of code and open source Biotech
It suddenly occurred to me that one of the best support sources for open source biotech would be the open source software movement. Google offers scholarships to students to take on summer coding projects with open source foundations. Is there any Bioinformatics in there? Just two that I can see.
GenMAPP (Gene Map Annotator and Pathway Profiler):
an academically based organization that develops and supports GenMAPP (Gene Map Annotator and Pathway Profiler), a visualization and analysis tool for biological data. GenMAPP illustrates the relationships between various genes and proteins to help researchers understand their data in terms of connected, biological pathways. Over 18,000 people from >70 countries have registered to download the GenMAPP program. There are over 360 publications that reference GenMAPP or use GenMAPP to display data in the context of biological pathways. GenMAPP is 100% open source. All new development is in Java, MySQL, Derby, XML, and Web technologies such as MediaWiki in collaboration with the UCSF library, BiGCaT Bioinformatics, and the Cytoscape Consortium. Our development team is composed of individuals who are both biologists and programmers, providing a unique perspective on building and using open source tools.
The NESCent (National Evolutionary Synthesis Centre):
NESCent facilitates synthetic research on grand challenge questions in evolutionary biology and also works to address critical needs in software infrastructure and education through promoting open, collaborative development of interoperable and standards-supporting open-source software. The Center is located in Durham, North Carolina, is jointly operated by Duke University, the University of North Carolina at Chapel Hill, and North Carolina State University, and receives its core funding from the National Science Foundation (NSF). Together with developers from open-source life-science programming toolkits (BioPerl, Biojava, Biopython, Bioruby, BioSQL; collectively referred to as the Bio* projects), evolutionary software packages, and recently developers of comparative phylogenetic methods NESCent has so far run two Hackathons, which continue to have significant and lasting impacts on the landscape of collaborative software development in our field. The Center is committed to FLOSS and sharing of scientific data (see for example the NESCent Data and Software Policy at http://www.nescent.org/informatics/data_software_policy.php); all software products of the Center are released as open source and established as collaborative projects on sites such as SourceForge. Members of the Center’s Informatics team are lead developers in several open-source projects, and one of our organization administrators has been active on the Board of the Open Bioinformatics Foundation (http://open-bio.org/), the umbrella organization for the Bio* projects, since seven years.
Well it’s a start. I need to look more into what these groups are doing.