GSOC 2009

For the third year in a row, I will participate in the Google Summer of Code with the GenMAPP organization. The first time I was a student, after that two times a mentor. In the coming weeks I’ll write some things about all the different student project that are going on this year.

About the GenMAPP organization itself: GenMAPP acts as an umbrella organization for GenMAPP, Cytoscape, PathVisio and WikiPathways, all four are bioinformatics tools that help with analysis of large biological datasets. Although these four tools have diverse origins they all work in the same problem space. It is really good to do this together for two reasons: first, we can pool our mentoring resources and second, this will encourage cooperation and integration between the tools, to create cohesion between all the parts. Integration is the most important problem in bioinformatics nowadays, and to solve that it’s important that we work together.

Integration is also what Adem’s project is all about this year. Adem Bilican is a french student who is planning to write a BioPAX plugin for PathVisio. BioPAX stands for “Biological Pathway Exchange”, and is aimed as a standard for exchanging pathway data between databases. Since PathVisio is about creating and visualizing pathways, it’s natural that we support this format. A BioPAX plugin would enable PathVisio to communicate directly with large pathway databases such as Reactome.

This is not going to be easy. PathVisio has been designed primarily with the visual aspects of pathways in mind, whereas BioPAX is all about biological semantics. So a successfull BioPAX plugin would have to cross the bridge between layout and content.

Adem will be keeping a blog about his progress here: Adem’s blog

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