We were very excited about participating in the Google Summer of Code this year for the first time. We, the Theoretical Biophysics Groups at the Humboldt University Berlin, pursue scientific research in the field of Systems Biology by the means of computational models. Our focus is on developing techniques and tools incorporating both new and well established knowledge in order to get a better understanding of the fundamentals of life. In particular, we focus on biological processes in Yeast, Bacillus subtilis, and mammalian cells. Our goal has been to develop a web tool that produces an optimized layout for biological reaction networks.
We were overwhelmed by a large number of extraordinary applications from all over the world and had a difficult time in choosing only three students to mentor for the summer, but we were very excited with our choices. Ben Ripkins created a javascript component which can visualize biological networks dynamically in the browser, Matthias Bock created a server component which retrieves biological networks from public databases, and Wei Jing dealt with the graph layout that determines where the network nodes should be located in the final visualization. We were really surprised how far our students were able to carry their projects given the complexity of the tasks. The results of the student’s work went into the biographer project. We have set up two showcases which demonstrate the interplay of the different student projects. At http://cheetah.biologie.hu-berlin.de/networkexplorer a large network compiled from the public databases Reactome and PID can be walked through and by simply clicking on the next node, the view will refocus thereby uncovering further parts of the network. At http://biographer.biologie.hu-berlin.de networks edited from scratch or loaded from several resources are visualized.
To sum it all up, this year's Google Summer of Code was a great success for all of us and we hope to be involved in future editions of the program.
By Thomas Handorf, Falko Krause, Marvin Schulz & Max Flottmann on behalf of the Theoretical Biophysics @ Humboldt University Organization
