GSoC/GCI Archive
Google Summer of Code 2011

Theoretical Biophysics @ Humboldt University

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The Theoretical Biophysics group pursues scientific research in the field of Systems Biology by the means of mathematical and computational models. We aim to develop new techniques, software, incorporate new and well established knowledge to get a better understanding of the fundamentals of life. In particular, we focus on biological processes in Yeast, Bacillus subtilis and mammalian cells.

At GSoC 2011 we are seeking skilled students for our projects aiming at an optimized layout for biological reaction networks and their in-browser visualization. See our ideas site for details.

Our code repository can be found here:


  • A JavaScript library for interactive reaction graphs Currently no library is available for client side visualization of reaction networks. As a result a JavaScript library for interactive reaction graphs is to be designed and developed. Besides presentation the framework should provide functionality for scrolling, dragging, zooming, modification and export to JPEG, PNG, SVG and PDF.
  • GSoC 2011 Application: A Graph Layout for Reaction Networks I am interested in “A Graph Layout for Reaction Networks”. My main motivation is that this project requires effective algorithms and data structures. Being well-versed in algorithm designing and interested in biology and organic chemistry, I am able to do good contribution to this OSS project. In my application, I will elaborate my motivation, my academic and working experience as well as personal information, my project proposal, and my time line.
  • Optimized Layout for Biological Reaction Networks I propose the setup of a server machine, placed at the Institute for Theoretical Biophysics at the Humboldt Universität zu Berlin, running Debian/GNU or Ubuntu Linux, and the development of the server software further described in the proposal, based upon the python web framework web2py, in order to create a web framework for the Visualization of Biological Reaction Networks.