GSoC/GCI Archive
Google Summer of Code 2012


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biographer is an open-source project for in-browser visualization of biological networks. It aims at providing a standard library which can be used as plugin in the vast variety of bioinformatics tools and platforms which need network visualization. Focus lies on the SBGN standard compliant visualization of reaction networks including an optimized automated layout which emphasizes on network function.

biographer is based on JavaScript, python, C++, HTML5 and SVG. The different students projects proposed this year however do not require all of these. Please refer to our ideas page for more details.

biographer is developed at the Theoretical Biophysics group which 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. At GSoC 2012 we are seeking skilled students for our projects which like to contribute to open-source in a research environment.


  • A javascript library of system biology formats The aim of the project is to implement a javascript library which can input and output common system biology file formats, such as SBGN-ML, jSBGN, SBML and BioPAX. The library will have clean APIs, comprehensive documents and a reasonable coverage of unit testing to ensure code quality.
  • Boolean Network Simulation The goal of this project is to extend biographer to support the simulation and analysis of boolean networks. The project involves writing modules for importing models in booleannet format and also automatically generating models for a reaction graph. An interface needs to be then provided for simulating the boolean network step by step using Biographer's existing UI. Simple tools that calculate the steady state, trajectory length and cyclic attractors will also be written
  • Performance Improvements and Mobile Device Support for Visualisation Allowing support for tablets and other portable devices such as smartphones will require the JavaScript code to be optimised to improve performance on less powerful devices so that the use of the software is as pleasant and enjoyable as possible. The interface must also be adapted to fit comfortably on a smaller screen. Touch based input must also be supported.