Team Freiburg Software

Synthetic Biology aims at constructing whole new genomes. Such an effort is pushed forward by many users and relies on modular combination of genetic elements. The genetic elements represent an increasing complexity by assembling parts to devices and then systems. The construction process needs to be transparent and even at final stages control at the basepair level is required. We propose to build a user environment able to analyze and construct genetic parts and ultimately genomes.

We will build the software suite on the Google-Wave format, which is currently in beta testing, and add molecular biology tools mainly from the BioJava library. The first goal is to provide basic molecular biology cloning functionality which appeals to the wet bench scientist. On top of that, we would like to add specific synthetic biology functionality such as biobrick database access and part annotation. The software for the Jamboree will not be feature complete, but demonstrate the principle use, with some molecular biology standard tasks, as well as the power of the wave approach for a distributed collaborative synthetic biology effort. Many wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico.

The first developments of 'SynBioWave' will lay the ground for a useful grouping of functionality for wave-robots, how the calling of robots and their functions is managed, how robots act on DNA or protein sequences, how intermediate results are stored, etc... The process should be open and clear so that users can add and share robots useful for synthetic biology.