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Team:Freiburg software
From 2009.igem.org
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.
As we do not want to reinvent the wheel we plan to build our first version on BioJava and the Google-Wave format, which is currently in beta testing. 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 within the next months 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.
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 people can add and share robots useful for synthetic biology.
