New technologies have been developed for the combinatorial assembly of genetic constructs from libraries of modular parts and thus have enabled synthetic biologists to explore design tradeoffs by assembling many variants of a construct. New computational approaches are needed to specify and prune the large construct design spaces that are possible with combinatorial assembly. To meet this need, we have developed a formal framework called GOLDBAR (Grammars for cOmbina-toriaL Design and Bio-Revision Assembly) which enables abstract, symbolic specifications of design spaces using a language consisting of atomic building blocks and operators that resemble those found in regular expressions.
provably correct. It is designed as a modular component and can operate standalone, but it can also parse and generate existing community standards such as the Synthetic Biology Open Language (SBOL) so that it is easily integrated with the synthetic biology community.
Parses GOLDBAR and SBOL
Visualization of design space
DARPA 1000 Molecules