Enumerate genetic designs through graphs that are mathematically rigorous

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.


Constellation is a JavaScript implementation of this formal framework for combinatorial design to satisfy questions such as “can a construct design or class of designs be assembled from a given part library?”. It can parse a rich set of operators as defined by GOLDBAR and enumerate genetic designs that satisfy user defined specifications through graphs that are mathematically rigorous and
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.

Key Features

  • Parses GOLDBAR and SBOL

  • Design enumeration

  • Visualization of design space

Funding

  • DARPA 1000 Molecules

Constellation is free to use. See the GitHub and CAD website located below:

Screen Shots

© Copyright 2020 CIDAR Lab – All Rights Reserved

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