Knox is a web-enabled repository for storing, modifying, and tracking changes to genetic design spaces encoding thousands of genetic design variants as directed graphs. Graph edges are labeled with sets of IDs for genetic parts such as promoters, coding sequences, and terminators. Each path from a start node to a stop node represents a combinatorial set of designs formed by concatenating one part from each edge in the path.
Knox provides operators for intersecting and merging genetic design spaces to determine what designs they have in common and to infer new designs based on their common structural motifs. Knox also tracks the application of its design space operators and provides revision control operators to branch and check out different versions of genetic design spaces.
Key Features
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RESTful API with endpoints for genetic design and revision control operators
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Import/export of genetic designs using the Synthetic Biology Open Language (SBOL) standard
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Dockerized Java application for easy cross-platform deployment
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Compatible with tools for Neo4j graph database instances
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Demo D3 web application for visualizing and operating on genetic design spaces
Funding
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The development of Knox was supported by DARPA Living Foundries award HR0011-15-C-0084.
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