BioCyc Support for Synthetic Biology

BioCyc supports the data and analytical needs of the synthetic biology community in multiple respects.

Chassis Genome Databases: BioCyc provides high-quality curated databases for the major synthetic biology chassis organisms. Each database combines the sequenced genome of an organism with its metabolic pathways, reactions, enzymes, and metabolites, and with additional organism-specific data such as protein features, genetic regulatory networks, and essential genes.

• EcoCyc -- Escherichia coli K-12 MG1655 – curated from 44,000 publications
• BsubCyc -– Bacillus subtilis 168
• Pseudomonas putida KT2440
• Cupriavidus necator H16
• Synechococcus elongatus PCC 7942
• YeastCyc -– Saccharomyces cerevisiae S288c
• Yarrowia lipolytica CLIB122 and CLIB89(W29)

Benefits for SynBio Researchers: Better Science, Faster. Bad decisions can send your team on a wild goose chase for weeks.

• We make significant improvements to several hundred annotations for most organisms we curate, giving an accurate foundation for decision making
• BioCyc performs a vast data integration to put diverse data at your fingertips
• Curators author mini-reviews that distill the literature on genes and pathways -- a huge time saver

MetaCyc Universal Pathway Database: MetaCyc contains 3,200 metabolic pathways from all domains of life, as well as 19,600 metabolic reactions and 14,000 enzymes. Curated from 78,000 publications, MetaCyc is a comprehensive metabolic parts catalog, listing metabolic enzymes that can be engineered into other organisms. MetaCyc enzyme data includes subunit composition, cofactors, activators, inhibitors, and kinetic parameters.

Software Tools for Pathway Design and More: BioCyc provides more than 40 software tools, ranging from a genome browser to a metabolic network browser to unique tools for comparative analysis and omics data analysis. The BioCyc RouteSearch tool designs novel metabolic pathways – given a starting metabolite and an ending metabolite, RouteSearch finds a minimal-cost path from the starting to the ending metabolite.

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