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Comparison of BioCyc to Pathway Tools -- Which to License?

Comparison of BioCyc to Pathway Tools -- Which to License?

BioCyc Subscription

A BioCyc subscription provides unlimited access to the BioCyc.org website. To obtain a BioCyc subscription please contact Phoenix Bioinformatics.

The BioCyc.org website provides:

  • 19,000 Pathway/Genome Databases (PGDBs) for sequenced organisms; 60 of those databases have been curated from 130,000 publications. Their data content includes:
    • Genomes, operons, regulatory networks
    • Metabolic pathways
    • Gene essentiality
    • Protein features, protein complexes
    • Extensive mini-reviews and literature citations

  • An extensive set of bioinformatics tools that address the following user tasks:
    • Information seeking
    • Comparative genomics
    • Transcriptomics data analysis
    • Metabolomics data analysis
    • Metabolic engineering / synthetic biology

Pathway Tools License

A Pathway Tools license enables licensees to download and install the Pathway Tools software on a local computer. To obtain a Pathway Tools subcription please contact

Pathway Tools runs as a desktop application (Mac, Windows, Linux) and as a web server (Mac, Linux). Once installed, in its web server mode the software enables licensees to create an internal mirror of the BioCyc website containing all BioCyc databases or of a subset of BioCyc databases. (The BioCyc website is powered by Pathway Tools.)

Pathway Tools provides features that go beyond what BioCyc.org provides including:

  • Provides an enterprise genome data management system that combines public genomes with private genomes
  • Private genomes can be processed by Pathway Tools to create new PGDBs including inferred metabolic networks and operons. All Pathway Tools operations can be applied to locally created PGDBs, such as comparative operations and omics-data analysis tools.
  • Development of quantitative metabolic models from PGDBs
  • Interactive updating of PGDBs