Download BioCyc Databases and Pathway Tools Software

We provide two types of downloadable materials for the BioCyc databases and Pathway Tools software.

Download BioCyc Data Files

We provide the BioCyc databases (such as EcoCyc and MetaCyc) as collections of data files in several alternative formats including the following.

• BioPAX format
• Pathway Tools attribute-value format
• Pathway Tools tabular format
• SBML format
• Gene Ontology annotations (EcoCyc only): [Download from GO Web site]

Click here for an exact listing of files provided and their formats.

Programmatic Access to BioCyc Data

We provide several APIs for accessing BioCyc data:

• The BioCyc Web Services interface
• SQL queries to the PublicHouse MySQL server
• Perl, Java, and Lisp APIs [details]

See also the advanced query interface via the Web menu command Search  →  Advanced.

Download EcoCyc iPad and iPhone Applications

iPad and iPhone applications for EcoCyc are available from the iTunes store.

These apps provides a streamlined mobile interaction for EcoCyc. Use EcoCyc-Mobile in the laboratory, in the classroom, at a conference, in the library, or while on travel.

Download Pathway Tools Software/Database Bundle

The software/database bundle is a program you install on your computer (Mac, PC, Linux) that combines the Pathway Tools software with sets of BioCyc databases. Program functionality includes:

• Create new BioCyc-like DBs for sequenced organisms, predicting their metabolic pathways
• Create steady-state metabolic flux models from those DBs
• Query and visualize BioCyc DBs
  • Runs in two modes: as a desktop application, and as a Web server. The desktop mode runs faster and has more functionality. Web mode allows you to run a Web server similar to BioCyc.org. [comparison of desktop mode and web mode]
• Analyze omics data (such as gene expression or metabolomics data) by painting data onto a full pathway map for an organism, onto the full genome, and onto a regulatory network diagram. Thus, a single omics dataset can be visualized from multiple perspectives.

A number of publications are available about Pathway Tools.

The software/database bundle can be downloaded with several alternative collections of Pathway/Genome Databases (PGDBs) including:

• Multiple E. coli and Shigella PGDBs
• Multiple Mycobacterium PGDBs
• Multiple Bacillus PGDBs
• The human, mouse, and cattle PGDBs
• All BioCyc PGDBs

If you want to use Pathway Tools with other PGDBs than the pre-built bundles listed above, you should download the bundle that is closest to your needs, and then download additional PGDBs from the PGDB registry using the Tools menu command Browse PGDB Registry.

How to Obtain Downloads

The software and databases are available through different license agreements; please choose the license that is best suited to your needs:

	Complete License	Data File License
Materials Provided	1. Software/Database Bundle 2. Data Files	Data files only
Licensing Speed	Online license reviewed by SRI, usually within one business day	Quick online licensing
License Terms	Free to academics for research purposes; fee for commercial use	Free to all
Obtain License	click here	click here