Download BioCyc Databases and Pathway Tools Software

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

Access to the BioCyc.org website and to BioCyc data files requires a paid BioCyc subscription, obtained from Phoenix Bioinformatics (although access to the EcoCyc and MetaCyc data files is free). Access to the Pathway Tools software is free to academic users and is available for a fee to commercial users (obtained from SRI International).

Download BioCyc Data Files

[Access to BioCyc data files requires (1) a license (see bottom of page), and (2) a paid BioCyc subscription (exceptions: access to the EcoCyc and MetaCyc data files is free, and access to two year old versions of all BioCyc data files is free; in both cases a license is required).]

Note that the BioCyc web-based SmartTables facility can save you significant time in answering large-scale data analysis questions, and is significantly easier to use than is downloading and parsing BioCyc files. See the SmartTables menu.

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

[Access to BioCyc data via APIs requires a paid BioCyc subscription (although access to the EcoCyc and MetaCyc data are free).]

We provide several APIs for accessing BioCyc data:

• The BioCyc Web Services interface
• Python, Perl, Java, R, and Lisp APIs [details]. This option requires local installation of the Pathway Tools software bundled with various BioCyc DBs.

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

Download EcoCyc iPad and iPhone Applications

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

These apps provides a streamlined mobile interaction to BioCyc databases, and to databases in other Pathway Tools based web servers. Access these database in the laboratory, in the classroom, at a conference, in the library, or while on travel.

Download Pathway Tools Software/Database Bundle

[Access to Pathway Tools requires a license (see bottom of page) and is freely available to academic users and available for a fee to commercial users. Use of Pathway Tools with subscription-only BioCyc databases, whether via the registry or via pre-built bundles, requires a paid BioCyc subscription for all users. ]

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 (source code available upon request) 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	EcoCyc and MetaCyc free. Remainder of BioCyc: paid subscription for latest version; 2 year old version free.
Obtain License	click here	click here