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 for all users, obtained from Phoenix Bioinformatics. Access to BioCyc also requires that you create a free account after a certain number of page views, even if you are a subscriber.

Access to the Pathway Tools software by academic users requires a free license (see table at bottom of this page). For access by commercial users, a fee is required (see table at bottom of this page).

A comparison of BioCyc.org versus Pathawy Tools is provided here.

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).]

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 at BioCyc.org.

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. Note that these files are not in a format suitable for importing into the Pathway Tools software.

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 obtained via the registry or via pre-built bundles, requires a paid BioCyc institutional 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 various pre-built sets of BioCyc databases. To use Pathway Tools with other PGDBs than the pre-built bundles we provide, you should download the bundle that is closest to your needs, and then download additional PGDBs from the PGDB registry using the command Browse PGDB Registry from the Tools menu. Pathway Tools functionality includes:

• Create new BioCyc-like DBs for sequenced organisms, predicting their metabolic reactions and pathways
• Create steady-state metabolic flux models from those DBs
• Query and visualize BioCyc DBs
  • Runs in two modes: as a desktop application (Mac, Windows, and Linux), and as a Web server (Mac and Linux). The desktop mode runs faster and has more functionality. Web mode allows you to run a Web server similar to BioCyc.org.
• Analyze omics data (such as gene expression or metabolomics data) via enrichment analysis and by painting data onto a full pathway map for an organism, onto the full genome, and onto the Omics Dashboard.

Programmatic Access to BioCyc Data

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

We provide several APIs for accessing BioCyc data:

• The BioCyc Web Services interface.
• Python, Perl, Java, R, and Lisp APIs [details]. These options require local installation of the Pathway Tools software bundled with various BioCyc DBs.
• The BioVelo query language.
• The advanced query interface via the Web menu command Search  →  Advanced.

How to Obtain Downloads

A paid subscription is required to access the BioCyc.org website and data files.

Pathway Tools and BioCyc databases are available through different license agreements; please choose the license below that is best suited to your needs.

	Software & Data-File License	Data-File License	BioCyc Subscription
Materials Provided	1. Pathway Tools Software/Database Bundle (source code available by request) 2. BioCyc data files	BioCyc data files only	Access BioCyc.org and BioCyc data files
Licensing Speed	Online license reviewed by SRI,usually within one business day	Quick online licensing	Purchase required
License Terms	1. Software is free to academics for research purposes; fee for commercial use 2. BioCyc data files: EcoCyc and MetaCyc free; paid subscription for remainder of BioCyc	EcoCyc and MetaCyc free. Remainder of BioCyc: paid subscription for latest version; 2 year old version free.	Paid subscription
Obtain License	click here	click here	click here