Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract BioCyc Database Collection is a collection of over 1,000 Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and 'metabolic pathways' of a single organism, with the exception of the MetaCyc database, which is a reference source on 'metabolic pathways' from hundreds of organisms.

The BioCyc collection of Pathway/Genome Databases (DBs) provides electronic reference sources on the pathways and genomes of different organisms. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received.

Tier 1 DBs -- have been created through intensive manual efforts and receive continuous updating. The BioCyc Tier 1 DBs are:

a) EcoCyc (see G6G Abstract Number 20231), which describes Escherichia coli K-12.

b) MetaCyc (see G6G Abstract Number 20232), which describes enzymes and metabolic pathways for more than 1,500 organisms. MetaCyc does Not seek to model the complete metabolic network of any one organism, but to provide a comprehensive collection of experimentally elucidated 'metabolic pathways'.

c) The BioCyc Open Chemical Database (BOCD) (see G6G Abstract Number 20233), an open collection of chemical compound data from the BioCyc databases. BOCD includes metabolites, enzyme activators, inhibitors, and cofactors.

Tier 2 DBs -- were computationally generated by the PathoLogic Pathway-Prediction program (see G6G Abstract Number 20235), and have undergone moderate amounts of review and updating.

There are over 30 DBs in Tier 2. HumanCyc (see G6G Abstract Number 20234) is an example of a Tier 2 Pathway/Genome Database (PGDB).

Tier 3 DBs -- were computationally generated by the PathoLogic pathway-prediction program and have undergone No review and updating. There are over 965 DBs in Tier 3.

Note: The manufacturer encourages scientists to adopt the Tier 2 and Tier 3 DBs for ongoing curation and updating.

Scientists can use the BioCyc Web site to visualize individual metabolic pathways or to view the complete metabolic map of an organism.

The latter diagram can be used to analyze gene expression, proteomics, or metabolomics data using the 'Pathway Tools Omics Viewer' (see G6G Abstract Number 20237), such as, to produce animated views of time-course gene-expression experiments.

The BioCyc Web site also provides genome browsing capabilities, and for the EcoCyc DB in particular, provides extensive information about transcriptional mechanisms of gene regulation.

The navigation capabilities of the software allow a user to move from a display of an enzyme to a display of a reaction that the enzyme catalyzes, or to the gene that encodes the enzyme.

The interface supports a variety of queries, such as generating a display of the map positions of all genes that code for enzymes within a given biochemical pathway.

As well as being used as a reference source to look up individual facts, BioCyc databases support computational studies of the metabolism, such as design of novel biochemical pathways for biotechnology, studies of the evolution of metabolic pathways, and simulation of metabolic pathways.

BioCyc DBs are linked to other biological databases containing protein and nucleic-acid sequence data, bibliographic data, protein structures, and descriptions of different strains.

System Requirements

Pathway Tools is now available for Linux x86_64 machines. Please note that these executables will only run on a Linux x86_64 machine. Please pay attention to the sizes of the Linux x86_64 executables that are listed in the table below. We recommend that the machine on which you run these images have an amount of RAM of at least the executable size. The 64-bit Linux version with all three tiers requires more than 4GB of RAM memory and has a long startup time. We only recommend downloading this version if you are planning to do large-scale comparative analyses.

Also please note that none of the built-in PGDBs of any tier are editable. If editable PGDBs are needed, a distribution containing few tiers should be chosen, and the PGDBs to be edited should be downloaded from the Registry.

Operating System

Most of the testing of Pathway Tools on the following operating systems has been done for 32-bit versions.

Linux on any AMD or Intel-based x86 system that uses a version 2.2 or higher kernel, OpenMotif (not LessTif), and glibc 2.1+ Known to work on:

It works on Ubuntu-6.06.

Known Problems:

On Suse-8.2 on a x86_64 system, one user reported that restarting the WWW server mode of Pathway Tools by means of automated scripts never got to work. The problem does not seem to occur on Suse-8.1.

Microsoft Windows NT, 2000, XP, or later versions

Solaris 8 (not tested on Solaris 9)


Processor: Minimum requirement = 1GHz

Memory (RAM) recommended


Manufacturer Web Site BioCyc

Price Free for academic institutions. Fee required for commercial use. Licence required.

G6G Abstract Number 20230

G6G Manufacturer Number 102506