BioCyc Database Collection
Encyclopedia
The BioCyc database collection is a set of biological databases. Databases within BioCyc describe genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

 and pathway
Biological pathway
A biological pathway is a number of biochemical steps, linked together, with a start and an end. The activity within a pathway should is a flow of molecules. Some typical types of biochemical pathways are metabolic pathways and signaling pathways. The Reactome is a curated information source, with...

 information for individual organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...

s. BioCyc is maintained by SRI International
SRI International
SRI International , founded as Stanford Research Institute, is one of the world's largest contract research institutes. Based in Menlo Park, California, the trustees of Stanford University established it in 1946 as a center of innovation to support economic development in the region. It was later...

, in Menlo Park, California
Menlo Park, California
Menlo Park, California is a city at the eastern edge of San Mateo County, in the San Francisco Bay Area of California, in the United States. It is bordered by San Francisco Bay on the north and east; East Palo Alto, Palo Alto, and Stanford to the south; Atherton, North Fair Oaks, and Redwood City...

.

Two databases within BioCyc are highly curated, meaning they have received extensive manual updating with information from the scientific literature. Those databases are EcoCyc
EcoCyc
EcoCyc is a bioinformatics database for the bacterium Escherichia coli K-12. The EcoCyc project performs literature-based curation of the E. coli genome, and of E. coli transcriptional regulation, transporters, and metabolic pathways....

 and MetaCyc
MetaCyc
The MetaCyc database contains extensive information on metabolic pathways and enzymes from many organisms. MetaCyc stores experimentally determined metabolic pathways....

. The remaining BioCyc databases were generated computationally to predict what metabolic pathway
Metabolic pathway
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...

s are present in these organisms. In some cases, the databases were refined manually after their generation. As of October 2010, BioCyc contained databases for 1,004 genomes.

The BioCyc website contains a variety of software tools for searching, visualizing, comparing, and analyzing genome and pathway information. It includes a genome browser, and browsers for metabolic and regulatory networks
Gene regulatory network
A gene regulatory network or genetic regulatory network is a collection of DNA segments in a cell whichinteract with each other indirectly and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA.In general, each mRNA molecule goes...

. The website also includes tools for painting large-scale ("omics") datasets onto metabolic and regulatory networks, and onto the genome.

BioCyc databases rely on a software system called Pathway Tools for their initial generation, subsequent updating, and for querying their content. The databases can also be installed locally.

All BioCyc databases share the same database schema, which facilitates comparisons across the databases.
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