BioCyc Microbial Genomes and Metabolic Pathways Web Portal

BioCyc Database Collection Logo




The BioCyc Microbial Genomes and Metabolic Pathways Web Portal is coming to the University of Cincinnati.

Beginning August 31st, researchers can access the full suite of databases in the BioCyc Database Collection. The BioCyc web portal from SRI International contains genome and metabolic-pathway information for over 10,000 microbes. BioCyc encyclopedias are unique in integrating a diverse range of data and providing a high level of curation for important microbes. BioCyc Pathway/Genome Databases (PGDB) describe the genome of an organism, as well as its biochemical pathways and (for a small fraction of organisms) its regulatory network. BioCyc bioinformatics tools combine unparalleled breadth and user friendliness and include a unique set of visualization tools to speed comprehension of its extensive and complex data.

BioCyc databases integrate extensive data for each organism, and provide platforms for analysis of large-scale datasets. BioCyc enables scientists to pursue several use cases:

  • BioCyc is a massive encyclopedic reference on microbial genes, metabolites, and pathways that integrates information from many sources. Scientists consult BioCyc to save large amounts of time finding, understanding, and synthesizing material from the primary literature.
  • BioCyc is a genome informatics and comparative genomics platform.
  • BioCyc enables exploration of a vast set of biological networks.
  • BioCyc provides gene-expression, metabolomics, and multi-omics analysis tools.
  • BioCyc provides executable metabolic models for a small but growing set of organisms.

BioCyc Informatics Tools

  • Search for genomes by name, taxonomy, phenotypic properties.
  • Gene information page
    • Retrieve amino-acid sequence and nucleotide sequence of arbitrary genome region.
    • Query genes by gene name, accession number, sequence length, replicon position, protein properties (pI, MW, protein features, subcellular location, ligand), GO terms.
  • Transcription-unit information page.
  • Genome Browser depicts genomic regions at user-selected resolution with semantic zooming that reveals new features at higher resolutions. Visible features include pseudogenes, promoters, transcription-factor binding sites, repeats, terminators, nucleotide sequence. Zoom to sequence. Generate genome poster.
  • BLAST search sequence-pattern search via patmatchMap SNPs to genes and show effects on translation.

Access this URL for more information about BioCyc databases and features:

Some additional links that may be helpful:


Guided tour:

User guide:

Data Sheet: BioCyc data sheet



Tiffany J. Grant, PhD
Interim, Assistant Director for Research and Informatics
Research Informationist
Co-Leader, Research Services
Health Sciences Library
Office: (513) 558-9153

Current Trials for AccessPediatrics, AccessPhysiotherapy, and More, Now in One Location

Be part of the acquisition decision-making process – visit the new HSL: Trials for New Electronic Resources guide.  This new guide will house the free trials of the electronic resources currently under consideration for acquisition.  Each trial includes a brief survey so you can add your voice to the decision-making process.

The electronic resources currently under consideration are the following:

We value your input.  Please take a look at the resource(s) under consideration that interest you and fill out the surveys.  Thank you.


CampusGuides: Taking Research Guides to the Next Level

The UC Blue Ash Library, in conjunction with UC Libraries, is transitioning the subject and class guides to a more user-friendly, robust CampusGuides interface during the 2011-2012 academic year. CampusGuides incorporate search boxes, RSS Feeds, embedded media, surveys and can be easily accessed on mobile devices. See the UCBA Psychology guide for an example of a new and improved guide. We look forward to your feedback and suggestions in order to make these guides as useful as possible for our users.  Continue reading


UPDATE: All services have been restored.

Please note that on Saturday, December 19th from 6:00 am to 12:00 pm electric power to Langsam Library will be out for planned maintenance. This power outage will cause the UC Libraries Web site, the Library Catalog, and Interlibrary Loan services through ILLiad to be inaccessible during this time.

In addition, UCit@Langsam will be closed 5:00 am to 1:00 pm because of the power outage.

Thank you for your patience.