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 Welcome To The CyberCell Database: CCDB

The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655). It is intended to provide sufficient information and querying capacity for biologists and computer scientists to use computers or detailed mathematical models to simulate all or part of a bacterial cell at a nanoscopic (10-9 m), mesoscopic (10-8 m) and microscopic (10-6 m) level.
The CCDB may be accessed by clicking on any of the hyperlinked buttons located at the top of this page. The CCDB database is actually several databases, one (CCDB) contains quantitative proteomic, genomic and metabolic information about E. coli. The CC3D database contains 3D structural data for E. coli structural proteomics work, the CCRD database contains detailed information on E. coli RNA molecules while the CCMD database contains quantitative information on E. coli metabolites. Each database is presented as a re-formattable synoptic table which allows users to casually browse the databases. Detailed information about each gene, protein, RNA, structure or metabolite may be obtained by clicking on the "*Card" button on the left column. Each card contains more than 60 fields concerning all aspects of the sequence, function or structure of a given molecule. CCDB users may also perform text searches (using the Search button), BLAST sequence searches (using the BLAST button) or conduct more detailed data extraction or relational data searches (using the Extract button). Statistical information and general information about E. coli are accessibile by clicking on the Statistics and About E.coli buttons. Flatfile versions of the CCDB entries, and useful pre-compiled lists of protein data can be found on the Download page. A complete listing of all of the electronic databases and programs used to construct and update CCDB can be found on the database summary page.
By its very nature the CCDB is continually evolving and will not be "complete" until sufficient data has been collected to perform all levels of the desired cellular simulations. CCDB is an integral part of Project CyberCell*, a large-scale multi-lab project based out the University of Alberta. The CCDB functions as an archival bioinformatics resource for Project CyberCell serving as a warehouse of prior or existing knowledge as well as a repository for newly acquired, experimental knowledge about E. coli. The CCDB is intended to be a community project and as such it provides facilities for E. coli researchers world-wide to submit, correct or add data to the database. Submissions, additions, corrections and comments are welcome.

* Project CyberCell is also part of the International E. coli Alliance, an multi-national project aimed at coordinating E. coli simulation and E. coli bioinformatics efforts across Canada (Project CyberCell), the US (EMC2), Japan (E-Cell) and the European Community (SiliconCell, GSK)

Please cite the following: Shan Sundararaj, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani,Paul Stothard, Michael Ellison,and David S. Wishart "The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli" Nucleic Acids Res. 2004 January 1; 32 (Database issue): D293.D295

  Webmaster: Shan Sundararaj and An Chi Guo

(Last CCDB Update: June 22, 2006)
(Copyright © 2001, 2002 and 2003, University of Alberta)

Funding for this project was provided by  , , and

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