WholeCellKB - Model Organism Databases for Comprehensive Whole-Cell Models

NAR Molecular Biology Database Collection entry number 1631
Karr, J.R.1, Sanghvi, J.C.2, Macklin, D.N.2, Arora, A.3 and Covert, M.W.2
1Graduate Program in Biophysics, Stanford University, 318 Campus Drive West, Stanford, CA 94305, USA. 2Department of Bioengineering and 3Department of Electrical Engineering, Stanford University, 318 Campus Drive West, Stanford, CA 94305, USA.

Database Description

WholeCellKB is a collection of open-access model organism databases specifically designed to enable whole-cell models. Currently, WholeCellKB contains a database of Mycoplasma genitalium, a Gram-positive bacterium and common human pathogen. The M. genitalium database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. The M. genitalium database was curated from over 900 primary research articles, reviews, books, and databases. The M. genitalium database is extensively cross-referenced to external resources including BioCyc, KEGG, and UniProt. WholeCellKB is also an open-source web-based software program for constructing model organism databases. The WholeCellKB software provides an extensive and fully customizable data model that fully describes individual species including the structure and function of each gene, protein, reaction, and pathway. WholeCellKB is freely accessible via a web-based user interface as well as via a RESTful web service.


This work was supported by an NIH Director’s Pioneer Award [5DP1LM01150-05] and a Hellman Faculty Scholarship (to M.W.C.); NDSEG, NSF and Stanford Graduate Fellowships (to J.R.K.); NSF and Bio-X Graduate Student Fellowships (to J.C.S.) and a Stanford Graduate Fellowship (to D.N.M.).


1. Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW. (2013) WholeCellKB: model organism databases for comprehensive whole-cell models, Nucleic Acids Res, 41.

2. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW. (2012) A whole-cell computational model predicts phenotype from genotype, Cell, 150, 389-401.

Subcategory: Metabolic pathways

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