WholeCellKB is a collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms.
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README.md

WholeCellKB

WholeCellKB is a collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including:

  • Cellular chemical composition,
  • Growth medium composition,
  • Gene locations, lengths, and directions,
  • Transcription unit organization and transcriptional regulation,
  • Macromolecule composition,
  • Reaction stoichiometry, kinetics, and catalysis, and
  • Extensive links and cross-links to all references used to construct each model organism database.

See the tutorial and the about page for more information about WholeCellKB how to use WholeCellKB as well as how it was design, implemented, and curated.

Installation and requirements

See the Developer's Guide.

Creating and editing model organism databases

See the Developer's Guide.

Customizing the WholeCellKB data model and user interface

See the Developer's Guide.

Need help?

Please view the tutorial, about page, or contact us at wholecell@lists.stanford.edu.

Citing WholeCellKB

Please use the following references to cite WholeCellKB:

  • Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW. WholeCellKB: Model Organism Databases for Comprehensive Whole-Cell Models. Nucleic Acids Research 41, D787-D792 (2013). PubMed
  • Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW. A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell 150 2, 389-401 (2012). PubMed

Development Team

WholeCellKB was developed by a team of three researchers at Stanford University:

  • Jonathan Karr, Graduate Student in Biophysics
  • Jayodita Sanghvi, Graduate Student in Bioengineering
  • Derek Macklin, Graduate Student in Bioengineering
  • Abhishek Arora, Graduate Student in Electrical Engineering
  • Markus Covert, Assistant Professor of Bioengineering

License

Copyright (c) 2012, Stanford University

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 
SOFTWARE.