About WholeCellSimDB

WholeCellSimDB is a database of whole-cell model simulations designed to make it easy for researchers to explore and analyze whole-cell model predictions including predicted:

  • Metabolite concentrations,

  • DNA, RNA and protein expression,

  • DNA-bound protein positions,

  • DNA modification positions, and

  • Ribome positions.

Getting started?

Please view the tutorial and help pages for help getting started.

Implementation

WholeCellSimDB is a hybrid SQL/HDF database implemented in Python. The Django framework was used to construct a MySQL database containing simulation metadata as well as links to HDF files containing the simulation predictions. The H5py package was used to read and write HDF files. Full text search over the simulation metadata was implemented using Xapian and Haystack. The web interface was run using Apache and mod_wsgi. The web interface was developed using flot, Google Fonts, jQuery, jqTree, jQWidgets, and FamFamFam Silk icons.

Data model

Citing WholeCellSimDB

Please see the following for more information or to cite WholeCellSimDB:

  • Karr JR, Phillips, NC, Covert MW. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database (2014). Database | 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, 389-401 (2012). Cell | PubMed

Development team

WholeCellSimDB was developed by researchers at Mount Sinai School of Medicine, Stanford University, and the University of Prince Edward Island:

Contact info

Please contact the development team at wholecell@lists.stanford.edu.

The MIT License

Copyright © 2013-2014 Covert Lab, 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.