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:
DNA, RNA and protein expression,
DNA-bound protein positions,
DNA modification positions, and
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.
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
WholeCellSimDB was developed by researchers at Mount Sinai School of Medicine, Stanford University, and the University of Prince Edward Island:
Please contact the development team at firstname.lastname@example.org.
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Copyright © 2013-2014 Covert Lab, Stanford University
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