WholeCellSimDB

Welcome to 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.

WholeCellSimDB provides a simple graphical interface to search and browse simulations, including all of the metadata needed to reproduce simulations. WholeCellSimDB also provides three simple plotting applets to enable researchers to preview simulations. In addition, WholeCellSimDB provides a Python API for more advanced analysis (see examples).

Reseachers can download entire simulations and groups of simulations from WholeCellKB in HDF5 format. In addition, researchers can obtain the simulation metadata needed to reproduce simulations in SED-ML format.

WholeCellSimDB currently contains data from a single whole-cell model of the Gram-positive bacterium and human pathogen Mycoplasma genitalium.

Content summary

Quantity Value
Organisms 2
Simulation batches 533
Simulations 2823
States 18
Properties 91
Processes 30
Parameters 271
Options 132
Investigators 1

Getting started?

Please use the "Browse" and "Search" menus at the top-left to browse and search simulations. Please use the basic plotting tool below to preview simulations. See the Python API gallery for examples how to use the Python API for more advanced analysis. Note: The Python API is not publicly accessible. Researchers must install WholeCellSimDB on their own machines to use the Python API.

Please view the tutorial and help pages for further help, or contact us at wholecell@lists.stanford.edu.

Preview simulations

1. Select simulations and predicted phenotypes

2. Visualize selected phenotypes

Visualize simulations

Researchers can use the Python API to construct more advanced visualizations. Please see the Python API gallery for examples. Note: The Python API is not publicly accessible. Researchers must install WholeCellSimDB on their own machines to use the Python API.

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

Need help?

Please contact us at wholecell@lists.stanford.edu.