WholeCellSimDB.org 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
- Ribosome 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.
Researchers 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.