Software

Whole-cell KB (WC-KB) is a data model for describing the experimental data needed to build, calibrate, and validate a whole-cell model. WC-KB includes a command line program and a Python API. Whole-cell KB

WC-KB-Gen is a Python framework for programmatically constructing knowledge bases for whole-cell models. WC-KB-Gen helps modelers retrieve data from external sources, organize this data, and record the provenance of this data. In turn, WC-KB-Gen helps modelers scalably, reproducibly, and comprehensibly discover and aggregate data for whole-cell models. Learn more

WC-Lang is a data model and a file format for describing composite, multi-algorithmic whole-cell models. WC-Lang includes a command line interface and a Python API. WC-Lang

WC-Model-Gen is a Python framework for programmatically constructing whole-cell models from large datasets described with WC-KB. WC-Model-Gen helps modelers retrieve data from a WC-KB and use the data to scalably design species and reactions. In turn, WC-Model-Gen helps modelers build models scalably, reproducibly, and comprehensibly. WC-Model-Gen on GitHub

WC-Rules is a formalism for describing composite, mixed-grained, multi-algorithmic WC models. WC-Rules provides modelers a high-level, biologically-intuitive language for describing models in terms of patterns of metabolite, DNA, RNA, and protein species, and rules for their interactions. Together, these species patterns and interaction rules enable modelers to describe the molecular complexity of any biochemical [...]

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 [...]

WholeCellViz.org is a web-based software program for visually analyzing whole-cell simulations. WholeCellViz enables users to interactively analyze many aspects of cell physiology including: Cell mass, volume, and shape, Metabolite, RNA, and protein copy numbers, Metabolic reaction fluxes, Molecular machine statuses – DNA polymerase, RNA polymerase, ribosome, FtsZ ring, and the Chromosome copy number, superhelicity, [...]