Jonathan Karr

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, [...]