libRoadRunner is a high-performance and portable simulation engine for systems and synthetic biology. It can run on many platforms including Windows, Mac OS, and Linux. libRoadRunner is a major rewrite of the original C# roadRunner developed by Frank Bergmann and Herbert Sauro. The same original functionality however remains, including the original C API, the [...]
VCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that are built on a central database and disseminated as a web application. VCell permits the construction of models, application of numerical solvers to perform simulations, and analysis of simulation results, offering the choice of multiple physical approximations and simulation technologies to [...]
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, [...]