The Random Whole-cell model generator is a tool for generating WC models that represent user-specified numbers of genes, RNA, proteins, and reactions of an archetypal bacterium. The models generated by the model generator represent the metabolism, replication, transcription, translation, RNA and protein degradation, and cell division of a typical bacterium. The archetypal bacterium model [...]
SemGen is an experimental software tool for automating the modular composition and decomposition of biosimulation models. SemGen facilitates the construction of complex, integrated models, and the swift extraction of reusable sub-models from larger ones. SemGen relies on the semantically-rich SemSim model description format to help automate these modeling tasks. With SemGen, users can: Visualize [...]
Tellurium (te.) is a Python environment based on spyder2 IDE. It combines a number of existing libraries, including libSBML, libRoadRunner (including libStruct), libAntimony, and is extensible via telPlugins. In addition, other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support. On Windows, Tellurium comes with pip, so [...]
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 [...]
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 [...]