H1 human embryonic stem cell whole-cell model

The H1 human embryonic stem cell (hESC) model is the first step toward whole-cell models of human cells. The model will represent the core cellular functions of all human cells including their metabolism, DNA replication, transcription, translation, protein complexation, RNA and protein degradation, and division. The model focuses on H1-hESCs because ESCs behave as individual [...]

May 2nd, 2018|Model|

Kinetic Datanator

Kinetic Datanator is a tool for discovering the data needed to build, calibrate, and validate whole-cell models. Kinetic Datanator is composed of an integrated database of experimental data for whole-cell modeling and tools for identifying relevant data for modeling a specific organism and environmental condition. Kinetic Datanator has a web-based graphical interface, a REST API, [...]

August 24th, 2017|Software, TR&D 1 - Software|


A high performance and portable simulation engine for systems and synthetic biology. I can run on many platforms including Windows, Mac OS, and Linux. libRoadRunner is 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 structural analysis code, [...]

September 12th, 2016|Software, TR&D 3 - Software|

Mycoplasma genitalium whole-cell model

The M. genitalium whole-cell model was the first model that represented each characterized gene function of an organism. The model is composed of 28 submodels of 28 cellular processes. In total, the model represents the functions of 401 genes, 722 compounds, 1,857 reactions, and 1,836 parameters. In addition to demonstrating the feasibility of whole-cell models, [...]

September 12th, 2016|Model|

Mycoplasma pneumoniae whole-cell model

The Mycoplasma pneumoniae whole-cell model will be the most comprehensive, most systematically constructed, and most extensible whole-cell model to date. The model will represent all of the major cellular functions of M. pneumoniae, including the function each characterized gene. The model will be based primarily on M. pneumoniae genomic data. The model will be used [...]

May 2nd, 2018|Model|

Random WC model generator

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 generator [...]

May 2nd, 2018|Model, Software, TR&D 1 - Software|


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.

September 12th, 2016|Software, TR&D 2 - Software|


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 you [...]

September 12th, 2016|Software|


VCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a web application. VCell permits 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 appropriately model [...]

September 12th, 2016|Software, TR&D 3 - Software|


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.

September 12th, 2016|Software, TR&D 1 - Software|