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, [...]

2019-09-17T10:32:18-07:00August 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, [...]

2019-09-17T10:34:31-07:00September 12th, 2016|Software, TR&D 3 - Software|

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 [...]

2019-09-17T10:43:29-07:00May 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.

2019-09-17T10:44:03-07:00September 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 [...]

2019-09-17T10:44:24-07:00September 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 [...]

2019-06-17T05:45:05-07:00September 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.

2019-09-17T10:16:40-07:00September 12th, 2016|Software, TR&D 1 - Software|


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.

2019-09-17T10:14:59-07:00May 2nd, 2018|Software, TR&D 1 - Software|


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.

2019-09-17T10:13:23-07:00May 2nd, 2018|Software, TR&D 1 - Software|