CompuCell3d multiscale modeling
Drs. Maciek Swat and James Glazier The Biocomplexity Institute Indiana University Bloomington, IN, USA
JWS Online modeling environment
Jacky Snoep Stellenbosch University Stellenbosch, South Africa
MiniCell – A model-driven approach to minimal cell engineering for medicine
Luis Serrano and Maria Lluch-Senar Center for Regulatory Genomics Barcelona, Spain Alain Blanchard and Carole Lartigue National Institute for Agricultural Research Bordeaux, France Jörg Stülke University of Göttingen Gottingen, Germany
PRiME: Program for Research on Immune Modeling and Experimentation
Stuart Sealfon Professor Neurology, Neurobiology, and Pharmacology & Systems Therapeutics Icahn School of Medicine at Mount Sinai New York, NY, USA
Simtk
Dr. Joy Ku Stanford University Stanford, CA, USA
Systems Biology Center New York
Ravi Iyengar Professor, Department of Pharmacology and Systems Therapeutics Icahn School of Medicine at Mount Sinai New York, NY, USA
Virtual Cell modeling environment
Leslie Loew Professor University of Connecticut Health Center Farmington, CT, USA
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 [...]
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 [...]
libRoadRunner
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 [...]