Cellware
Cellware has been designed to conduct modeling and simulation of gene regulatory and metabolic pathways and also offer an integrated environment for diverse mathematical representations, parameter estimation and optimization. In addition, a user-friendly
CytoScape
Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimit
E-Cell 3
E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.
Gepasi
Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and l
