Tool type | Tools | Description | Relation to MetaReg |
---|---|---|---|
Network or model visualization tools | Cytoscape [28] Visant [29] CellDesigner [30] Reviewed in [31] | Tools for constructing visualizations of interaction and regulatory networks. These networks can then be integrated with high-throughput data | These tools offer powerful visualization aids and other analysis aids, but they do not address regulatory logics and do not offer model evaluation or refinement mechanisms |
Kinetic and continuous modeling tools | Gepasi [32] BioNetS [33] Dynetica [34] PyBioS [35] Reviewed in [36-38] | Tools allowing detailed dynamical modeling with kinetic parameters and differential equations | These tools can perform detailed model analysis by accurate dynamical simulations, but they cannot discover new mechanisms and rely on detailed mechanistic understanding of the system1 |
Logical modeling tools | BIOCHAM [39] Bionet [40] CellNetAnalyzer [41] GINsim [42] | Tools for modeling regulatory systems using various formalisms, for example, Boolean, discrete, fuzzy logic and so on | Allow model evaluation through simulations, but are not designed for model evaluation and refinement in accordance with high throughput data |