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Table 1 Available tools related to MetaReg

From: MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data

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
  1. 1 In several cases the kinetic and continuous modeling tools have parameter optimization capabilities, but only for the given differential equations included in the model. Hence, these tools lack MetaReg's ability to discover unknown mechanism of reaction and changes in model topology. Furthermore, kinetic and continuous modeling approaches require either detailed mechanistic understanding or known model parameters (e.g., reaction constants), which are commonly unknown, even in well studied systems (e.g., the Leucine biosynthesis pathway studied here).