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Table 2 Modeling formalisms and implemented features

From: Modeling formalisms in Systems Biology

  BN Bay PN PA CB DE RB ISM CA AB
Visualization + + +     + + + +
Topology + + +   +      
Modularity    + +    + +   
Hierarchy    e e     +   
Multi-state    e     + + + +
Compartments     e    + +   +
Spatial       e e   + +
Qualitative + + + + +   +    
Synchronized +   e       +  
Stochastic e + e +   e + + + +
Continuous    e    + +    
  1. Modeling formalisms and implemented features. (+) Supported feature; (e) Available through extension; (BN) Boolean networks; (Bay) Bayesian networks; (PN) Petri nets; (PA) Process algebras; (CB) Constraint-based models; (DE) Differential equations; (RB) Rule-based models; (ISM) Interacting state machines; (CA) Cellular automata; (AB) Agent-based models.