From: Modelling with ANIMO: between fuzzy logic and differential equations
Tool | Formalism | Domain-specific interface | Visual modeling | Qualitative parameters | Tight coupling with topology | User-chosen granularity |
---|---|---|---|---|---|---|
GINsim [40] | Boolean Networks | Yes | Yes | Yes | Yes | Yes ^{a} |
BooleSim [41] | Boolean Networks | Yes | Yes | No | No | No |
CytoCopteR [35] | Fuzzy logic ^{b} | Yes | Yes | Yes | Yes | Yes ^{c} |
ANIMO [10] | Timed Automata | Yes | Yes | Yes | Yes | Yes |
Odefy [42] | Logic-based ODE | No | Yes ^{d} | Yes | No | No |
COPASI [43] | ODE, stochastic models | No ^{e} | No | No | No | No |
CellDesigner [44] | ODE | Yes | Yes | No | Yes | No |
GNA [45] | PLDE | Yes | Yes | Yes | Yes | Yes ^{a} |
Virtual Cell [46] | ODE, PDE, stochastic models | Yes | Yes | No | Yes | No |
Bio-PEPA Workbench [47] | Bio-PEPA | No | No | No | No | Yes |
COSBI LAB [48] | BlenX | Yes | Yes | No | Yes | No |
Cell Illustrator [49] | Petri Nets | Yes | Yes | No | Yes | No |