Skip to main content

Advertisement

Table 1 Comparison between ANIMO and some existing approaches to modelling biological systems

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
  1. A “Yes” under a column indicates that the modelling tool (mostly) fulfils the parameter, “No” indicates very limited or no fulfilment
  2. aThe user can choose the number of levels for each reactant, allowing to define multi-level models based on Boolean reaction dynamics
  3. bBoolean logic and logic-based ODE models are also available
  4. cThe choice for the type of logic to be used determines also the granularity of the model
  5. dOnly if coupled with the yEd [50] graph editor
  6. eWhile visual network modeling is absent, the MultiState Model Builder (MSMB [51]) editor provides an interactive support during the phase of model definition