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Table 1 A comparison of MONALISA and Snoopy

From: MONALISA for stochastic simulations of Petri net models of biochemical systems

 

Snoopy

MonaLisa

Availability

closed source

open source

Biological terminology

no

yes

Annotation facilities

no

MIRIAM Identifier and SBO terms

Supported analysis techniques1

no

P-Invariants, T-Invariants, Maximal Common Transitions sets, distance matrix, T-Cluster, Knock-out, Minimal Cut sets, node degrees

Color highlighting of analysis results

no

yes - for Invariants, MCT-sets, and Knock-outs

Supported simulation modes

P/T-net animation, Gillespie, FAU

Asynchronous, Synchronous, Stochastic, (Gillespie)

Supported Petri net classes

19 - for example: P/T-net, Fault Tree, Extended Fault Tree, Freestyle Net

P/T-nets

Supported input file formats

ANDL, CANDL, APNN, SBML, PED, PNML, TINA, CSV, DNF

APNN, KEGG, METATOOL, PNML, PNT, SBML, SPEED

Supported output file formats

19 - for example: ANDL, CANDL, Maria, PEP, Prod

APNN, METATOOL, PNML, SBML, SVG, PNG, TXT, PNT

Supported Operation Systems

Windows, MacOS X, Linux (selected distributions)

Windows, MacOS, Linux

Software Platform

C++

Java

Editor UI

yes

yes

  1. 1Snoopy does not involve analysis techniques. These have to be approached via different file formats for other tools.