Table 2.

Petri Net Tools Characterized by the Typical Biological Systems That They Can Represent and by the Biological Questions That They Can Answer

	Mobius	TimeNET	Design/CPN	Genomic Object Net	Woflan
Typical process characteristics
Abstractions of complex processes	+ Composition		+ hierarchy
Populations	++ Composition gates	+ Arc weight	+ Arc weight	+ Arc weight
Genetic variation			+*
Substrates, products, catalysts	+ I/O place	+ I/O place	+ I/O place	+ I/O place	+ I/O place
Stoichiometric coefficients	+	+	+	+
Reaction rates	+++	++	+	+++
Inhibitors and allosteric effectors	Competing cases	+ Inhibitory arcs	Competing transitions	Competing transitions	Competing transitions
Typical kinetic behavior	+	+	+	+
Competing reactions with different probabilities	+	Probabilities not working	Not directly supported	Not working
Concurrent processes	+	+	+	+	+
Typical questions
Active processes					+*
Network structure		+*
Network behavior/interactive simulation		+	+	+
Reachable states		Not working
Kinetic profile	++	+++	Not directly supported	+++
Process utilization	+		Not directly supported	+
Equilibrium state	+++	+++	Not directly supported	+++

The number of + signs indicates the level of support.

CPN = Colored Petri Net; I/O = input or output.

^*Features that are supported by at most a single tool.