ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

BMC Bioinformatics

Table 4 Software Comparison

	Steady State Analysis	Limit Cycle Analysis	Input Format	System Requirements
ADAM	Yes^‡	Yes^◊	Boolean (or polynomial) functions Logical Models (GINsim)	None, web based
GINsim	Yes^‡	For small models	Parameters (non-zero truth tables) Logical Model	Java virtual machine^○
BoolNet R package	For small ^† models	For small ^† models	Boolean functions	R statistics software
DDLab	For small models	For small models	Logical tables	○
BN/PBN Matlab Toolbox	For small models	For small models	Logical tables	Matlab

Comparison of different software tools regarding attractor analysis: ‡ less than 1 second on published gene regulatory networks with up to 72 variables; ◊ only for short limit cycles; † heuristic methods are available for larger networks; ○ installation necessary, available for common operating systems.

ISSN: 1471-2105