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Table 1 Summary of available ChemChains parameters.

From: ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

Parameter Description
General parameters used with all running modes
-ispecs filename Simulation specification file name
-ilogic filename Network descriptor file name
-v Verbose mode
Parameters used with FileConversion mode
-TT2ND Creates a network descriptor file from a set of truth tables
-ND2TT Converts the network descriptor into a set of truth tables
-itables path File path for list of truthtables, and the nodelist
-inodelist filename File for List of Nodes, Used with TT2ND
-o filename Specifies the location of FileConversion output
Parameters used with Visual mode
-vis filename Instantiates ChemChains in the visual mode and saves the output file provided by filename
-A Output all nodes
Parameters used with Calculation mode
-calc experimentname instantiates ChemChains in the calculation mode
-n xxx Number of consecutive simulations
-noBits Suppress printing of bit files
-rand_init randomly selects initial states for all nodes and creates new logic file
Parameters used with Pattern analysis extension
-patterns runs pattern analysis after each simulation
-isettings xxx Patterns file with node activity range settings
-inodes xxx File with nodes to be analyzed