Table 1 Summary of available ChemChains parameters.

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