# README FILE FOR bnsim - simple Boolean Network Simulator
# Written by Pau Rué, Antonio J Pons Rivero and N Domedel-Puig
# LICENSE ... whatever
# DATE


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# INSTALLATION INSTRUCTIONS
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Download and untar the bnsim archive bnsim-0.1.tar.gz
BNsim is ready to run.

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# USER-SPECIFIED SETTINGS
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The executable file bnsim needs 4 parameters to run:

'-r <filename>.rules':  rules file. This file defines the nodes and logic rules of the boolean network

'-c <filename>.condis': simulation conditions file. This file defines the simulation conditions of the network.

	Parameter Num_New_Iterations: defines the number of iterations to perform.
	Parameter <node>*: defines the update rule of input node <node>.
		The current implementation of bnsim accepts two types of input node:
			Periodic inputs are specificed by: 
				<node>* Sequence <periodic sequence> <error probability>. For example:
				A* = Sequence 111000 0.0
				See also example 2.
			Chatter inputs are specificed by: 
				<node>* Sequence <one-digit default value> <error probability>. For example:
				A* Sequence 0 0.50
				See also example 3.
				
'-s <filename>.states': states file. This file defines the initial values of the network nodes, given in the same order as the node names given in the hash-commented line.

'-o <filename>.out': output file. This file defines the location and name of the output file. The output file is formatted such that there is one hash-commented initial row with node information, followed by one row of states values per iteration.