CWC Simulator Files

CWC Simulator (ver. 0.5)
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This is a C++ implementation of CWC, a calculus for the representation and simulation of biological systems.
After a successful installation (see INSTALL) you'll be able to run simulations over CWC models.



* Features
- Gillespie-like algorithm over CWC models;
- multiple rating functions (mass action, Michaelis-Menten, Hill);
- hybrid stochastic/deterministic semantics;
- dynamic cutoff-based reconfiguration;
- multiple instances of simulation;
- online statistics (mean and variance under Grubb's test, quantiles, clustering);
- optimization for multicore architectures based on FastFlow framework.



* (Command-line) Interface
As a generic user, you should run:

<scwc>
	-i model.cwc
	-o statistics
	-t <time_limit>
	-s <sampling_frequency>
	-n <runs>
	-r <rate_cutoff>
	-p <population_cutoff>
	-q <quantiles>
	-c <clusters>
	-w <workers>

where:
- <scwc> is the name of the executable (scwc or scwc_hybrid);
- model.cwc is the CWC program (see examples);
- statistics is the prefix for the output files;
- <time_limit> is the time-limit for the simulation (i.e. 30);
- <sampling_frequency> is the sampling frequency;
- <runs> is the number of instances of simulation;
- <rate_cutoff> is the minimum-rate cutoff
- <population_cutoff> is the minimum-population cutoff
- <quantiles> is the number of quantiles;
- <clusters> is the number of clusters;
- <workers> has usually to match the number of cores of your system (i.e. 2 for dual-core CPU).

Notes:
- <rate_cutoff> and <population_cutoff> are available only with the hybrid version
- to get NP (i.e. 250) sampling points, the sampling period should be set at: <time_limit> / NP (i.e. 0.12)



* Output
The tool produces:
- some .dat files (the sampled output of the simulations)
- some gnuplot scripts to draw statistical analyses