CWC Simulator Files

CWC Simulator (ver. 0.5.1)
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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, as shown in some examples (see examples directory).



* Features
- Gillespie SSA algorithm over CWC models;
- hybrid stochastic/deterministic semantics;
- dynamic cutoff-based reconfiguration;
- labelled CWC compartments;
- multiple instances of simulation with online statistics;
- optimization for multicore architectures based on FastFlow framework.



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

<scwc>
	-i model.cwc
	-o statistics.dat
	-t <time>
	-s <sampling_rate>
	-n <runs>
	-r <rate_cutoff>
	-p <population_cutoff>
	-c <confidence>
	-q <quantiles>
	-w <workers>

where:
- <scwc> is the name of the executable (default: scwc);
- model.cwc is the CWC program (see examples);
- statistics.dat is the output file;
- <time> is the time-limit for the simulation (i.e. 30);
- <sampling_frequency> is the sampling frequency (i.e. 0.12 to get 250 points with time-limit=30);
- <runs> is the number of instances of simulation;
- <rate_cutoff> is the minimum rate cutoff
- <population_cutoff> is the minimum population cutoff
- <confidence> is the confidence-level for the statistical estimations (i.e. 95 to get 95%-confidence intervals);
- <quantiles> is the number of quantiles;
- <workers> has usually to match the number of cores of your system (i.e. 4 for quad-core CPU).



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