CWC Simulator Files

CWC Simulator (ver. 0.8)
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This is a C++ tool for the simulation-analysis workflow based on CWC, a calculus for the representation and simulation of biological systems.
After building (see BUILD.ME) you'll be able to run simulations over CWC models, as shown in some examples (see examples/).
A prototypal JAVA GUI is included.



* Features
- Gillespie SSA algorithm over CWC models
- hybrid stochastic/deterministic semantics
- multiple rating semantics (mass action, Michaelis-Menten, Hill etc.)
- multiple instances of simulation with online statistics
- optimization for multicore architectures based on FastFlow framework
- both shared-memory and distributed versions
- extensible statistical framework (mean-variance, filtered clustering etc.)



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

<scwc>
	-i model.cwc
	-o <statistics>
	-t <time>
	-s <sampling_period>
	-n <runs>
	-c <clusters>
	--qt-threshold <threshold>
	-q <quantiles>
	-w <workers>

where:
- <scwc> is the name of the executable (default: scwc);
- model.cwc is the input CWC program (see examples);
- statistics is the output-files prefix;
- <time> is the simulation-time limit;
- <sampling_period> is the sampling period (i.e. 0.12 to get 250 points with time-limit=30);
- <runs> is the number of instances of simulation;
- <clusters> is the number of clusters for k-means
- <threshold> is the threshold for QT clustering
- <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).

For a full list of the allowed parameters, run:
<scwc> -h
      
	
            



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



We're working at a comprehensive user manual.