CWC Simulator 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/).
(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
- < hreshold > 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).
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.
Product's homepage
Here are some key features of "CWC Simulator":
· Gillespie SSA algorithm over CWC models
· Hybrid stochastic/deterministic semantics
· Multiple instances of simulation with online statistics
· Optimization for multicore architectures based on FastFlow framework
· Extensible statistical framework (mean-variance, filtered clustering etc.)
· Multiple rating semantics (mass action, Michaelis-Menten, Hill etc.)
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