# CWC Simulator 0.6

C++ implementation for the simulation of bio systems

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/).

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).

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.

**(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.

### Main features:

- 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.)

- last updated on:
- July 13th, 2011, 13:33 GMT
- price:
- FREE!
- developed by:
**Maurizio Drocco**- license type:
- GPL (GNU General Public License)
- category:
- ROOT \ Science and Engineering \ Bioinformatics

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