CWC Simulator 0.6

C++ implementation for the simulation of bio systems
CWC Simulator
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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.

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!
homepage:
sourceforge.net
license type:
GPL (GNU General Public License) 
developed by:
Maurizio Drocco
category:
ROOT \ Science and Engineering \ Bioinformatics
CWC Simulator
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