Computational Systems Biology
Sauro Lab
University of Washington
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Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
4. WinSCAMP
5. Matlab Interface
6. Optimization
6. Bifurcation
 
maintained by Frank Bergmann
 
 
 
 

Simulation Tool

The Simulation Tool is one of the main entry points into SBW. The tool has the following features:

  • Time course simulation with load, simulate and reset. Set time start, end and number of points. Select X and Y axis variables, including concentrations, fluxes, rates of changes, volumes, parameters and time.
  • Continuous time course with panning graph.
  • Steady State, compute and reset with optional pre-simulation. Compute eigenvalues as well as steady state values for concentration, fluxes, flux control coefficients, concentration control coefficients and elasticities (all unscaled or scaled).
  • Frequency Analysis: Plots the amplitude and phase of sinusoidal signals injected into the system.
  • Structural Analysis: obtain the stoichiometry matrix, conservation matrix, K and L matrices together with reduced forms. Copy to clipboard or save to file.
  • Plot reaction rates versus species, useful for obtaining reaction rate profiles.
  • Parameter scans at steady state or time course simulations.
  • Apply pulse and ramp inputs to systems
  • Extract the current Jacobian matrix
  • *All* analyses can be controlled via sliders

The simulation tool also has a plugin architecture allowing other developers to add new functionality to the tool.

:sbw:simdrivernet.png

Installation

The Simulation Tool is installed with SBW. For more information see the SBW installation page.

The Simulation Tool module is fully supported on Windows and Linux, and partially supported on Mac OS X.

Documentation & Help

SimDriver FAQ

[[fbergman@kgi.edu|Frank Bergmann 2006/08/01 13:07

 
sbw/simdriver.txt · Last modified: 2010/05/10 20:32 by hsauro
 

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