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
 
 
 
 

JarnacLite

JarnacLite is a portable module (Windows, Linux and Mac OS) that supports the model description language of Jarnac. It does not support the Jarnac control language. JarnacLite can thus be used to edit or build models. It is particularly useful when a user wishes to edit a model in a module which has no model editing capabilities. Thus a user would move to JarnacLite from one module (via the SBW menu), edit the model, and move back. Any SBW enabled application will have access to JarnacLite (eg, JDesigner, CellDesigner, Copasi, Oscill8).

The Jarnac definition language currently supports:

  1. Reaction schemes
  2. Arbitrary rate laws
  3. Compartments
  4. Assignment Rules

Examples:

p = defn cell
     A -> B; k1*A;
     B -> A; k2*B;
end;
 
p.A = 1.0; p.B = 0.0;
p.k1 = 0.1; p.k2 = 0.34;

p = defn myModel
 
    // Declare a compartment
    vol cytosol;
    var ATP in cytosol, ADP in cytosol, AMP in cytosol;
    // Declare an external (boundary) species
    ext Pi;
 
    // Define an assignment rule
    AdenylateKinase = k1*ATP*AMP - k2*ADP^2;
 
    ATP + AMP -> 2ADP; AdenylateKinase;
    ATP -> ADP + Pi;   kATPase*ATP;   // ATP utilization
end;

This screen shots shows JarnacLite and a sample model (Brussleator) in Jarnac model definition language.

:sbw:jarnaclite.png

Installation

JarnacLite is installed with SBW. For more information see the SBW installation page.

JarnacLite is fully supported on Windows and Linux, and partially supported on Mac OS X.

Documentation & Help

 
sbw/jarnaclite.txt · Last modified: 2007/01/10 23:54 (external edit)
 

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