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 small cross-platform application that supports the reaction definition syntax for of the Jarnac syntax. The examples below illustrate some Jarnaclite scripts:

The following code describe a simple linear pathway. The kinetic laws are free format.

p = defn cell
     $Xo -> S1;  k1*Xo;
      S1 -> S2;  k2*S1 - k3*S2;
      S2 -> $X1; Vmax*S2/(Km + S2);
end;

p.k1 = 0.1;
p.k2 = 0.2;
p.k3 = 0.15;
p.Vmax = 5.5;
p.Km = 0.5;

p.Xo = 10;
p.X1 = 0;

The following example illustrates a new syntax which allows users to include discrete events in a model. In this case, a bolus of input is applied at time = 10 and is then returned to the original value at time = 20. The graph that follows illustrate a simulation from this model. The function gt() means greater then.

p = defn newModel
      $Xo -> S1;  v;
       S1 -> $X1; k*S1;
  
       at(gt(time,10)): v = 2;
       at(gt(time,20)): v = 1;
end;

p.v = 1;
p.k = 0.5;
p.Xo = 0.5; 

 
sysbio/sbwdevelopers.txt · Last modified: 2009/08/30 14:21 by hsauro
 

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