Q1 How do I set the random number generator seed?

Use the command:

rndseed (timer);

Q2 How do I output data to a file?

The following code will generate a matlab formated matrix to a file.

f = createfile ("c:\\data.txt");
f.write ("m = [");
for i = 1 to rows (m) do
    begin
    for j = 1 to columns (m) do
        f.write (m[i,j]);
    f.write (";\n");
    end;
f.write ("]\n");
f.close;

Q3 How do I make multiple plots on one graph?

Plotting is accomplished by the graph (m) command, where m is matrix. To plot multiple graphs, use the setghold (true) command to prevent the previous graph from being erased. Use setghold (false) to release the hold.

graph (m1);       // Plot the data in matrix m1
setghold (true);  // Hold the graph (i.e do not erase) 
graph (m2);       // Plot matrix m2 and overlay on previous graph
setghold(false);  // Release the hold

Q4 How do I run a stochastic simulation?

// This will run multiple Gillespie simulations 
// at different parameter values and plot the 
// resulting runs on one graph. 
P = defn myModel 

    $Xo -> S1; k1*Xo; 
    S1 -> $X1; k2*S1; 
end; 

p.Xo = 10; 
p.S1 = 0; 
p.X1 = 0; 
p.k1 = 0.23; p.k2 = 0.56; 

// Load the model into the Gillespie solver
gillLoadSBML (p.xml); 

// Run a simulation and plot the results
m = gillSimulate (0, 50, 1); 
graph (m);
// Hold the current graph, ie do not erase next time we plot 
setghold (true);
 
// Loop over a set of parameter value and carry out a simulation
// Each time plot the results on the held graph.
k1 = 0.1; 
for i = 1 to 5 do 
    begin 
    gillSetParameter ("k1", k1); 
    m = gillSimulate (0, 50, 1); 
    graph (m); 
    k1 = k1 + 2; 
    end; 
// Release the graph hold
setghold (false);