Cellular Models

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Model Repository

Other SBML repositories: ERATO

UPDATED (12-January-03)

NOTE: All the following models can be read by SBML Level 1 Compatible Simulation tools, eg Jarnac, Gepasi, JDesigner and Cellerator

Simple Model Models
 

Linear Model
Branch Model
Simple Cycle Model
Two Cycle Model

Real-World Models (These models can be rendered by JDesigner)

Theoretical Models (These models can be rendered by JDesigner)

The Following Models were taken from the Gepasi site (with permission)

The following were taken from the Gepasi site at www.gepasi.org to illustrate the ease with which it is now possible to interchange models between different simulators. The SBML models at gepasi.org were loaded into JDesigner, and adjusted by hand so that the networks were more ordered on screen.

Taken from the Gepasi site with permission and modified for JDesigner display, see www.gepasi.org for details.

Documentation for sbml can be obtained from:

ERATO XMl Spec - Second Draft 

Sample Script from Jarnac to generate SBML

Here is an example of the sort of script that can be used to generate SBML files:

// Declare the model, $Xn represent boundary fixed species
// Lines starting with // are comments

p = defn SimpleExample

        // Describe a three step linear pathway
        $X0 -> S1;  k1*X0;
         S1 -> S2;  k2*S1;
         S2 -> $X1; k3*S2;
end;

// Write out the xml file
p.xml ("simple.xml");

To read the SBML back in, one can use the script:

p = network ("simple.xml");