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SBW/JARNAC TUTORIAL

Herbert M Sauro (hsauro@u.washington.edu)

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INSTALLATIONInstall from the web site sys-bio.org

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INSTALLATIONFrom http://sourceforge.net/projects/sbw/

Group Meeting

INSTALLATIONFrom http://sourceforge.net/projects/sbw/

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Systems Biology Workbench

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Systems Biology Workbench

Auto Update

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Systems Biology Workbench

A main entry point for many users

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Systems Biology Workbench

Other possible entry points

Jarnac: Script based modeling toolJarnacLite: Small version of aboveJDesigner: Visual design tool

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Systems Biology Workbench

Access to biomodels

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Systems Biology Workbench

Layout networks

General Network Viewer

Models Translators to:Matlab, C, Java, C#, Jarnac, etc

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Jarnac

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Jarnac

Jarnac:

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Try a Simple SimulationThe model editing window should appear,type the following in the window:

p = defn cell S1 -> S2; k1*S1; S2 -> S3; k2*S2;end;

p.S1 = 10;p.S2 = 0;p.S3 = 0;

p.k1 = 0.34;p.k2 = 1.3;

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Jarnac: Run the Model

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Running a Model

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Running a Model

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Using the Script to Run a Modelp = defn cell

S1 -> S2; k1*S1;

S2 -> S3; k2*S2;

end;

p.S1 = 10;

p.S2 = 0;

p.S3 = 0;

p.k1 = 0.34;

p.k2 = 1.3;

m = p.sim.eval (0, 10, 100);

graph (m);

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Now start on the Jarnac Tutorials

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General Simulation Tool

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Try a Simple Simulation1. Start the Simulation Tool

2. Click on the new button (top left)

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Try a Simple SimulationMove the mode to the simulationTool by clicking on:

Third button from the right.

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Try a Simple Simulation

Click to run simulation

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Access Data

Copy simulation data tothe clipboard or load into Excel