Kinetics Intro to Synthetic Biology, 424 1 Copyright © 2008: Sauro.
Herbert M Sauro ([email protected])h. Install from the web site sys-bio.org.
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Transcript of Herbert M Sauro ([email protected])h. Install from the web site sys-bio.org.
Group Meeting
INSTALLATIONInstall from the web site sys-bio.org
Group Meeting
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