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SBW/ Jarnac Tutorial

Herbert M Sauro ( h sauro@u.washington.edu ). SBW/ Jarnac Tutorial. Install from the web site sys-bio.org. Installation. From http://sourceforge.net/projects/sbw/. Installation. From http://sourceforge.net/projects/sbw/. Installation. Systems Biology Workbench.

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SBW/ Jarnac Tutorial

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  1. Herbert M Sauro (hsauro@u.washington.edu) SBW/JarnacTutorial

  2. Install from the web site sys-bio.org Installation

  3. From http://sourceforge.net/projects/sbw/ Installation

  4. From http://sourceforge.net/projects/sbw/ Installation

  5. Systems Biology Workbench

  6. Systems Biology Workbench Auto Update

  7. Systems Biology Workbench A main entry point for many users

  8. Systems Biology Workbench Other possible entry points Jarnac: Script based modeling tool JarnacLite: Small version of above JDesigner: Visual design tool

  9. Systems Biology Workbench Access to biomodels

  10. Systems Biology Workbench Layout networks General Network Viewer Models Translators to: Matlab, C, Java, C#, Jarnac, etc

  11. Jarnac

  12. Jarnac Jarnac:

  13. Try a Simple Simulation The 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;

  14. Jarnac: Run the Model

  15. Running a Model

  16. Running a Model

  17. Using the Script to Run a Model 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; m = p.sim.eval (0, 10, 100); graph (m);

  18. Now start on the Jarnac Tutorials

  19. General Simulation Tool

  20. Try a Simple Simulation Start the Simulation Tool 2. Click on the new button (top left)

  21. Try a Simple Simulation Move the mode to the simulation Tool by clicking on: Third button from the right.

  22. Try a Simple Simulation Click to run simulation

  23. Access Data Copy simulation data to the clipboard or load into Excel

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