SBW/ Jarnac Tutorial

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