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

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

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

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

5. Systems Biology Workbench 5

6. 6 Auto Update

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

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

9. Systems Biology Workbench 9 Access to biomodels

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

11. Jarnac 11

12. Jarnac 12 Jarnac:

13. 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 14

15. Running a Model 15

16. Running a Model 16

17. Using the Script to Run a Model 17 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 18

19. 19 General Simulation Tool

20. 20 Try a Simple Simulation 1.Start the Simulation Tool 2. Click on the new button (top left)

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

22. 22 Try a Simple Simulation Click to run simulation

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