1 / 23

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.

cybele
Télécharger la présentation

SBW/ Jarnac Tutorial

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related