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Installing and Using Systems Biology Workbench: Jarnac Tutorial for Simulations

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This guide provides detailed instructions for installing the Systems Biology Workbench (SBW) and using the Jarnac modeling tool for system simulations. Users can download SBW from the specified SourceForge link and learn to navigate various entry points, including Jarnac and JarnacLite. The tutorial includes step-by-step processes for running a simple model, utilizing simulation tools, and exporting data for further analysis. Ideal for researchers and students engaged in systems biology.

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Installing and Using Systems Biology Workbench: Jarnac Tutorial for Simulations

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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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