Copasi

Introduction

Copasi is an open source software package for modeling and simulation of biochemical reaction networks. Copasi can import and export SBML (Systems Biology Markup Language), which is a file format for exchanging models with other systems biology software.

Model Creation

1. Click the "Model" tab from the side of the home page.
2. Rename the model.
3. Adjust the units according to your needs.
4. Write any comments in the large text box
5. Choose the biochemical tab from the side underneath the "Model" tab. Choose "Compartment" from the drop down list.
6. Rename the compartment and and double click on the compartment.
7. Once the compartment is adjusted to your needs, click on the "Reactions" tab.
8. Double-Click the reaction to rename and then double-click the reaction again to put in the chemical equation. Using the equal sign means the reaction is reversible. -> means the reaction is irreversible.
9. Press the new button to create a new reaction.
10. Adjust rate law according to your needs.
11. If the rate law you need is not in the list, select the "New Rate Law" button.
12. Enter the mathematical formula into the "Formula" box.
13. Press the "Commit" button when finished with the rate law.
14. Click the "Reactions" tab to see a summary of the information you have entered.
15. Select the "Species" tab to see all of the species.
16. Double-click on a species to edit the simulation type, initial concentration, rate and reactions for that species.
17. Select "Parameter of Review" from the side tabs to review all of the information.
18. Select the "File" tab to save the model.

Time Course Simulation

1. Select the "File" tab and then click "file" to load a model.
2. Select the triangle next to "Tasks" to expand the drop-down menu.
3. Select "Time Course" then hit "Run."
4. Select "Result" from the "Time Course" drop-down to see a table of the data. Select "Save" to create a txt file for the data.

To get a plot...

1. Select the "Output Assistant" button on the the "Time Course" page.
2. Select the predesigned plot value and click "Create."
3. Check the "Active" box to make sure the plot appears next time the program is run.
4. Click "Time Course" then "Run" to see the plot.

Duration

• Setting the duration to suppress before a certain time gives the simulation "time to settle in."
• Larger intervals speed up the run.

Helpful Tips

• If a box is highlighted pink in copasi, there is an error with that information.
• Make sure the duration is long enough for the plot to oscillate if the plot is oscillating.

References

Copasi Website