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
- Click the "Model" tab from the side of the home page.
- Rename the model.
- Adjust the units according to your needs.
- Write any comments in the large text box
- Choose the biochemical tab from the side underneath the "Model" tab. Choose "Compartment" from the drop down list.
- Rename the compartment and and double click on the compartment.
- Once the compartment is adjusted to your needs, click on the "Reactions" tab.
- 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.
- Press the new button to create a new reaction.
- Adjust rate law according to your needs.
- If the rate law you need is not in the list, select the "New Rate Law" button.
- Enter the mathematical formula into the "Formula" box.
- Press the "Commit" button when finished with the rate law.
- Click the "Reactions" tab to see a summary of the information you have entered.
- Select the "Species" tab to see all of the species.
- Double-click on a species to edit the simulation type, initial concentration, rate and reactions for that species.
- Select "Parameter of Review" from the side tabs to review all of the information.
- Select the "File" tab to save the model.
Time Course Simulation
Basic Plotting
Steady State
Reports
Parameter Scanning and Sampling
Metabolic Control Analysis
Helpful Tips
- If a box is highlighted pink in copasi, there is an error with that information.