Difference between revisions of "Copasi"
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Line 99: | Line 99: | ||
* If a box is highlighted pink in copasi, there is an error with that information. | * 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. | * Make sure the duration is long enough for the plot to oscillate if the plot is oscillating. | ||
+ | * For Steady-State, if you only want to use one method, the other methods can be set to 0. | ||
==References== | ==References== | ||
[http://copasi.org/Support/Video_Tutorials/ Copasi Website] | [http://copasi.org/Support/Video_Tutorials/ Copasi Website] |
Revision as of 18:31, 1 July 2019
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
A model must be created before creating a time course simulation.
- Select the "File" tab and then click "file" to load a model.
- Select the triangle next to "Tasks" to expand the drop-down menu.
- Select "Time Course" then hit "Run."
- 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...
- Select the "Output Assistant" button on the the "Time Course" page.
- Select the pre-designed plot value and click "Create."
- Check the "Active" box to make sure the plot appears next time the program is run.
- 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.
Basic Plotting
A model must be created before creating a plot.
- Load a model.
- Run a Time Course of the model.
- Select "Output Assistant."
- Select the type of plot desired and press "Create."
- Click "Run."
Phase Space Diagram
Diagram of one variable vs. the other where time is no longer explicit.
- Click the "Output Specifications" tab.
- Select "Plots" from the drop down menu.
- Rename the plot and select "New Curve."
- Define the X axis as a "Transient Concentration" of one of the species.
- Define the Y axis as a "Transient Concentration" of the other species.
- Change the title of the curve and press "Commit."
- Run a time course of the model.
Histogram
- Click the "Output Specifications" tab.
- Select "Plots" from the drop down menu.
- Rename the plot and select "New Histogram."
- Choose the variable from "Species" --> "Transient Concentrations."
- Choose the increment or "bin size."
- Change the title of the histogram and press "Commit."
- Run a time course of the model.
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.
- Make sure the duration is long enough for the plot to oscillate if the plot is oscillating.
- For Steady-State, if you only want to use one method, the other methods can be set to 0.