List FAQs
Questions
Answers
Q:
What is the relation between COPASI and Gepasi?
A:
COPASI is based on Gepasi, however most of the program has been rewritten. In particular the front-end has been entirely rewritten with the QT toolkit and is now portable across many computer architectures. COPASI is able to read Gepasi files, so it is backwards compatible.
Q:
Why do the results for Stability Analysis differ in COPASI and Gepasi?
A:
In systems in which Mass Conservation occurs the Jacobian is incorrectly calculated in Gepasi. This problem only effects the stability analysis and does not effect the dynamics of the system. A more detailed discussion of how COPASI calculates the Jacobian can be found in:
Stability Analysis
Q:
Is the COPASI file format documented?
Q:
Why are some rate laws in SBML files exported by COPASI multiplied by the compartment volume?
A:
This is done to convert from traditional rate laws, which specify concentration change, to the SBML format, which requires the kinetic law to specify particle number change. A more detailed explanation may be found in:
COPASI's and SBML's Kinetic Law Representation
Q:
Why does COPASI refuse to import an SBML file it just exported?
A:
COPASI version prior and including COPASI RC1 contain a bug in the SBML export. If the user chooses to export a model that has the substance units set to "#" (items), COPASI will export an SBML file where the scale of the substance unit is set to 1 instead of 0.
Since COPASI does not do SBML unit conversion upon import yet, it will refuse to read those files.
In order to correct such a file, open it in a text editor and change the scale on the substance unit (in the <ListOfUnitDefinitions> tag) from 1 to 0.
Versions of COPASI newer than RC1 will point you to this FAQ if they encounter such a file.
Q:
Does COPASI support fractional stochiometries?
A:
Yes, COPASI allows the user to enter non integer numbers for stoichiometries. However, it is not possible to use a quotient like 1/4 in a reaction instead one needs to write 0.25.
Q:
How can I change the starting values for Optimization or Parameter Estimation parameters, when I am stuck in a local minimum?
A:
In the Optimization or Parameter Estimation widget you may select a any combination of parameters. If you are stuck in a local minimum it is best to select all parameters by first selecting the first and then clicking on the last while pressing the shift key. After you have selected the parameters you would like to change use the tool button to the right of the "Start Value" and press "Random". You may also revert to the current model parameters or change the start values individually.
Q:
Do I have to reference COPASI in a scientific publication and if how do I do it?
A:
Yes, you have to reference COPASI in a scientific pulication if you used COPASI to optain your results. The correct way is to use the reference below.
Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., and Kummer, U. (2006). COPASI — a COmplex PAthway SImulator. Bioinformatics 22, 3067-74.
Q:
I have developed an application using COPASI source code. Is it possible to distribute my software?
A:
Yes, you may distribute any software you developed with COPASI source code as long as you adhere to the COPASI
license. We suggest that you read the article
Redistribution of 3rd Party Software, which clarifies some of the main issues.
Q:
How do I add the total amount of substance of a mass conservation law (moiety) to a report or mathematical expression?
A:
COPASI does not know about the amount of substance for a mass conservation law. However, you may select the value of a moiety in the expert mode of the selection widget. This value is the total particle number of the mass conversation law, i.e., the conserved value. You can convert this value with the help of a global quantity of type assignment to your desired units or to concentration.
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