If you click on the Model branch of the object tree which was explained in the COPASI GUI Elements section, you activate the dialog that lets you specify certain parameters for your model like its name and the units that are to be used for time, volume and concentration quantities throughout the current model. You can also give a textual description of your model that is more expressive than reactions and equations. You could for example state which part of the metabolism the model describes (e.g. glycolysis) and add some references to articles related to the model. This will help others (and yourself) to understand and identify your models.

Dialog for general model settings

COPASI internally represents amounts of species by particle numbers. If a concentration has to be displayed or is needed for some output this is calculated from the particle number, the volume of the compartment the species belongs to and Avogadro's number ( ). Lets assume that you have set your default volume units to fl and your default substance units to nMol and species A is present in the amount of . Further assuming that the volume of the compartment containing A is set to (fl), A would be present in a concentration of . Since the default substance unit is set to nMol instead of Mole we have to multiply the result by . So COPASI would display a concentration of .

You are able to easily change the display between concentrations and particle numbers by selecting the drop down list in the menu bar at the top. COPASI, per default, displays the concentrations.

With the drop down list labeled Rate Law Interpretation you can specify how COPASI should interpret the kinetic rate laws you specify for your reactions. Per default, COPASI will interpret all rate laws as deterministic rate laws. Since COPASI allows the user to simulate a model either deterministically or stochastically, COPASI has to make some corrections to deterministic rate laws when using them for a stochastic simulation. This functionality sometimes interferes with rate laws that have been written for stochastic simulation and where the before mentioned corrections have already been made by the modeler. So if you have a model with rate laws that have been written be used in a stochastic simulation, you have to specify this by selecting stochastic from this drop down list. If you do this, COPASI will not apply any corrections to the rate laws specified in the model when doing stochastic simulation.

With the edit field labeled Time (s) under the text of Initial the user can tell COPASI to take the given value as the initial time for tasks like time course. For example, if you already have run a time course simulation for 1000 seconds in another program and your model values reflect the state of the model after those 1000 seconds of simulation, you can continue your simulation at that time point by setting the initial time to 1000. (This assumes that the models time units in the same widget are set to seconds.) If you run a time course simulation and check the update model box there, COPASI will automatically set the initial time to the end time of the time course simulation after running it. For more information on running time course simulation is COPASI see Time Course Simulation