General Model Settings

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.



COPASI internally represents amounts of species by particle numbers. If a concentration must be displayed or is needed for output, COPASI calculates it from the particle number, the volume of the compartment the species belongs to, and Avogadro's number $6.022140857 \cdot {10}^{23}\,\frac{\mbox{particles}}{\mbox{mol}}$. Suppose your default volume units are $fl$ and your default substance units are $nmol$, and species $A$ has an amount of $1.0 \cdot {10}^{15}\,\mbox{particles}$. If the compartment containing $A$ has a volume of $1.0~fl$, the concentration will be $\frac{1.0 \cdot {10}^{15} \, \mbox{particles}}{6.022140857 \cdot {10}^{23}\,\frac{\mbox{particles}}{\mbox{mol}}\,\cdot 1.0\, \mbox{fl}}$. Since the default substance unit is nmol (not mol), multiply the result by $1.0 \cdot {10}^{9}$. COPASI would therefore display a concentration of $1.661\,\frac{\mbox{nmol}}{\mbox{fl}}$.

You can easily change the display between concentrations and particle numbers by selecting the drop-down list in the menu bar at the top. By default, COPASI displays concentrations.


The checkbox labeled "Rate Law Interpretation" lets you specify how COPASI should interpret the kinetic rate laws for your reactions. By default, COPASI interprets all rate laws as deterministic rate laws. Since COPASI allows simulation either deterministically or stochastically, it must make corrections to deterministic rate laws when using them for stochastic simulation. Sometimes, rate laws have already had these corrections applied by the modeler for stochastic simulation. If this is the case, you should uncheck the checkbox. With this setting, COPASI will not apply further corrections to the rate laws in the model during stochastic simulations.

In the field labeled `Initial Time` the user can tell COPASI to take the given value as the initial time for tasks like time course. This field is only enabled for editing for non-autonomous models, i.e., models which use the value of time explicitly in an ODE, an assignment, a rate law, or an event. COPASI automatically detects whether a model is non-autonomous. If you have a non-autonomous model you can set the start time of a time course by adjusting this field. For more information on running time course simulation is COPASI see Time Course Simulation.

The field `Time` displays the current time of the model (e.g. the end point of the simulation last run).