Parasim GUI Tutorial
This page describes how to create a parasim project and perform some basic analysis. It does not include creating properties -- signal temporal logic formulae (see Experiment File Format for their definition) or creating model in SBML.
For the purposes of this tutorial we will re-analyse SIR model (included in experiments). We will need:
Execute parasim (for example using parasim-gui.sh script). Two windows should appear:
- reduced project manager window (left) -- only toolbar and menu
- logger window (right) -- this one is unimportant right now
Open "new project" dialog either clicking on "new" button (with document icon), using menu ("Project -> New") or pressing "CTRL+N".
In the upper file chooser dialog enter the parasim experiments folder. Then enter "SIR" folder, change file filter to "XML files" and choose the file sir.model.xml. Create a new empty folder and select it in the lower file chooser. Click "OK". After a moment, an empty project should open in the project manager window.
To perform an analysis, it is necessary to import properties and create configurations
First, let us import some properties. Click on the "Import" button in the "Properties" panel (upper right corner of project manager window). The following dialog should appear:
Enter parasim experiments folder, the "SIR" folder and choose outbreak5.formula.xml. Rename it to "outbreak5" in the text area at the bottom of dialog (you may rename it anytime in the "Properties" panel) and click "OK".
Repeat this process with outbreakM50.formula.xml (rename it to "outbreakM50").
The "Properties" panel should now contain two properties.
When you hover over them, you may find out, what they mean (note, 5 is itial value of infected).
| Property | Formula | Explanation |
|---|---|---|
| outbreak5 | F[1,5](I>5) |
sometime between 1 s and 5 s there are more than 5 infected |
| outbreakM50 | F[1,5](I>50) |
sometime between 1 s and 5 s there are more than 50 infected |
Select the first property and click "Use". It should appear in the "Experiment" panel (upper right corner of project manager window). If it does not, we will correct it later.
Next, let us have a look at the "Simulation" panel (lower left corner of the project manager window).
The default values seem to be pretty decent. Simulation Start should generally be 0 and 100 s (1E2) for Simulation End should be ok too (note: the actual simulation length depends on used property). We do not know much about the model, so leave Time Step and **Maximal relative error" at 0.1 (1E-1). Should you need to simulate the model more precisely, you may change them later. The same goes for Abs error (maximum absolute error).
Now, as for Minimum and Maximum bounds for each model variable (S, I, R), we note that there are 100 individuals in the model as a whole, none die and none are born. Therefore, the minima should be 0 and maxima 100.
Click on "Save" button in the "Simulation" panel and choose a name for this configuration. Then click on "Use" button. This configuration should appear in the "Experiment" panel.