Using a simple model to verify correct ProcessDB installation:

Log on to ProcessDB at www.integrativebioinformatics.com. Enter your login name and password. Select the Diagrams radio button. Click Launch.

Confirm your database connection to the server by clicking OK.

You will then be connected and the Database pane will be populated with a list of currently available models.

Double-click catalytic subunit cAPK to load the model diagram.

A Model Realization (MR) is a quantitative model corresponding to the diagram. If necessary, expand the directory tree for catalytic subunit cAPK. Then double-click MR242 to open its diagram.

Later you can come back and explore the model realization properties, but for this installation verification test, just click "MOE 334" to open the corresponding Model of Experiment. This take you to the Model of Experiments (MOE) screen when the quantitative model corresponding to the diagram has been combined with a simple experimental protocol involving Fluorescence Recovery After Photobleaching (FRAP).

Again, you can return later to explore the features of this screen, but to continue the installation verification, just right-click on the MOE and select Export to Solver. This opens the Launch Solver dialog.

The only thing you must do here is enter a file name for the exported Madonna file that encodes the model of experiments (MOE334).

Click the Launch Solver button. This converts the quantitative model and its associated experimental protocols to a native Berkeley Madonna file, downloads the file to your computer, and launches it in your locally installed copy of Berkeley Madonna (available at www.berkeleymadonna.com).

To check that the installation is complete, you can run the model and plot its solution. First define the graph you want to see by clicking the Graph menu and selecting New Window.

Double click the gray graph area to open the select variables dialog. Scroll down the variable list to the bottom.

Double-click "nuclearFRAP" and "Fnucleus_81" to put these variables on the Y-axis.

Click OK to accept this graph definition.

Click the Run button (upper left of graph window) to see the model solution for the FRAP experiment.

Congratulations! If you see this graph, ProcessDB and Berkeley Madonna are installed and working properly. You've also stepped through the basics of our software and you're ready to begin your own project.