Step by step model
Getting Started with a Sample Model
Log on to ProcessDB. Enter your login name and password. Click Launch. You will then be connected and the Database pane will be populated with a list of currently available models. In the Display pulldown list below the models, select "Public". This will show you all public models in our database.
Scroll down to the model named "catalytic subunit cAPK", which has a model ID of 375. Double click the model 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 MR241 to open its diagram.
Later you can come back and explore the model realization properties, but for this installation verification test, just click "MOE 309" to open the corresponding Model of Experiment. This takes 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 Solve. You will be prompted to select a parameter set; select parameter set zero and click OK. This will launch the parameter explorer with an initial solution.
If you want to test your model by running it in Berkeley Madonna, right click on the MOE and select "Export to Solver". Enter a file name for the exported Madonna file that encodes the model of experiments (MOE309).
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.
