Morpheus

Multiscale modeling often involves the integration of existing models. For example, combining an existing cell-based CPM model (CPM.xml) with an ODE model (ODE.xml) regulating, say, the cell cycle of each cell.

Morpheus lets you copy and paste parts of a model between different documents.

This allows you to copy the System from ODE.xml containing the ODE equations and parameters (right-click → Copy). And then paste it inside the CellType element in the CPM.xml document (right-click → Copy).

You can paste elements only in appropriate places, otherwise it will be greyed out. This ensures validity of the model.

All copied elements are shown in the ClipBoard.

Testing models frequently involves switch things on and off to observe their effects. Morpheus allow you to do this without losing your contents by using Right-Click → Disable. The selected element and everything below it will be commented out in the XML file.

This mechanism also allows you to compare submodels. If you want to compare two versions of an ODE system, you can have both System elements in your model, with one disabled. Switching ODE systems then only involves enabling/disabling both. This provides a quick way to compare submodels within exactly the same context.

During model construction and testing, graphical output and visual feedback is important to debugging, spot erros and guide development.

Yet, during serious simulation (production work), you do not want to be bothered by pop-up windows and graphics that slow down simulation.

Morpheus therefore distuingishes between an interactive and local simulation execution mode.

Overview