Step-by-Step Example

To show SBML support in Morpheus as of version 2.1 in practice, we give a step-by-step example of how to download, import and extend an SBML model. 1. Get an SBML Model from BioModels First, we browse the BioModels model repository and select a model.

Coupled ODE Lattice: Lateral Signaling

Morpheus Model ID: M0004 Open in Morpheus History Persistent Identifier Use this permanent link to cite or share this Morpheus model: Copy Introduction This example model cell fate decisions during early patterning of the pancreas (de Back et al.


Let’s go through an example. We’ll construct a model in which an intracellular cell cycle network (ODE) regulates the division of motile cells which (CPM) release a diffusive cytokine (PDE) which, in turn, controls the cell cycle (ODE).

Relative Time Scales

At this point, you may be asking yourself: ‘All nice and well, but how can I control the relative time scales between the various models?’ And I’d respond:

Equation vs. Rule vs. Function

“What is the difference between an Equation, a Rule and a Function ?” All three are algebraic expressions, however: An Equation is an equality relation the simulator is expected to keep throughout simulation time.