Overview

VCell provides two styles of developing computational models:

BioModels
MathModels

Each uses a different methodology of model creation that best suits a given user's experience.

BioModel

A BioModel is a computational model defined and built through defining biological concepts within a graphical interface. BioModels consist of:

a model's biological system, including cellular structures, species and biochemical reactions ("Physiology")
one or more sets of constraints and conditions imposed on the model ("Application")

Each Application allows the user to define the quantitative values needed to define, run and visualize a Virtual Experiment (i.e. numerical simulation). Thus, an Application includes:

Geometry
Specifications (e.g. species, reactions)
Protocols (e.g. events, electrical mapping)
one or more Simulations
Parameter Estimation (if applicable)

MathModel

MathModels define Virtual Experiments using the Virtual Cell Markup Language (VCML). A MathModel consists of: