Generated Math

The Virtual Cell automatically converts the biological description defined in a BioModel into a corresponding mathematical system of equations (e.g. ordinary and/or partial differential equations). Once an application is created in a BioModel, The Virtual Cell automatically generates the Math Description upon saving a model or running a simulation.

Choose View:

• Math Equations button The Equation Viewer displays all the equations generated from the geometric mapping of the model. It is displayed in a tree-structured directory so you can view the math description's defined constants, functions, volume domains, and membrane domains. The Show parameter: Name/Value radio buttons select whether math parameters are displayed by name or associated value (e.g named constants).
• Math Description Language button The Equation Viewer displays the math in VCell Markup Language (vcml) format. This all in one representation is the same used when defining MathModels. Although the text in this view is not editable a search tool is provided at the bottom of the panel to quickly highlight fragments of text to aid in locating information.
• Refresh Math button The math is not constantly updated as you create your model (e.g. add species, edit geometry, etc...). Press the "Refresh Math" button to view a fully updated view of the math. (Note: math is refreshed automatically when a model is saved or a simulation is run.)
• Create Math Model button Click this button to create a math model by using the math description generated in the current BioModel application. A new window will open to load the newly created MathModel. The new MathModel is editable as a vcml document and is completely independent of the original BioModel application. Any changes will not effect the original.
• Note: Math Equations View and Math Description Language View are for viewing purposes only. Nothing can be changed or edited in either view.