PhysioML

PhysioML is an Extensible Marup Language (XML) for physiological modeling. It has tags to describe the model parameters and variables and associated units. Initial conditions can be specified as well. Finally it has tags to describe the user interface: placement of parameters and variables on the interface and graphical representation of the results of the simulation.

At the moment there is no means to incorporate the model description (functions) in the XML, although eventually it is envisioned that that will be accomplished using MathML.

Here is a description of the main tags used in PhysioML.

display user interface definition
panel defines a window panel
image URL for screen image
label screen display

model model defintion
variable define variable (name, initial value)
transfer transfer matrix
box define a compartment
boxstuff image displayed in compartment
boxtrigger threshold for compartment

Examples of PhysioML model descriptions developed by Ming Gu, at the time a student intern from Grinnell College.

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display		user interface definition
	panel	defines a window panel
	image	URL for screen image
	label	screen display
model		model defintion
	variable	define variable (name, initial value)
	transfer	transfer matrix
	box	define a compartment
	boxstuff	image displayed in compartment
	boxtrigger	threshold for compartment