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CPP

Seminar

CellML language and tools supporting the cardiac physiome

Nielsen, P (Auckland)
Friday 24 July 2009, 10:45-11:00

Meeting Room 2, CMS

Abstract

The CellML language is an established standard designed to encode lumped parameter mathematical models of biological processes. CellML supports the sharing of models by including information about model structure, mathematics, and metadata. It makes use of existing standards for encoding mathematics (Content MathML ) and representing metadata (Resource Description Framework ). Model reuse is facilitated by the element, enabling new models to be constructed by combining existing models to form model hierarchies. Almost 400 CellML models from peer-reviewed publications are currently available in the Physiome Model Repository . The repository contains models of biological processes ranging from gene regulation, ion channel electrophysiology, signal transduction, and metabolic pathways to bioengineering constitutive laws and larger scale systems physiology processes. A major focus of the CellML effort involves the development of tools to facilitate the curation and annotation of models within the repository. The aim of this effort is to link entities and processes described in CellML models to their corresponding definitions in, for example, biological and biophysical ontologies. Doing so enables richer searching, automatic rule checking, and the ability to produce biologically meaningful visual representations of models.

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