Tutorial on CellML, OpenCOR, & the Physiome Model Repository

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Tutorial on CellML, OpenCOR, & the Physiome Model Repository

This tutorial shows you how to install and run the OpenCOR software [1], to author and edit CellML models [2] and to use the Physiome Model Repository (PMR) [3]. We start by giving a brief background on the VPH-Physiome project. We then create a simple model, save it as a CellML file and run model simulations. We next try opening existing CellML models, both from a local directory and from the Physiome Model Repository. The various features of CellML [4] and OpenCOR are then explained in the context of increasingly complex biological models. A simple linear first order ODE model and a nonlinear third order model are introduced. Ion channel gating models are used to introduce the way that CellML handles units, components, encapsulation groups and connections. More complex potassium and sodium ion channel models are then developed and subsequently imported into the Hodgkin-Huxley 1952 squid axon neural model using the CellML model import facility. The Noble 1962 model of a cardiac cell action potential is used to illustrate importing of units and parameters. The tutorial finishes with sections on model annotation and the facilities available on the CellML website and the Physiome Model Repository to support model development, including the links to bioinformatic databases. There is a strong emphasis in the tutorial on establishing ‘best practice’ in the creation of CellML models and using the PMR resources, particularly in relation to modular approaches (model hierarchies) and model annotation.

The PDF tutorial document is accessed via the download link below.

1. Garny A and Hunter PJ. OpenCOR: a modular and interoperable approach to computational biology. Frontiers in Physiology 6, 26 (2015).
2. Cuellar AA, Lloyd CM, Nielsen PF, Halstead MDB, Bullivant DP, Nickerson DP and Hunter PJ. An overview of CellML 1.1, a biological model description language. SIMULATION: Transactions of the Society for Modeling and Simulation 79(12):740-747, 2003
3. Yu T et al. The Physiome Model Repository 2. Bioinformatics 27, 743–744, 2011.
4. Hunter PJ. The IUPS Physiome Project: a framework for computational physiology. Progress in Biophysics and Molecular Biology 85, 551–569, 2004.