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Newcastle University

GOLD MEDAL WINNER 2008

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Introduction to CellML

The programming language chosen for modelling was CellML (CellML, 2003). CellML has mainly been used to model biological pathways and the molecules involved in these (CellML model repository, 2008). CellML models are based on a modular structure, which is appropriate when modelling the behaviour of biological parts (Rouilly, et al., 2007). CellML is accepted as a standard by members of the Physiome project (The Physiome Project, 2006).

CellML looks to model the mathematics behind this system (Schilstra, et al., 2006). This is beneficial when capturing information but the implications are that the mathematics behind the behaviour must be clearly defined and understood. An aim of CellML was to overcome some of the limitations of SBML (Lloyd, et al., 2004). Particularly, the modularity of CellML allows it to be utilised on a large scale. Whole models or components of parts of models can be integrated successfully to produce larger models whilst maintaining the language structure (Lloyd, et al., 2004).

Model generation and simulation

Modelling in the CellML language was carried out in the Cellular Open Resource (COR) (Garny, et al., 2003). COR is a free resource available in Microsoft Windows. This provides an editor to write in COR language, which has easier readability than the mark-up language. The text is converted into CELLML by the program, which complies and runs models as they are created. Once models were generated in COR, they were loaded into PCEnv for simulation.

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+==Introduction to CellML==
+The programming language chosen for modelling was CellML (CellML, 2003). CellML has mainly been used to model biological pathways and the molecules involved in these (CellML model repository, 2008).  CellML models are based on a modular structure, which is appropriate when modelling the behaviour of biological parts (Rouilly, et al., 2007).  CellML is accepted as a standard by members of the Physiome project (The Physiome Project, 2006).
+CellML looks to model the mathematics behind this system (Schilstra, et al., 2006).  This is beneficial when capturing information but the implications are that the mathematics behind the behaviour must be clearly defined and understood. An aim of CellML was to overcome some of the limitations of SBML (Lloyd, et al., 2004). Particularly, the modularity of CellML allows it to be utilised on a large scale.  Whole models or components of parts of models can be integrated successfully to produce larger models whilst maintaining the language structure (Lloyd, et al., 2004).
+==Model generation and simulation==
+Modelling in the CellML language was carried out in the Cellular Open Resource (COR) (Garny, et al., 2003).  COR is a free resource available in Microsoft Windows.  This provides an editor to write in COR language, which has easier readability than the mark-up language. The text is converted into CELLML by the program, which complies and runs models as they are created. Once models were generated in COR, they were loaded into PCEnv for simulation.