Multiscale information modelling for heart morphogenesis, Abdulla IMEKO 2010

Multiscale Information Modelling for Heart Morphogenesis

Tariq Abdulla13th IMEKO TC1-TC7 Joint Symposium

02/09/2010

Outline

Heart Morphogenesis – what happens? Information Modelling – what do we mean? Multiscale Modelling - how do we do it? Conclusion and Future Work

Heart Morphogenesis: what happens?

Rear View

Outline

Heart Morphogenesis – what happens? Information Modelling – what do we mean? Multiscale Modelling - how do we do it? Conclusion and Future Work

Information Modelling – what do we mean?

The concepts, relationships and constraints in a domain - these are ontologies

Use the same information models across multiple data sources

Thus we know how one piece of information relates to another

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Basic Formal Ontology

Cell, Protein, Eye,Endocardial Cushion

Red, Hypertrophic, Discontinuous

Morphogenesis, Death,

Development,Signaling,Growth

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Mammalian Phenotype Ontology

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Phenotype and Trait Ontology (PATO)

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Human Developmental Anatomy(EHDA)

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Post-composition

Outline

Heart Morphogenesis – what happens? Information Modelling – what do we mean? Multiscale Modelling - how do we do it? Conclusion and Future Work

Multiscale Modelling – how do we do it?

Different types of computational model are suitable for different levels of biological scale

E.g. Biochemical reactions can be represented as networks or ODEs. Cellular behaviour can be modelled with agent based models.

Use models at one level of scale, to pass information to models at another level of scale

Conclusion and Future Work

Gene to phenotype annotation tends to use a surgical or anatomical perspective – but we know very little about mechanism or causes

Post-compositional annotation allows a link between multiscale measurement and multiscale modelling

Future plans include scale-linking between SBML models and agent based models, for simulation of Endocardial Cushion Growth

Questions?