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Multiscale Information Modelling for Heart Morphogenesis

Multiscale Information Modelling for Heart Morphogenesis. Tariq Abdulla 13 th 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.

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Multiscale Information Modelling for Heart Morphogenesis

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  1. Multiscale Information Modelling for Heart Morphogenesis Tariq Abdulla 13th IMEKO TC1-TC7 Joint Symposium 02/09/2010

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

  3. Heart Morphogenesis: what happens? Rear View

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

  5. 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

  6. Basic Formal Ontology Morphogenesis, Death, Development, Signaling, Growth Cell, Protein, Eye, Endocardial Cushion Red, Hypertrophic, Discontinuous

  7. Mammalian Phenotype Ontology

  8. Phenotype and Trait Ontology (PATO)

  9. Human Developmental Anatomy (EHDA)

  10. Post-composition

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

  12. 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

  13. 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

  14. Questions?

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