Multiscale information modelling for heart morphogenesis, Abdulla IMEKO 2010
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Transcript of Multiscale information modelling for heart morphogenesis, Abdulla IMEKO 2010
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Multiscale Information Modelling for Heart Morphogenesis
Tariq Abdulla13th IMEKO TC1-TC7 Joint Symposium
02/09/2010
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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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Heart Morphogenesis: what happens?
Rear View
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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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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
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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 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
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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
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Questions?