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MODEL1002160000 - Gomez-Cabrero2011_Atherogenesis

 

The following model is part of the non-curated branch of BioModels Database. While the syntax of the model has been verified, its semantics remains unchecked. Any annotation present in the models is not a product of BioModels' annotators. We are doing our best to incorporate this model into the curated branch as soon as possible. In the meantime, we display only limited metadata here. For further information about the model, please download the SBML file.


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Reference Publication
Publication ID: 22670212
Gomez-Cabrero D, Compte A, Tegner J.
Workflow for generating competing hypothesis from models with parameter uncertainty.
Interface Focus 2011 Jun; 1(3): 438-449
Department of Medicine, Karolinska Institutet , Unit of Computational Medicine, Centre for Molecular Medicine , Solna, Stockholm , Sweden.  [more]
Model
Original Model: Atherosclerosis Model
Submitter: David Gomez-Cabrero
Submission Date: 16 Feb 2010 17:38:08 UTC
Last Modification Date: 16 Feb 2012 14:30:03 UTC
Creation Date: 16 Feb 2012 12:16:57 UTC
Encoders:
bqbiol:isVersionOf Gene Ontology response to cholesterol
Experimental Factor Ontology 0003914
bqbiol:hasTaxon Taxonomy Homo sapiens
Notes

This model is from the article:
Workflow for generating competing hypothesis from models with parameter uncertainty.
David Gomez-Cabrero, Albert Compte and Jesper Tegner Interface Focus 6 June 2011 vol. 1 no. 3 438-449; doi: 10.1098/rsfs.2011.0015
Abstract:
Mathematical models are increasingly used in life sciences. However, contrary to other disciplines, biological models are typically over-parametrized and loosely constrained by scarce experimental data and prior knowledge. Recent efforts on analysis of complex models have focused on isolated aspects without considering an integrated approach-ranging from model building to derivation of predictive experiments and refutation or validation of robust model behaviours. Here, we develop such an integrative workflow, a sequence of actions expanding upon current efforts with the purpose of setting the stage for a methodology facilitating an extraction of core behaviours and competing mechanistic hypothesis residing within underdetermined models. To this end, we make use of optimization search algorithms, statistical (machine-learning) classification techniques and cluster-based analysis of the state variables' dynamics and their corresponding parameter sets. We apply the workflow to a mathematical model of fat accumulation in the arterial wall (atherogenesis), a complex phenomena with limited quantitative understanding, thus leading to a model plagued with inherent uncertainty. We find that the mathematical atherogenesis model can still be understood in terms of a few key behaviours despite the large number of parameters. This result enabled us to derive distinct mechanistic predictions from the model despite the lack of confidence in the model parameters. We conclude that building integrative workflows enable investigators to embrace modelling of complex biological processes despite uncertainty in parameters.

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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

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