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Metabolic Model Generalization

hal.structure.identifierModels and Algorithms for the Genome [ MAGNOME]
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
dc.contributor.authorZHUKOVA, Anna
dc.date.accessioned2024-04-15T09:43:03Z
dc.date.available2024-04-15T09:43:03Z
dc.date.conference2013-06-03
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/197731
dc.description.abstractEnGenome-scale metabolic models for new organisms include thousands of reactions that are generated automatically: by inferring them from databases of reactions and pathways, existing models for similar organisms, etc. This process includes several iterations of the draft model analysis, error detection, and improvement; starting from more general issues and going deeper into details. Especially in the first iterations model evaluation by a human expert is important. But genome-scale models are targeted for computer simulation and analysis, and are too detailed and complicated to be easily understood by a human. For example, in the beta-oxidation of fatty acids pathway, a reaction missing for a particular fatty-acyl-CoA type (e.g. decanoyl-CoA) is a more specific issue than missing a whole enoyl-CoA hydratase step (which could happen if the corresponding enzyme is not found). But the abundance of reactions in the model (e.g. those corresponding to other beta-oxidation steps and presented for each of the different types of fatty-acyls-CoA) may hide this fact from the human. That is why we developed a method for knowledge-based scaling of metabolic models, providing a higher-level view of a model, keeping its essential structure and omitting the details.
dc.language.isoen
dc.typeAutre communication scientifique (congrès sans actes - poster - séminaire...)
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
bordeaux.hal.laboratoriesLaboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800*
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionBordeaux INP
bordeaux.institutionCNRS
bordeaux.conference.titleInternational Course in Yeast Systems Biology
bordeaux.countrySE
bordeaux.conference.cityGothenburg
bordeaux.peerReviewedoui
hal.identifierhal-00859442
hal.version1
hal.conference.end2013-06-10
hal.popularnon
hal.audienceInternationale
dc.title.itMetabolic Model Generalization
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-00859442v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=ZHUKOVA,%20Anna&rft.genre=conference


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