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Por favor, use este identificador para citar o enlazar a este item: http://hdl.handle.net/10261/114011
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dc.contributor.authorVillaverde, A. F.-
dc.contributor.authorHenriques, David-
dc.contributor.authorBalsa-Canto, Eva-
dc.contributor.authorBanga, Julio R.-
dc.date.accessioned2015-04-22T12:16:49Z-
dc.date.available2015-04-22T12:16:49Z-
dc.date.issued2015-02-20-
dc.identifier.citationBMC Systems Biology 9:8 (2015)es_ES
dc.identifier.urihttp://hdl.handle.net/10261/114011-
dc.description15 páginas, 2 tablas, 6 figuras.-- Alejandro F. Villaverde ... et al.-- This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.es_ES
dc.description.abstract[Background] Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model calibration) and optimal experimental design are particularly challenging. The community has already developed many methods and software packages which aim to facilitate these tasks. However, there is a lack of suitable benchmark problems which allow a fair and systematic evaluation and comparison of these contributions.es_ES
dc.description.abstract[Results] Here we present BioPreDyn-bench, a set of challenging parameter estimation problems which aspire to serve as reference test cases in this area. This set comprises six problems including medium and large-scale kinetic models of the bacterium E. coli, baker’s yeast S. cerevisiae, the vinegar fly D. melanogaster, Chinese Hamster Ovary cells, and a generic signal transduction network. The level of description includes metabolism, transcription, signal transduction, and development. For each problem we provide (i) a basic description and formulation, (ii) implementations ready-to-run in several formats, (iii) computational results obtained with specific solvers, (iv) a basic analysis and interpretation.-
dc.description.abstract[Conclusions] This suite of benchmark problems can be readily used to evaluate and compare parameter estimation methods. Further, it can also be used to build test problems for sensitivity and identifiability analysis, model reduction and optimal experimental design methods. The suite, including codes and documentation, can be freely downloaded from the BioPreDyn-bench website, https://​sites.​google.​com/​site/​biopredynbenchma​rks/​.-
dc.description.sponsorshipThis work was supported by the EU project “BioPreDyn” (EC FP7-KBBE-2011-5, grant number 289434). We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).es_ES
dc.language.isoenges_ES
dc.publisherBioMed Centrales_ES
dc.relationinfo:eu-repo/grantAgreement/EC/FP7/289434-
dc.relation.isversionofPublisher's versiones_ES
dc.rightsopenAccesses_ES
dc.subjectDynamic modellinges_ES
dc.subjectModel calibrationes_ES
dc.subjectParameter estimationes_ES
dc.subjectOptimizationes_ES
dc.subjectBenchmarkses_ES
dc.subjectLarge-scalees_ES
dc.subjectMetabolismes_ES
dc.subjectTranscriptiones_ES
dc.subjectSignal transductiones_ES
dc.subjectDevelopmentes_ES
dc.titleBioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biologyes_ES
dc.typeartículoes_ES
dc.identifier.doi10.1186/s12918-015-0144-4-
dc.description.peerreviewedPeer reviewedes_ES
dc.relation.publisherversionhttp://dx.doi.org/10.1186/s12918-015-0144-4es_ES
dc.identifier.e-issn1752-0509-
dc.rights.licensehttp://creativecommons.org/licenses/by/4.0es_ES
dc.contributor.funderEuropean Commission-
dc.contributor.funderCSIC - Unidad de Recursos de Información Científica para la Investigación (URICI)-
dc.relation.csicSíes_ES
dc.identifier.funderhttp://dx.doi.org/10.13039/501100000780es_ES
dc.identifier.pmid25880925-
dc.type.coarhttp://purl.org/coar/resource_type/c_6501es_ES
item.grantfulltextopen-
item.cerifentitytypePublications-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.languageiso639-1en-
item.fulltextWith Fulltext-
item.openairetypeartículo-
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