BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology
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- dc.contributor.author Villaverde, Alejandro Fca
- dc.contributor.author Henriques, Davidca
- dc.contributor.author Smallbone, Kieranca
- dc.contributor.author Bongard, Sophiaca
- dc.contributor.author Schmid, Joachimca
- dc.contributor.author Cicin Sain, Damjanca
- dc.contributor.author Crombach, Antonca
- dc.contributor.author Sáez Rodríguez, Julioca
- dc.contributor.author Mauch, Klausca
- dc.contributor.author Balsa Canto, Evaca
- dc.contributor.author Mendes, Pedroca
- dc.contributor.author Jaeger, Johannes, 1973-ca
- dc.contributor.author Banga, Julio R.ca
- dc.date.accessioned 2015-11-09T15:50:01Z
- dc.date.available 2015-11-09T15:50:01Z
- dc.date.issued 2015
- 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. 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. 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/biopredynbenchmarks/.en
- dc.description.sponsorship This work was supported by the EU project “BioPreDyn” (EC FP7-KBBE-2011-5, grant number 289434).en
- dc.format.mimetype application/pdfca
- dc.identifier.citation Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D et al. BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology. 2015;9:8. DOI: 10.1186/s12918-015-0144-4ca
- dc.identifier.doi http://dx.doi.org/10.1186/s12918-015-0144-4
- dc.identifier.issn 1752-0509
- dc.identifier.uri http://hdl.handle.net/10230/25024
- dc.language.iso engca
- dc.publisher BioMed Centralca
- dc.relation.ispartof BMC Systems Biology. 2015;9:8
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/289434
- dc.rights © 2015 Villaverde et al.; licensee BioMed Central. 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.ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by/4.0ca
- dc.subject.keyword Dynamic modellingen
- dc.subject.keyword Model calibrationen
- dc.subject.keyword Parameter estimationen
- dc.subject.keyword Optimizationen
- dc.subject.keyword Benchmarksen
- dc.subject.keyword Large-scaleen
- dc.subject.keyword Metabolismen
- dc.subject.keyword Transcriptionen
- dc.subject.keyword Signal transductionen
- dc.subject.keyword Developmenten
- dc.subject.other Metabolismeca
- dc.title BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biologyca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca