{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T08:22:54Z","timestamp":1774426974477,"version":"3.50.1"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T00:00:00Z","timestamp":1546905600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Ministry of Education and Research","award":["FKZ 031L0080"],"award-info":[{"award-number":["FKZ 031L0080"]}]},{"name":"SYS-Stomach","award":["01ZX1310B"],"award-info":[{"award-number":["01ZX1310B"]}]},{"name":"INCOME","award":["FKZ 01ZX1705A"],"award-info":[{"award-number":["FKZ 01ZX1705A"]}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["TRR179"],"award-info":[{"award-number":["TRR179"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["INST 35\/1134-1 FUGG"],"award-info":[{"award-number":["INST 35\/1134-1 FUGG"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Dynamic models are used in systems biology to study and understand cellular processes like gene regulation or signal transduction. Frequently, ordinary differential equation (ODE) models are used to model the time and dose dependency of the abundances of molecular compounds as well as interactions and translocations. A multitude of computational approaches, e.g. for parameter estimation or uncertainty analysis have been developed within recent years. However, many of these approaches lack proper testing in application settings because a comprehensive set of benchmark problems is yet missing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a collection of 20 benchmark problems in order to evaluate new and existing methodologies, where an ODE model with corresponding experimental data is referred to as problem. In addition to the equations of the dynamical system, the benchmark collection provides observation functions as well as assumptions about measurement noise distributions and parameters. The presented benchmark models comprise problems of different size, complexity and numerical demands. Important characteristics of the models and methodological requirements are summarized, estimated parameters are provided, and some example studies were performed for illustrating the capabilities of the presented benchmark collection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The models are provided in several standardized formats, including an easy-to-use human readable form and machine-readable SBML files. The data is provided as Excel sheets. All files are available at https:\/\/github.com\/Benchmarking-Initiative\/Benchmark-Models, including step-by-step explanations and MATLAB code to process and simulate the models.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz020","type":"journal-article","created":{"date-parts":[[2019,1,6]],"date-time":"2019-01-06T15:07:21Z","timestamp":1546787241000},"page":"3073-3082","source":"Crossref","is-referenced-by-count":84,"title":["Benchmark problems for dynamic modeling of intracellular processes"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0577-2432","authenticated-orcid":false,"given":"Helge","family":"Hass","sequence":"first","affiliation":[{"name":"Center for Systems Biology (ZBSA), University of Freiburg , Freiburg 79104, Germany"},{"name":"Institute of Physics, University of Freiburg , Freiburg 79104, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3680-0627","authenticated-orcid":false,"given":"Carolin","family":"Loos","sequence":"additional","affiliation":[{"name":"Helmholtz Zentrum M\u00fcnchen \u2013 German Research Center for Environmental Health, Institute of Computational Biology , Neuherberg 85764, Germany"},{"name":"Technische Universit\u00e4t M\u00fcnchen, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems , Garching 85748, Germany"}]},{"given":"Elba","family":"Raim\u00fandez-\u00c1lvarez","sequence":"additional","affiliation":[{"name":"Helmholtz Zentrum M\u00fcnchen \u2013 German Research Center for Environmental Health, Institute of Computational Biology , Neuherberg 85764, Germany"},{"name":"Technische Universit\u00e4t M\u00fcnchen, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems , Garching 85748, Germany"}]},{"given":"Jens","family":"Timmer","sequence":"additional","affiliation":[{"name":"Center for Systems Biology (ZBSA), University of Freiburg , Freiburg 79104, Germany"},{"name":"Institute of Physics, University of Freiburg , Freiburg 79104, Germany"},{"name":"Center for Data Analysis and Modelling (FDM), University of Freiburg , Freiburg 79104, Germany"},{"name":"BIOSS Centre for Biological Signalling Studies, University of Freiburg , Freiburg 79104, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4935-3312","authenticated-orcid":false,"given":"Jan","family":"Hasenauer","sequence":"additional","affiliation":[{"name":"Helmholtz Zentrum M\u00fcnchen \u2013 German Research Center for Environmental Health, Institute of Computational Biology , Neuherberg 85764, Germany"},{"name":"Technische Universit\u00e4t M\u00fcnchen, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems , Garching 85748, Germany"}]},{"given":"Clemens","family":"Kreutz","sequence":"additional","affiliation":[{"name":"Center for Systems Biology (ZBSA), University of Freiburg , Freiburg 79104, Germany"},{"name":"Institute of Physics, University of Freiburg , Freiburg 79104, Germany"},{"name":"Center for Data Analysis and Modelling (FDM), University of Freiburg , Freiburg 79104, Germany"}]}],"member":"286","published-online":{"date-parts":[[2019,1,8]]},"reference":[{"key":"2023062711312073100_btz020-B1","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1039\/b918098b","article-title":"Sloppy models, parameter uncertainty, and the role of experimental design","volume":"6","author":"Apgar","year":"2010","journal-title":"Mol. 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