{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T16:51:18Z","timestamp":1770569478020,"version":"3.49.0"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3007,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets simultaneously. Multi-experiment-fitting is a powerful approach to estimate parameter values, to check the validity of a given model, and to discriminate competing model hypotheses. It requires high-performance integration of ordinary differential equations and robust optimization.<\/jats:p>\n               <jats:p>Results: We here present the comprehensive modeling framework Potters-Wheel (PW) including novel functionalities to satisfy these requirements with strong emphasis on the inverse problem, i.e. data-based modeling of partially observed and noisy systems like signal transduction pathways and metabolic networks. PW is designed as a MATLAB toolbox and includes numerous user interfaces. Deterministic and stochastic optimization routines are combined by fitting in logarithmic parameter space allowing for robust parameter calibration. Model investigation includes statistical tests for model-data-compliance, model discrimination, identifiability analysis and calculation of Hessian- and Monte-Carlo-based parameter confidence limits. A rich application programming interface is available for customization within own MATLAB code. Within an extensive performance analysis, we identified and significantly improved an integrator\u2013optimizer pair which decreases the fitting duration for a realistic benchmark model by a factor over 3000 compared to MATLAB with optimization toolbox.<\/jats:p>\n               <jats:p>Availability: PottersWheel is freely available for academic usage at http:\/\/www.PottersWheel.de\/. The website contains a detailed documentation and introductory videos. The program has been intensively used since 2005 on Windows, Linux and Macintosh computers and does not require special MATLAB toolboxes.<\/jats:p>\n               <jats:p>Contact: \u00a0maiwald@fdm.uni-freiburg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn350","type":"journal-article","created":{"date-parts":[[2008,7,10]],"date-time":"2008-07-10T00:25:55Z","timestamp":1215649555000},"page":"2037-2043","source":"Crossref","is-referenced-by-count":183,"title":["Dynamical modeling and multi-experiment fitting with PottersWheel"],"prefix":"10.1093","volume":"24","author":[{"given":"Thomas","family":"Maiwald","sequence":"first","affiliation":[{"name":"1 Freiburg Center for Data Analysis and Modeling, Freiburg University, Eckerstr. 1, 79104 Freiburg and 2Institute of Physics, Freiburg University, Hermann Herder Str. 3, 79104 Freiburg, Germany"},{"name":"1 Freiburg Center for Data Analysis and Modeling, Freiburg University, Eckerstr. 1, 79104 Freiburg and 2Institute of Physics, Freiburg University, Hermann Herder Str. 3, 79104 Freiburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens","family":"Timmer","sequence":"additional","affiliation":[{"name":"1 Freiburg Center for Data Analysis and Modeling, Freiburg University, Eckerstr. 1, 79104 Freiburg and 2Institute of Physics, Freiburg University, Hermann Herder Str. 3, 79104 Freiburg, Germany"},{"name":"1 Freiburg Center for Data Analysis and Modeling, Freiburg University, Eckerstr. 1, 79104 Freiburg and 2Institute of Physics, Freiburg University, Hermann Herder Str. 3, 79104 Freiburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,7,9]]},"reference":[{"key":"2023020211114057300_B1","first-page":"267","article-title":"Information theory and an extension of the maximum likelihood principle","volume-title":"2nd International Symposium on Information Theory.","author":"Akaike","year":"1973"},{"key":"2023020211114057300_B2","doi-asserted-by":"crossref","first-page":"e30","DOI":"10.1371\/journal.pcbi.0040030","article-title":"Stimulus design for model selection and validation in cell signaling","volume":"4","author":"Apgar","year":"2008","journal-title":"PLoS Comput. 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