{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T07:19:06Z","timestamp":1722755946390},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":476,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Here, we present REDEMPTION (Reduced Dimension Ensemble Modeling and Parameter estimation), a toolbox for parameter estimation and ensemble modeling of ordinary differential equations (ODEs) using time-series data. For models with more reactions than measured species, a common scenario in biological modeling, the parameter estimation is formulated as a nested optimization problem based on incremental parameter estimation strategy. REDEMPTION also includes a tool for the identification of an ensemble of parameter combinations that provide satisfactory goodness-of-fit to the data. The functionalities of REDEMPTION are accessible through a MATLAB user interface (UI), as well as through programming script. For computational speed-up, REDEMPTION provides a numerical parallelization option using MATLAB Parallel Computing toolbox.<\/jats:p>\n               <jats:p>Availability and implementation: REDEMPTION can be downloaded from http:\/\/www.cabsel.ethz.ch\/tools\/redemption.<\/jats:p>\n               <jats:p>Contact: \u00a0rudi.gunawan@chem.ethz.ch<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv365","type":"journal-article","created":{"date-parts":[[2015,6,16]],"date-time":"2015-06-16T00:30:31Z","timestamp":1434414631000},"page":"3387-3389","source":"Crossref","is-referenced-by-count":6,"title":["REDEMPTION: reduced dimension ensemble modeling and parameter estimation"],"prefix":"10.1093","volume":"31","author":[{"given":"Yang","family":"Liu","sequence":"first","affiliation":[{"name":"1 Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland and"},{"name":"2 Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erica","family":"Manesso","sequence":"additional","affiliation":[{"name":"1 Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland and"},{"name":"2 Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rudiyanto","family":"Gunawan","sequence":"additional","affiliation":[{"name":"1 Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland and"},{"name":"2 Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,6,14]]},"reference":[{"key":"2023020202314848000_btv365-B1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.mbs.2009.03.002","article-title":"Recent developments in parameter estimation and structure identification of biochemical and genomic systems","volume":"219","author":"Chou","year":"2009","journal-title":"Math. Biosci."},{"key":"2023020202314848000_btv365-B2","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1049\/iet-syb:20070030","article-title":"Challenges in lin-log modelling of glycolysis in Lactococcus lactis","volume":"2","author":"del Rosario","year":"2008","journal-title":"IET Syst. Biol."},{"key":"2023020202314848000_btv365-B3","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.cor.2009.05.003","article-title":"An evolutionary method for complex-process optimization","volume":"37","author":"Egea","year":"2010","journal-title":"Comput. Oper. Res."},{"key":"2023020202314848000_btv365-B4","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1186\/1752-0509-6-142","article-title":"Incremental parameter estimation of kinetic metabolic network models","volume":"6","author":"Jia","year":"2012","journal-title":"BMC Syst. Biol."},{"key":"2023020202314848000_btv365-B5","doi-asserted-by":"crossref","first-page":"891","DOI":"10.3390\/metabo2040891","article-title":"Ensemble kinetic modeling of metabolic networks from dynamic metabolic profiles","volume":"2","author":"Jia","year":"2012","journal-title":"Metabolites"},{"key":"2023020202314848000_btv365-B6","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1186\/s12918-014-0127-x","article-title":"Parameter estimation of dynamic biological network models using integrated fluxes","volume":"8","author":"Liu","year":"2014","journal-title":"BMC Syst. Biol."},{"key":"2023020202314848000_btv365-B7","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.jbiotec.2010.02.019","article-title":"Parameter identifiability of power-law biochemical system models","volume":"149","author":"Srinath","year":"2010","journal-title":"J. Biotechnol."},{"key":"2023020202314848000_btv365-B8","doi-asserted-by":"crossref","first-page":"1670","DOI":"10.1093\/bioinformatics\/bth140","article-title":"Decoupling dynamical systems for pathway identification from metabolic profiles","volume":"20","author":"Voit","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020202314848000_btv365-B9","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1186\/1752-0509-5-142","article-title":"Efficient characterization of high-dimensional parameter spaces for systems biology","volume":"5","author":"Zamora-Sillero","year":"2011","journal-title":"BMC Syst. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/20\/3387\/49035963\/bioinformatics_31_20_3387.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/20\/3387\/49035963\/bioinformatics_31_20_3387.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:50:38Z","timestamp":1675309838000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/20\/3387\/195825"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,6,14]]},"references-count":9,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2015,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv365","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,10,15]]},"published":{"date-parts":[[2015,6,14]]}}}