{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,3]],"date-time":"2025-08-03T04:35:01Z","timestamp":1754195701690},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Structural kinetic modeling (SKM) enables the analysis of dynamical properties of metabolic networks solely based on topological information and experimental data. Current SKM-based experiments are hampered by the time-intensive process of assigning model parameters and choosing appropriate sampling intervals for Monte-Carlo experiments. We introduce a toolbox for the automatic and efficient construction and evaluation of structural kinetic models (SK models). Quantitative and qualitative analyses of network stability properties are performed in an automated manner. We illustrate the model building and analysis process in detailed example scripts that provide toolbox implementations of previously published literature models.<\/jats:p>\n               <jats:p>Availability: The source code is freely available for download at http:\/\/bioinformatics.uni-potsdam.de\/projects\/skm.<\/jats:p>\n               <jats:p>Contact: \u00a0girbig@mpimp-golm.mpg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts473","type":"journal-article","created":{"date-parts":[[2012,7,31]],"date-time":"2012-07-31T06:55:55Z","timestamp":1343717755000},"page":"2546-2547","source":"Crossref","is-referenced-by-count":6,"title":["A MATLAB toolbox for structural kinetic modeling"],"prefix":"10.1093","volume":"28","author":[{"given":"Dorothee","family":"Girbig","sequence":"first","affiliation":[{"name":"1 Bioinformatics Group, Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany and 2Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany"}]},{"given":"Joachim","family":"Selbig","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany and 2Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany"},{"name":"1 Bioinformatics Group, Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany and 2Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany"}]},{"given":"Sergio","family":"Grimbs","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany and 2Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany"}]}],"member":"286","published-online":{"date-parts":[[2012,7,30]]},"reference":[{"key":"2023012513143877300_bts473-B1","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/bioinformatics\/btn051","article-title":"Libsbml: an api library for SBML","volume":"24","author":"Bornstein","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012513143877300_bts473-B2","doi-asserted-by":"crossref","first-page":"e34686","DOI":"10.1371\/journal.pone.0034686","article-title":"Systematic analysis of stability patterns in plant primary metabolism","volume":"7","author":"Girbig","year":"2012","journal-title":"PLoS One"},{"key":"2023012513143877300_bts473-B3","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/msb4100186","article-title":"The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks","volume":"3","author":"Grimbs","year":"2007","journal-title":"Mol. Syst. Biol."},{"key":"2023012513143877300_bts473-B4","article-title":"Data Mining Tools See5 and C5.0","author":"Quinlan","year":"2012"},{"key":"2023012513143877300_bts473-B5","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/j.jtbi.2010.07.023","article-title":"On the stability of metabolic cycles","volume":"266","author":"Reznik","year":"2010","journal-title":"J. Theor. Biol."},{"key":"2023012513143877300_bts473-B6","doi-asserted-by":"crossref","first-page":"11868","DOI":"10.1073\/pnas.0600013103","article-title":"Structural kinetic modeling of metabolic networks","volume":"103","author":"Steuer","year":"2006","journal-title":"Proc. Natl. Acad. Sci. 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