{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T19:57:00Z","timestamp":1760731020818,"version":"3.37.3"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,11,23]],"date-time":"2017-11-23T00:00:00Z","timestamp":1511395200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["UH 66\/13"],"award-info":[{"award-number":["UH 66\/13"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The modeling language ML-Rules allows specifying and simulating complex systems biology models at multiple levels of organization. The development of such simulation models involves a wide variety of simulation experiments and the replicability of generated simulation results requires suitable means for documenting simulation experiments. Embedded domain-specific languages, such as SESSL, cater to both requirements. With SESSL, the user can integrate diverse simulation experimentation methods and third-party software components into an executable, readable simulation experiment specification. A newly developed SESSL binding for ML-Rules exploits these features of SESSL, opening up new possibilities for executing and documenting simulation experiments with ML-Rules models.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ML-Rules is implemented in Java, SESSL and its bindings are implemented in Scala. The source code is available under open-source licenses:<\/jats:p>\n                  <jats:p>ML-Rules\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2002\u2003git.informatik.uni-rostock.de\/mosi\/mlrules2<\/jats:p>\n                  <jats:p>ML-Rules Quickstart (Graphical Editor)\u2003git.informatik.uni-rostock.de\/mosi\/mlrules2-quickstart<\/jats:p>\n                  <jats:p>SESSL\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003git.informatik.uni-rostock.de\/mosi\/sessl and sessl.org<\/jats:p>\n                  <jats:p>SESSL Quickstart (Experiment Template)\u2003git.informatik.uni-rostock.de\/mosi\/sessl-quickstart<\/jats:p>\n                  <jats:p>Furthermore, Maven-compatible compiled packages of ML-Rules, SESSL, and the SESSL bindings are available from the Maven Central Repository at maven.org (org.sessl:* and org.jamesii: mlrules).<\/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\/btx741","type":"journal-article","created":{"date-parts":[[2017,11,22]],"date-time":"2017-11-22T20:13:53Z","timestamp":1511381633000},"page":"1424-1427","source":"Crossref","is-referenced-by-count":7,"title":["Reproducible and flexible simulation experiments with ML-Rules and SESSL"],"prefix":"10.1093","volume":"34","author":[{"given":"T","family":"Warnke","sequence":"first","affiliation":[{"name":"Modeling and Simulation group, Institute of Computer Science, University of Rostock, Rostock, Germany"}]},{"given":"T","family":"Helms","sequence":"additional","affiliation":[{"name":"Modeling and Simulation group, Institute of Computer Science, University of Rostock, Rostock, Germany"}]},{"given":"A M","family":"Uhrmacher","sequence":"additional","affiliation":[{"name":"Modeling and Simulation group, Institute of Computer Science, University of Rostock, Rostock, Germany"}]}],"member":"286","published-online":{"date-parts":[[2017,11,23]]},"reference":[{"key":"2023012713010056300_btx741-B1","doi-asserted-by":"crossref","first-page":"3289","DOI":"10.1093\/bioinformatics\/bth378","article-title":"BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains","volume":"20","author":"Blinov","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012713010056300_btx741-B2","first-page":"H144","article-title":"Bridging experiments, models and simulations: an integrative approach to validation in computational cardiac electrophysiology","volume":"303","author":"Carusi","year":"2012","journal-title":"Am. 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