{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:09Z","timestamp":1772138049473,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T00:00:00Z","timestamp":1632355200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The National Resource for Network Biology (NRNB) and Google Inc"},{"DOI":"10.13039\/100009139","name":"German Center for Infection Research","doi-asserted-by":"crossref","award":["8020708703"],"award-info":[{"award-number":["8020708703"]}],"id":[{"id":"10.13039\/100009139","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections"},{"DOI":"10.13039\/501100002347","name":"Federal Ministry of Education and Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Systems Medicine of the Liver [LiSyM","award":["031L0054"],"award-info":[{"award-number":["031L0054"]}]},{"name":"DFG within the Research Unit Programme","award":["5151"],"award-info":[{"award-number":["5151"]}]},{"name":"Complex Resection\u2014A Systems Medicine Approach)","award":["436883643"],"award-info":[{"award-number":["436883643"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Studying biological systems generally relies on computational modeling and simulation, e.g., model-driven discovery and hypothesis testing. Progress in standardization efforts led to the development of interrelated file formats to exchange and reuse models in systems biology, such as SBML, the Simulation Experiment Description Markup Language (SED-ML) or the Open Modeling EXchange format. Conducting simulation experiments based on these formats requires efficient and reusable implementations to make them accessible to the broader scientific community and to ensure the reproducibility of the results. The Systems Biology Simulation Core Library (SBSCL) provides interpreters and solvers for these standards as a versatile open-source API in JavaTM. The library simulates even complex bio-models and supports deterministic Ordinary Differential Equations; Stochastic Differential Equations; constraint-based analyses; recent SBML and SED-ML versions; exchange of results, and visualization of in silico experiments; open modeling exchange formats (COMBINE archives); hierarchically structured models; and compatibility with standard testing systems, including the Systems Biology Test Suite and published models from the BioModels and BiGG databases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SBSCL is freely available at https:\/\/draeger-lab.github.io\/SBSCL\/ and via Maven Central.<\/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\/btab669","type":"journal-article","created":{"date-parts":[[2021,9,20]],"date-time":"2021-09-20T15:21:27Z","timestamp":1632151287000},"page":"864-865","source":"Crossref","is-referenced-by-count":7,"title":["The systems biology simulation core library"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9466-1675","authenticated-orcid":false,"given":"Hemil","family":"Panchiwala","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, Indian Institute of Technology , Roorkee, IN 247667, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1406-3577","authenticated-orcid":false,"given":"Shalin","family":"Shah","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Duke University , Durham, NC 27701, USA"},{"name":"Bloomberg , New York, NY 10022, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6536-0782","authenticated-orcid":false,"given":"Hannes","family":"Planatscher","sequence":"additional","affiliation":[{"name":"Signatope GmbH , Reutlingen 72770, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2792-0512","authenticated-orcid":false,"given":"Mykola","family":"Zakharchuk","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1725-179X","authenticated-orcid":false,"given":"Matthias","family":"K\u00f6nig","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Biology, Humboldt University of Berlin , Berlin 10115, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1240-5553","authenticated-orcid":false,"given":"Andreas","family":"Dr\u00e4ger","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany"},{"name":"Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of T\u00fcbingen , T\u00fcbingen 72076, Germany"},{"name":"German Center for Infection Research (DZIF), Partner Site T\u00fcbingen , T\u00fcbingen 72076, Germany"},{"name":"Cluster of Excellence \u2018Controlling Microbes to Fight Infections,\u2019 University of T\u00fcbingen , T\u00fcbingen 72076, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,9,23]]},"reference":[{"key":"2023020108470826200_btab669-B1","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1186\/s12859-014-0369-z","article-title":"COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project","volume":"15","author":"Bergmann","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023020108470826200_btab669-B2","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/1471-2105-9-356","article-title":"FERN \u2013 a Java framework for stochastic simulation and evaluation of reaction networks","volume":"9","author":"Erhard","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023020108470826200_btab669-B3","doi-asserted-by":"crossref","first-page":"e9110","DOI":"10.15252\/msb.20199110","article-title":"SBML Level 3: an extensible format for the exchange and reuse of biological models","volume":"16","author":"Keating","year":"2020","journal-title":"Mol. 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