{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T00:22:38Z","timestamp":1779927758121,"version":"3.53.1"},"publisher-location":"Cham","reference-count":32,"publisher":"Springer Nature Switzerland","isbn-type":[{"value":"9783031426964","type":"print"},{"value":"9783031426971","type":"electronic"}],"license":[{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023]]},"DOI":"10.1007\/978-3-031-42697-1_9","type":"book-chapter","created":{"date-parts":[[2023,9,8]],"date-time":"2023-09-08T09:02:29Z","timestamp":1694163749000},"page":"124-143","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Core SBML and\u00a0Its Formal Semantics"],"prefix":"10.1007","author":[{"given":"Joachim","family":"Niehren","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C\u00e9dric","family":"Lhoussaine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ath\u00e9na\u00efs","family":"Vaginay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,9,9]]},"reference":[{"key":"9_CR1","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1007\/978-3-030-31304-3_14","volume-title":"Computational Methods in Systems Biology","author":"E Allart","year":"2019","unstructured":"Allart, E., Niehren, J., Versari, C.: Computing difference abstractions of metabolic networks under kinetic constraints. In: Bortolussi, L., Sanguinetti, G. (eds.) CMSB 2019. LNCS, vol. 11773, pp. 266\u2013285. Springer, Cham (2019). https:\/\/doi.org\/10.1007\/978-3-030-31304-3_14"},{"issue":"1","key":"9_CR2","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1137\/141000671","volume":"59","author":"J Bezanson","year":"2017","unstructured":"Bezanson, J., Edelman, A., Karpinski, S., Shah, V.B.: Julia: a fresh approach to numerical computing. SIAM Rev. 59(1), 65\u201398 (2017). https:\/\/doi.org\/10.1137\/141000671","journal-title":"SIAM Rev."},{"issue":"14","key":"9_CR3","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.1093\/bioinformatics\/btl172","volume":"22","author":"L Calzone","year":"2006","unstructured":"Calzone, L., Fages, F., Soliman, S.: BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22(14), 1805\u20131807 (2006). https:\/\/doi.org\/10.1093\/bioinformatics\/btl172","journal-title":"Bioinformatics"},{"key":"9_CR4","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1181","author":"V Chelliah","year":"2015","unstructured":"Chelliah, V., et al.: BioModels: ten-year anniversary. Nucl. Acids Res. (2015). https:\/\/doi.org\/10.1093\/nar\/gku1181","journal-title":"Nucl. Acids Res."},{"issue":"11","key":"9_CR5","doi-asserted-by":"publisher","first-page":"1455","DOI":"10.1093\/bioinformatics\/btp170","volume":"25","author":"A Dr\u00e4ger","year":"2009","unstructured":"Dr\u00e4ger, A., et al.: Sbml2latex: conversion of sbml files into human-readable reports. Bioinformatics 25(11), 1455\u20131456 (2009)","journal-title":"Bioinformatics"},{"key":"9_CR6","unstructured":"Euler, L.: Institutionum Calculi Integralis. No. vol. 1 in Institutionum Calculi Integralis, imp. Acad. imp. Sa\u00e8nt. (1768)"},{"issue":"1","key":"9_CR7","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1016\/j.tcs.2008.04.024","volume":"403","author":"F Fages","year":"2008","unstructured":"Fages, F., Soliman, S.: Abstract interpretation and types for systems biology. Theor. Comput. Sci. 403(1), 52\u201370 (2008)","journal-title":"Theor. Comput. Sci."},{"key":"9_CR8","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.tcs.2014.07.032","volume":"599","author":"F Fages","year":"2015","unstructured":"Fages, F., Gay, S., Soliman, S.: Inferring reaction systems from ordinary differential equations. Theor. Comput. Sci. 599, 64\u201378 (2015). https:\/\/doi.org\/10.1016\/j.tcs.2014.07.032","journal-title":"Theor. Comput. Sci."},{"key":"9_CR9","doi-asserted-by":"publisher","unstructured":"Feinberg, M.: Chemical reaction network structure and the stability of complex isothermal reactors-I. the deficiency zero and deficiency one theorems. Chem. Eng. Sci. 42(10), 2229\u20132268 (1987). https:\/\/doi.org\/10.1016\/0009-2509(87)80099-4. http:\/\/www.sciencedirect.com\/science\/article\/pii\/0009250987800994","DOI":"10.1016\/0009-2509(87)80099-4"},{"key":"9_CR10","doi-asserted-by":"publisher","unstructured":"Glass, L., Kauffman, S.A.: The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol. 39(1), 103\u2013129 (1973). https:\/\/doi.org\/10.1016\/0022-5193(73)90208-7. https:\/\/www.sciencedirect.com\/science\/article\/pii\/0022519373902087","DOI":"10.1016\/0022-5193(73)90208-7"},{"issue":"3","key":"9_CR11","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/0167-6423(87)90035-9","volume":"8","author":"D Harel","year":"1987","unstructured":"Harel, D.: Statecharts: a visual formalism for complex systems. Sci. Comput. Program. 8(3), 231\u2013274 (1987). https:\/\/doi.org\/10.1016\/0167-6423(87)90035-9","journal-title":"Sci. Comput. Program."},{"issue":"24","key":"9_CR12","doi-asserted-by":"publisher","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","volume":"22","author":"S Hoops","year":"2006","unstructured":"Hoops, S., et al.: Copasi-a complex pathway simulator. Bioinformatics 22(24), 3067\u20133074 (2006)","journal-title":"Bioinformatics"},{"key":"9_CR13","doi-asserted-by":"publisher","unstructured":"Hucka, M., et al.: The systems biology markup language (SBML): language specification for level 3 version 2 core release 2. J. Integrat. Bioinf. 16(2), 20190021 (2019). https:\/\/doi.org\/10.1515\/jib-2019-0021. https:\/\/www.degruyter.com\/view\/j\/jib.ahead-of-print\/jib-2019-0021\/jib-2019-0021.xml","DOI":"10.1515\/jib-2019-0021"},{"issue":"2","key":"9_CR14","doi-asserted-by":"publisher","first-page":"271","DOI":"10.2390\/biecoll-jib-2015-271","volume":"12","author":"M Hucka","year":"2015","unstructured":"Hucka, M., et al.: Systems biology markup language (SBML) level 2 version 5: structures and facilities for model definitions. J. Integrat. Bioinf. 12(2), 271 (2015). https:\/\/doi.org\/10.2390\/biecoll-jib-2015-271","journal-title":"J. Integrat. Bioinf."},{"key":"9_CR15","unstructured":"Jelliffe, R.: Schematron (2006). iSO\/IEC 19757\u20133"},{"key":"9_CR16","unstructured":"Joachim, N., Lhoussaine, C., Aht\u00e9na\u00efs, V.: Core SBML and its formal semantics. In: CMSB: 21th International Conference on Formal Methods in Systems Biology, Luxembourg, Luxembourg (2023). https:\/\/inria.hal.science\/hal-04125922"},{"key":"9_CR17","doi-asserted-by":"crossref","unstructured":"John, M., Nebut, M., Niehren, J.: Knockout prediction for reaction networks with partial kinetic information. In: 14th International Conference on Verification, Model Checking, and Abstract Interpretation, Rome, Italy, pp. 355\u2013374 (2013). http:\/\/hal.inria.fr\/hal-00692499","DOI":"10.1007\/978-3-642-35873-9_22"},{"key":"9_CR18","unstructured":"Kay, M.: The saxon xslt and xquery processor (2004). https:\/\/www.saxonica.com"},{"key":"9_CR19","doi-asserted-by":"publisher","unstructured":"Keating, S.M., et al.: SBML level 3 community members: SBML level 3: an extensible format for the exchange and reuse of biological models. Molec. Syst. Biol. 16(8), e9110 (2020). https:\/\/doi.org\/10.15252\/msb.20199110","DOI":"10.15252\/msb.20199110"},{"key":"9_CR20","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1007\/978-3-319-10398-3_7","volume-title":"Formal Methods in Macro-Biology","author":"G Madelaine","year":"2014","unstructured":"Madelaine, G., Lhoussaine, C., Niehren, J.: Attractor equivalence: an observational semantics for reaction networks. In: Fages, F., Piazza, C. (eds.) FMMB 2014. LNCS, vol. 8738, pp. 82\u2013101. Springer, Cham (2014). https:\/\/doi.org\/10.1007\/978-3-319-10398-3_7"},{"issue":"D1","key":"9_CR21","doi-asserted-by":"publisher","first-page":"D407","DOI":"10.1093\/nar\/gkz1055","volume":"48","author":"RS Malik-Sheriff","year":"2020","unstructured":"Malik-Sheriff, R.S., et al.: BioModels-15 years of sharing computational models in life science. Nucl. Acids Res. 48(D1), D407\u2013D415 (2020). https:\/\/doi.org\/10.1093\/nar\/gkz1055","journal-title":"Nucl. Acids Res."},{"key":"9_CR22","doi-asserted-by":"crossref","unstructured":"Mendes, P., Hoops, S., Sahle, S., Gauges, R., Dada, J., Kummer, U.: Computational modeling of biochemical networks using copasi. Methods Molec. Biol. (Clifton, N.J.) 500, 17\u201359 (2009)","DOI":"10.1007\/978-1-59745-525-1_2"},{"issue":"1","key":"9_CR23","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1109\/TCBB.2018.2850901","volume":"16","author":"A Mizera","year":"2019","unstructured":"Mizera, A., Pang, J., Qu, H., Yuan, Q.: Taming asynchrony for attractor detection in large Boolean networks. IEEE\/ACM Trans. Comput. Biol. Bioinf. 16(1), 31\u201342 (2019). https:\/\/doi.org\/10.1109\/TCBB.2018.2850901","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf."},{"key":"9_CR24","doi-asserted-by":"publisher","unstructured":"Niehren, J., Vaginay, A., Versari, C.: Abstract simulation of reaction networks via boolean networks. In: Petre, I., Paun, A. (eds.) Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Bucharest, Romania, 14\u201316 September 2022, Proceedings. Lecture Notes in Computer Science, vol. 13447, pp. 21\u201340. Springer, Heidelberg (2022). https:\/\/doi.org\/10.1007\/978-3-031-15034-0_2","DOI":"10.1007\/978-3-031-15034-0_2"},{"key":"9_CR25","doi-asserted-by":"crossref","unstructured":"Niehren, J., Versari, C., John, M., Coutte, F., Jacques, P.: Predicting changes of reaction networks with partial kinetic information. BioSystems 149, 113\u2013124 (2016). https:\/\/hal.inria.fr\/hal-01239198","DOI":"10.1016\/j.biosystems.2016.09.003"},{"key":"9_CR26","doi-asserted-by":"publisher","unstructured":"Paulev\u00e9, L., Kol\u00e7\u00e0, J., Chatain, T., Haar, S.: Reconciling qualitative, abstract, and scalable modeling of biological networks. Nat. Commun. 11 (2020). https:\/\/doi.org\/10.1038\/s41467-020-18112-5. https:\/\/hal.archives-ouvertes.fr\/hal-02518582","DOI":"10.1038\/s41467-020-18112-5"},{"key":"9_CR27","doi-asserted-by":"publisher","unstructured":"Thomas, R.: Boolean formalization of genetic control circuits. J. Theor. Biol. 42(3), 563\u2013585 (1973). https:\/\/doi.org\/10.1016\/0022-5193(73)90247-6. https:\/\/www.sciencedirect.com\/science\/article\/pii\/0022519373902476","DOI":"10.1016\/0022-5193(73)90247-6"},{"key":"9_CR28","unstructured":"Thompson, H.S., Beech, D., Maloney, M., Mendelsohn, N.: Xml schema part 1: Structures, 2nd edn. (2004). http:\/\/www.w3.org\/TR\/xmlschema-1\/"},{"issue":"1","key":"9_CR29","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1007\/s41109-022-00505-8","volume":"7","author":"A Vaginay","year":"2022","unstructured":"Vaginay, A., Boukhobza, T., Sma\u00efl-Tabbone, M.: From quantitative SBML models to Boolean networks. Appl. Netw. Sci. 7(1), 73 (2022). https:\/\/doi.org\/10.1007\/s41109-022-00505-8","journal-title":"Appl. Netw. Sci."},{"key":"9_CR30","volume-title":"XML Schema","author":"E van der Vlist","year":"2003","unstructured":"van der Vlist, E.: XML Schema. O\u2019Reilly, Beijing (2003)"},{"key":"9_CR31","unstructured":"Van der Vlist, E.: RELAX NG: A Simpler Schema Language for XML, 1. aufl edn.. O\u2019Reilly & Assoc. (2004)"},{"key":"9_CR32","unstructured":"W3C: XSL transformations (XSLT) version 3.0 (2017). https:\/\/www.w3.org\/TR\/xslt-30"}],"container-title":["Lecture Notes in Computer Science","Computational Methods in Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-42697-1_9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,8]],"date-time":"2023-09-08T09:03:34Z","timestamp":1694163814000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-42697-1_9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023]]},"ISBN":["9783031426964","9783031426971"],"references-count":32,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-42697-1_9","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023]]},"assertion":[{"value":"9 September 2023","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"CMSB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Computational Methods in Systems Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Luxembourg City","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Luxembourg","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2023","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"13 September 2023","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"15 September 2023","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"21","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"cmsb2023","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/cmsb2023.uni.lu\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Easychair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"28","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"14","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"50% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3.72 (regular), 3 (tool)","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}