{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,22]],"date-time":"2025-03-22T12:21:30Z","timestamp":1742646090221},"reference-count":15,"publisher":"The Open Journal","issue":"90","license":[{"start":{"date-parts":[[2023,10,15]],"date-time":"2023-10-15T00:00:00Z","timestamp":1697328000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,10,15]],"date-time":"2023-10-15T00:00:00Z","timestamp":1697328000000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,10,15]],"date-time":"2023-10-15T00:00:00Z","timestamp":1697328000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JOSS"],"published-print":{"date-parts":[[2023,10,15]]},"DOI":"10.21105\/joss.05553","type":"journal-article","created":{"date-parts":[[2023,10,15]],"date-time":"2023-10-15T19:50:42Z","timestamp":1697399442000},"page":"5553","source":"Crossref","is-referenced-by-count":6,"title":["BASICO: A simplified Python interface to COPASI"],"prefix":"10.21105","volume":"8","author":[{"ORCID":"http:\/\/orcid.org\/0000-0001-5553-4702","authenticated-orcid":false,"given":"Frank T.","family":"Bergmann","sequence":"first","affiliation":[]}],"member":"8722","reference":[{"key":"bergmann_2017","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbiotec.2017.06.1200","article-title":"COPASI and its applications in\nbiotechnology","volume":"261","author":"Bergmann","year":"2017","unstructured":"Bergmann, F. T., Hoops, S., Klahn,\nB., Kummer, U., Mendes, P., Pahle, J., & Sahle, S. (2017). COPASI\nand its applications in biotechnology. Journal of Biotechnology, 261,\n215\u2013220.\nhttps:\/\/doi.org\/10.1016\/j.jbiotec.2017.06.1200","journal-title":"Journal of Biotechnology"},{"issue":"24","key":"hoops_2006","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btl485","article-title":"COPASI\u2014a complex pathway\nsimulator","volume":"22","author":"Hoops","year":"2006","unstructured":"Hoops, S., Sahle, S., Gauges, R.,\nLee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., &\nKummer, U. (2006). COPASI\u2014a complex pathway simulator. Bioinformatics,\n22(24), 3067\u20133074.","journal-title":"Bioinformatics"},{"issue":"4","key":"Hucka_2003","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a\nmedium for representation and exchange of biochemical network\nmodels","volume":"19","author":"Hucka","year":"2003","unstructured":"Hucka, M., Finney, A., Sauro, H. M.,\nBolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J.,\nBray, D., Cornish-Bowden, A., Cuellar, A. A., Dronov, S., Gilles, E. D.,\nGinkel, M., Gor, V., Goryanin, I. I., Hedley, W. J., Hodgman, T. C.,\nHofmeyr, J.-H., \u2026 SBML Forum:, the rest of the. (2003). The systems\nbiology markup language (SBML): a medium for representation and exchange\nof biochemical network models. Bioinformatics, 19(4), 524\u2013531.\nhttps:\/\/doi.org\/10.1093\/bioinformatics\/btg015","journal-title":"Bioinformatics","ISSN":"http:\/\/id.crossref.org\/issn\/1367-4803","issn-type":"print"},{"issue":"8","key":"keating_sbml_2020","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20199110","article-title":"SBML Level 3: An extensible format for the\nexchange and reuse of biological models.","volume":"16","author":"Keating","year":"2020","unstructured":"Keating, S. M., Waltemath, D., K\u00f6nig,\nM., Zhang, F., Dr\u00e4ger, A., Chaouiya, C., Bergmann, F. T., Finney, A.,\nGillespie, C. S., Helikar, T., Hoops, S., Malik-Sheriff, R. S., Moodie,\nS. L., Moraru, I. I., Myers, C. J., Naldi, A., Olivier, B. G., Sahle,\nS., Schaff, J. C., \u2026 Hucka, M. (2020). SBML Level 3: An extensible\nformat for the exchange and reuse of biological models. Molecular\nSystems Biology, 16(8), e9110.\nhttps:\/\/doi.org\/10.15252\/msb.20199110","journal-title":"Molecular systems biology","ISSN":"http:\/\/id.crossref.org\/issn\/1744-4292","issn-type":"print"},{"issue":"2","key":"BioModels2015b","doi-asserted-by":"publisher","DOI":"10.1002\/psp4.3","article-title":"BioModels: Content, Features, Functionality,\nand Use: BioModels: Content, Features, Functionality, and\nUse","volume":"4","author":"Juty","year":"2015","unstructured":"Juty, N., Ali, R., Glont, M.,\nKeating, S., Rodriguez, N., Swat, M., Wimalaratne, S., Hermjakob, H., Le\nNov\u00e8re, N., Laibe, C., & Chelliah, V. (2015). BioModels: Content,\nFeatures, Functionality, and Use: BioModels: Content, Features,\nFunctionality, and Use. CPT: Pharmacometrics & Systems Pharmacology,\n4(2), 55\u201368. https:\/\/doi.org\/10.1002\/psp4.3","journal-title":"CPT: Pharmacometrics & Systems\nPharmacology"},{"issue":"13","key":"JWS","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth200","article-title":"Web-based kinetic modelling using JWS\nonline","volume":"20","author":"Olivier","year":"2004","unstructured":"Olivier, B. G., & Snoep, J. L.\n(2004). Web-based kinetic modelling using JWS online. Bioinformatics,\n20(13), 2143\u20132144.\nhttps:\/\/doi.org\/10.1093\/bioinformatics\/bth200","journal-title":"Bioinformatics"},{"key":"SWIG","article-title":"SWIG: An easy to use tool for integrating\nscripting languages with c and c++","author":"Beazley","year":"1996","unstructured":"Beazley, D. M. (1996). SWIG: An easy\nto use tool for integrating scripting languages with c and c++.\nProceedings of the 4th Conference on USENIX Tcl\/Tk Workshop, 1996 -\nVolume 4, 15\u201315.\nhttp:\/\/dl.acm.org\/citation.cfm?id=1267498.1267513","journal-title":"Proceedings of the 4th conference on USENIX\ntcl\/tk workshop, 1996 - volume 4"},{"issue":"74","key":"pyABC","doi-asserted-by":"publisher","DOI":"10.21105\/joss.04304","article-title":"pyABC: Efficient and robust easy-to-use\napproximate bayesian computation","volume":"7","author":"Sch\u00e4lte","year":"2022","unstructured":"Sch\u00e4lte, Y., Klinger, E., Alamoudi,\nE., & Hasenauer, J. (2022). pyABC: Efficient and robust easy-to-use\napproximate bayesian computation. Journal of Open Source Software,\n7(74), 4304. https:\/\/doi.org\/10.21105\/joss.04304","journal-title":"Journal of Open Source\nSoftware"},{"key":"sbmltoodejax","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2307.08452","article-title":"SBMLtoODEjax: Efficient simulation and\noptimization of ODE SBML models in JAX","author":"Etcheverry","year":"2023","unstructured":"Etcheverry, M., Levin, M.,\nMoulin-Frier, C., & Oudeyer, P.-Y. (2023). SBMLtoODEjax: Efficient\nsimulation and optimization of ODE SBML models in JAX.\nhttps:\/\/doi.org\/10.48550\/arXiv.2307.08452"},{"key":"mendes2023reproducibility","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2023.1201673","article-title":"Reproducibility and FAIR principles: The case\nof a segment polarity network model","volume":"11","author":"Mendes","year":"2023","unstructured":"Mendes, P. (2023). Reproducibility\nand FAIR principles: The case of a segment polarity network model.\nFrontiers in Cell and Developmental Biology, 11.\nhttps:\/\/doi.org\/10.3389\/fcell.2023.1201673","journal-title":"Frontiers in Cell and Developmental\nBiology","ISSN":"http:\/\/id.crossref.org\/issn\/2296-634X","issn-type":"print"},{"key":"pandas","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.8092754","article-title":"Pandas-dev\/pandas: pandas","author":"pandas development team","year":"2023","unstructured":"pandas development team. (2023).\nPandas-dev\/pandas: pandas (Version v2.0.3). Zenodo.\nhttps:\/\/doi.org\/10.5281\/zenodo.8092754"},{"key":"libCombine","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.7408732","article-title":"Sbmlteam\/libCombine: Release\n0.2.20","author":"Bergmann","year":"2022","unstructured":"Bergmann, F., K\u00f6nig, M., Karr, J.,\nKeegan, L., & Plesn\u00edkov\u00e1, J. (2022). Sbmlteam\/libCombine: Release\n0.2.20 (Version v0.2.20). Zenodo.\nhttps:\/\/doi.org\/10.5281\/zenodo.7408732"},{"key":"libSEDML","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.6619620","article-title":"Fbergmann\/libSEDML: Release\n2.0.32","author":"Bergmann","year":"2022","unstructured":"Bergmann, F., Smith, L., Nickerson,\nD., Garny, A., Medley, K., & Marakasov, D. (2022).\nFbergmann\/libSEDML: Release 2.0.32 (Version v2.0.32). Zenodo.\nhttps:\/\/doi.org\/10.5281\/zenodo.6619620"},{"issue":"1","key":"bergmann2014combine","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-014-0369-z","article-title":"COMBINE archive and OMEX format: One file to\nshare all information to reproduce a modeling project","volume":"15","author":"Bergmann","year":"2014","unstructured":"Bergmann, F. T., Adams, R., Moodie,\nS., Cooper, J., Glont, M., Golebiewski, M., Hucka, M., Laibe, C.,\nMiller, A. K., Nickerson, D. P., & others. (2014). COMBINE archive\nand OMEX format: One file to share all information to reproduce a\nmodeling project. BMC Bioinformatics, 15(1), 1\u20139.\nhttps:\/\/doi.org\/10.1186\/s12859-014-0369-z","journal-title":"BMC bioinformatics"},{"issue":"3","key":"SCHABER2012183","doi-asserted-by":"publisher","DOI":"10.1016\/j.biosystems.2012.09.003","article-title":"Easy parameter identifiability analysis with\nCOPASI","volume":"110","author":"Schaber","year":"2012","unstructured":"Schaber, J. (2012). Easy parameter\nidentifiability analysis with COPASI. Biosystems, 110(3), 183\u2013185.\nhttps:\/\/doi.org\/10.1016\/j.biosystems.2012.09.003","journal-title":"Biosystems","ISSN":"http:\/\/id.crossref.org\/issn\/0303-2647","issn-type":"print"}],"container-title":["Journal of Open Source Software"],"original-title":[],"link":[{"URL":"https:\/\/joss.theoj.org\/papers\/10.21105\/joss.05553.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2023,10,15]],"date-time":"2023-10-15T19:50:51Z","timestamp":1697399451000},"score":1,"resource":{"primary":{"URL":"https:\/\/joss.theoj.org\/papers\/10.21105\/joss.05553"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,15]]},"references-count":15,"journal-issue":{"issue":"90","published-online":{"date-parts":[[2023,10]]}},"alternative-id":["10.21105\/joss.05553"],"URL":"https:\/\/doi.org\/10.21105\/joss.05553","relation":{"has-review":[{"id-type":"uri","id":"https:\/\/github.com\/openjournals\/joss-reviews\/issues\/5553","asserted-by":"subject"}],"references":[{"id-type":"doi","id":"10.5281\/zenodo.8189386","asserted-by":"subject"}]},"ISSN":["2475-9066"],"issn-type":[{"value":"2475-9066","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,15]]}}}