{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T02:10:02Z","timestamp":1780107002514,"version":"3.54.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,7,22]],"date-time":"2021-07-22T00:00:00Z","timestamp":1626912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Smoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C\/C++ application programming interface (API), which were convenient, but limited extensibility.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We added a Python API to Smoldyn to improve integration with other software tools, such as Jupyter notebooks, other Python code libraries and other simulators. It includes low-level functions that closely mimic the existing C\/C++ API and higher-level functions that are more convenient to use. These latter functions follow modern object-oriented Python conventions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Smoldyn is open source and free, available at http:\/\/www.smoldyn.org and can be installed with the Python package manager pip. It runs on Mac, Windows and Linux.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>\u2002<\/jats:title>\n                    <jats:p>Documentation is available at http:\/\/www.smoldyn.org\/SmoldynManual.pdf and https:\/\/smoldyn.readthedocs.io\/en\/latest\/python\/api.html.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab530","type":"journal-article","created":{"date-parts":[[2021,7,21]],"date-time":"2021-07-21T15:12:49Z","timestamp":1626880369000},"page":"291-293","source":"Crossref","is-referenced-by-count":0,"title":["Python interfaces for the Smoldyn simulator"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4645-3211","authenticated-orcid":false,"given":"Dilawar","family":"Singh","sequence":"first","affiliation":[{"name":"Subconscious Compute Pvt. 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