Python interfaces for the Smoldyn simulator

Python interfaces for the Smoldyn simulator

Abstract Motivation 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 extensib...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Bioinformatics 2021-12, Vol.38 (1), p.291-293
Hauptverfasser: Singh, Dilawar, Andrews, Steven S
Format: Artikel
Sprache:eng
Schlagworte:
Documentation
Software
Systems Biology
Online-Zugang:Volltext bestellen
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 293
container_issue 1
container_start_page 291
container_title Bioinformatics
container_volume 38
creator Singh, Dilawar
Andrews, Steven S
description Abstract Motivation 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. Results 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. Availability and implementation 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.   Documentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html.
doi_str_mv 10.1093/bioinformatics/btab530
format Article
fullrecord <record><control><sourceid>proquest_TOX</sourceid><recordid>TN_cdi_proquest_miscellaneous_2555112117</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/bioinformatics/btab530</oup_id><sourcerecordid>2555112117</sourcerecordid><originalsourceid>FETCH-LOGICAL-c348t-9a6c96ebb4a5b884dc033919adf4e62627651f85219aba606added89a2b4b1e73</originalsourceid><addsrcrecordid>eNqNkE1LAzEQhoMotlb_QtmjIGsz-ermKMUvKCio55BkszSyu6lJ9tB_75ZWwZunGYbnfQcehOaAbwFLujA--L4JsdPZ27QwWRtO8QmaAhO4JJjL03GnYlmyCtMJukjpE2MOjLFzNKGMSAoYT9HN6y5vQl_4PrvYaOtSMbYWeeOKty609a4vku-GVucQL9FZo9vkro5zhj4e7t9XT-X65fF5dbcuLWVVLqUWVgpnDNPcVBWrLaZUgtR1w5wggiwFh6biZDwZLbDQde3qSmpimAG3pDN0fejdxvA1uJRV55N1bat7F4akCOccgADsUXFAbQwpRdeobfSdjjsFWO1Fqb-i1FHUGJwffwymc_Vv7MfMCMABCMP2v6XfxUF7TQ</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2555112117</pqid></control><display><type>article</type><title>Python interfaces for the Smoldyn simulator</title><source>Access via Oxford University Press (Open Access Collection)</source><creator>Singh, Dilawar ; Andrews, Steven S</creator><contributor>Martel, Pier Luigi</contributor><creatorcontrib>Singh, Dilawar ; Andrews, Steven S ; Martel, Pier Luigi</creatorcontrib><description>Abstract Motivation 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. Results 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. Availability and implementation 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.   Documentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btab530</identifier><identifier>PMID: 34293100</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Documentation ; Software ; Systems Biology</subject><ispartof>Bioinformatics, 2021-12, Vol.38 (1), p.291-293</ispartof><rights>The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2021</rights><rights>The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c348t-9a6c96ebb4a5b884dc033919adf4e62627651f85219aba606added89a2b4b1e73</cites><orcidid>0000-0002-4645-3211 ; 0000-0002-4576-8107</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,1604,27924,27925</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/btab530$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34293100$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Martel, Pier Luigi</contributor><creatorcontrib>Singh, Dilawar</creatorcontrib><creatorcontrib>Andrews, Steven S</creatorcontrib><title>Python interfaces for the Smoldyn simulator</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract Motivation 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. Results 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. Availability and implementation 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.   Documentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html.</description><subject>Documentation</subject><subject>Software</subject><subject>Systems Biology</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkE1LAzEQhoMotlb_QtmjIGsz-ermKMUvKCio55BkszSyu6lJ9tB_75ZWwZunGYbnfQcehOaAbwFLujA--L4JsdPZ27QwWRtO8QmaAhO4JJjL03GnYlmyCtMJukjpE2MOjLFzNKGMSAoYT9HN6y5vQl_4PrvYaOtSMbYWeeOKty609a4vku-GVucQL9FZo9vkro5zhj4e7t9XT-X65fF5dbcuLWVVLqUWVgpnDNPcVBWrLaZUgtR1w5wggiwFh6biZDwZLbDQde3qSmpimAG3pDN0fejdxvA1uJRV55N1bat7F4akCOccgADsUXFAbQwpRdeobfSdjjsFWO1Fqb-i1FHUGJwffwymc_Vv7MfMCMABCMP2v6XfxUF7TQ</recordid><startdate>20211222</startdate><enddate>20211222</enddate><creator>Singh, Dilawar</creator><creator>Andrews, Steven S</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4645-3211</orcidid><orcidid>https://orcid.org/0000-0002-4576-8107</orcidid></search><sort><creationdate>20211222</creationdate><title>Python interfaces for the Smoldyn simulator</title><author>Singh, Dilawar ; Andrews, Steven S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c348t-9a6c96ebb4a5b884dc033919adf4e62627651f85219aba606added89a2b4b1e73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Documentation</topic><topic>Software</topic><topic>Systems Biology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Singh, Dilawar</creatorcontrib><creatorcontrib>Andrews, Steven S</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Singh, Dilawar</au><au>Andrews, Steven S</au><au>Martel, Pier Luigi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Python interfaces for the Smoldyn simulator</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2021-12-22</date><risdate>2021</risdate><volume>38</volume><issue>1</issue><spage>291</spage><epage>293</epage><pages>291-293</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract Motivation 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. Results 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. Availability and implementation 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.   Documentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>34293100</pmid><doi>10.1093/bioinformatics/btab530</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0002-4645-3211</orcidid><orcidid>https://orcid.org/0000-0002-4576-8107</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext_linktorsrc
identifier ISSN: 1367-4803
ispartof Bioinformatics, 2021-12, Vol.38 (1), p.291-293
issn 1367-4803
1460-2059
1367-4811
language eng
recordid cdi_proquest_miscellaneous_2555112117
source Access via Oxford University Press (Open Access Collection)
subjects Documentation
Software
Systems Biology
title Python interfaces for the Smoldyn simulator
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-28T23%3A55%3A42IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_TOX&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Python%20interfaces%20for%20the%20Smoldyn%20simulator&rft.jtitle=Bioinformatics&rft.au=Singh,%20Dilawar&rft.date=2021-12-22&rft.volume=38&rft.issue=1&rft.spage=291&rft.epage=293&rft.pages=291-293&rft.issn=1367-4803&rft.eissn=1460-2059&rft_id=info:doi/10.1093/bioinformatics/btab530&rft_dat=%3Cproquest_TOX%3E2555112117%3C/proquest_TOX%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2555112117&rft_id=info:pmid/34293100&rft_oup_id=10.1093/bioinformatics/btab530&rfr_iscdi=true