{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T03:10:59Z","timestamp":1688958659176},"reference-count":2,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: A host of formal, textual languages for modeling cellular processes have recently emerged, but their simulation tools often require an installation process which can pose a barrier for use. Bio Simulators is a framework for easy online deployment of simulators, providing a uniform web-based user interface to a diverse pool of tools. The framework is demonstrated through two plugins based on the KaSim Kappa simulator, one running directly in the browser and another running in the cloud.<\/jats:p><jats:p>Availability: Web tool: bsims.azurewebsites.net. KaSim client side simulator: github.com\/NicolasOury\/KaSimJS. KaSim cloud simulator: github.com\/mdpedersen\/KaSimCloud.<\/jats:p><jats:p>Contact: \u00a0michael.d.pedersen@gmail.com or Andrew.Phillips@microsoft.com<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu050","type":"journal-article","created":{"date-parts":[[2014,1,28]],"date-time":"2014-01-28T01:56:48Z","timestamp":1390874208000},"page":"1491-1492","source":"Crossref","is-referenced-by-count":2,"title":["Bio Simulators: a web UI for biological simulation"],"prefix":"10.1093","volume":"30","author":[{"given":"Michael","family":"Pedersen","sequence":"first","affiliation":[{"name":"1 Department of Plant Sciences, Cambridge University, Cambridge CB2 3EA, UK, 2School of Informatics, Edinburgh University, Edinburgh EH8 9AB, Scotland and 3Microsoft Research, Cambridge CB1 2FB, UK"},{"name":"1 Department of Plant Sciences, Cambridge University, Cambridge CB2 3EA, UK, 2School of Informatics, Edinburgh University, Edinburgh EH8 9AB, Scotland and 3Microsoft Research, Cambridge CB1 2FB, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicolas","family":"Oury","sequence":"additional","affiliation":[{"name":"1 Department of Plant Sciences, Cambridge University, Cambridge CB2 3EA, UK, 2School of Informatics, Edinburgh University, Edinburgh EH8 9AB, Scotland and 3Microsoft Research, Cambridge CB1 2FB, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colin","family":"Gravill","sequence":"additional","affiliation":[{"name":"1 Department of Plant Sciences, Cambridge University, Cambridge CB2 3EA, UK, 2School of Informatics, Edinburgh University, Edinburgh EH8 9AB, Scotland and 3Microsoft Research, Cambridge CB1 2FB, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Phillips","sequence":"additional","affiliation":[{"name":"1 Department of Plant Sciences, Cambridge University, Cambridge CB2 3EA, UK, 2School of Informatics, Edinburgh University, Edinburgh EH8 9AB, Scotland and 3Microsoft Research, Cambridge CB1 2FB, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,1,27]]},"reference":[{"key":"2023041302470148000_","doi-asserted-by":"crossref","DOI":"10.1007\/978-94-007-6803-1_9","article-title":"Innovations of the rule-based modeling approach","volume-title":"Systems Biology: integrative biology and simulation tools","author":"Chylek","year":"2013"},{"key":"2023041302470148000_","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-540-74407-8_3","article-title":"Rule-based modelling of cellular signalling","author":"Danos","year":"2007"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/10\/1491\/49860409\/bioinformatics_30_10_1491.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/10\/1491\/49860409\/bioinformatics_30_10_1491.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T02:48:48Z","timestamp":1688957328000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/10\/1491\/267657"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1,27]]},"references-count":2,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2014,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu050","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,5,15]]},"published":{"date-parts":[[2014,1,27]]}}}