{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T16:28:34Z","timestamp":1759940914112},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments.<\/jats:p>\n               <jats:p>Availability and implementation: ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http:\/\/protocolnavigator.org\/index.html under the GPL v2 license.<\/jats:p>\n               <jats:p>Contact: \u00a0wpciak@cf.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu554","type":"journal-article","created":{"date-parts":[[2014,8,23]],"date-time":"2014-08-23T04:14:10Z","timestamp":1408767250000},"page":"3440-3442","source":"Crossref","is-referenced-by-count":8,"title":["ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments"],"prefix":"10.1093","volume":"30","author":[{"given":"Imtiaz A.","family":"Khan","sequence":"first","affiliation":[{"name":"1 School of Medicine, Cardiff University, Cardiff, UK, 2Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and 3School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK"},{"name":"1 School of Medicine, Cardiff University, Cardiff, UK, 2Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and 3School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam","family":"Fraser","sequence":"additional","affiliation":[{"name":"1 School of Medicine, Cardiff University, Cardiff, UK, 2Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and 3School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark-Anthony","family":"Bray","sequence":"additional","affiliation":[{"name":"1 School of Medicine, Cardiff University, Cardiff, UK, 2Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and 3School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul J.","family":"Smith","sequence":"additional","affiliation":[{"name":"1 School of Medicine, Cardiff University, Cardiff, UK, 2Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and 3School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nick S.","family":"White","sequence":"additional","affiliation":[{"name":"1 School of Medicine, Cardiff University, Cardiff, UK, 2Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and 3School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne E.","family":"Carpenter","sequence":"additional","affiliation":[{"name":"1 School of Medicine, Cardiff University, Cardiff, UK, 2Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and 3School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rachel J.","family":"Errington","sequence":"additional","affiliation":[{"name":"1 School of Medicine, Cardiff University, Cardiff, UK, 2Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and 3School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,8,22]]},"reference":[{"key":"2023012712024397400_btu554-B1","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/483531a","article-title":"Drug development: raise standards for preclinical cancer research","volume":"483","author":"Begley","year":"2012","journal-title":"Nature"},{"key":"2023012712024397400_btu554-B2","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1126\/science.331.6018.692","article-title":"Challenges and opportunities","volume":"331","author":"Editorial","year":"2011","journal-title":"Science"},{"key":"2023012712024397400_btu554-B3","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1038\/496398a","article-title":"Reducing our irreproducibility","volume":"496","author":"Editorial","year":"2013","journal-title":"Nature"},{"key":"2023012712024397400_btu554-B4","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1080\/09505430701872814","article-title":"Standardising the unknown:practicable pluripotency as doable futures","volume":"17","author":"Eriksson","year":"2008","journal-title":"Sci. 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Data sharing and reuse in the long tail of science and technology","volume":"8","author":"Wallis","year":"2013","journal-title":"PLoS One"},{"key":"2023012712024397400_btu554-B9","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/nar\/gkt328","article-title":"The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud","volume":"41","author":"Wolstencroft","year":"2013","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/23\/3440\/48931841\/bioinformatics_30_23_3440.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/23\/3440\/48931841\/bioinformatics_30_23_3440.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:00:17Z","timestamp":1674824417000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/23\/3440\/207149"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,8,22]]},"references-count":9,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2014,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu554","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,12,1]]},"published":{"date-parts":[[2014,8,22]]}}}