{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,8]],"date-time":"2024-08-08T13:51:05Z","timestamp":1723125065192},"reference-count":2,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2020,5,29]],"date-time":"2020-05-29T00:00:00Z","timestamp":1590710400000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Skyline Targeted Proteomics Environment","award":["R01 GM103551"],"award-info":[{"award-number":["R01 GM103551"]}]},{"name":"Library of Integrated Network-Based Cellular Signatures","award":["U54 HG008097"],"award-info":[{"award-number":["U54 HG008097"]}]},{"name":"A Sustainable Cloud Solution for Mass Spectrometry Data","award":["R01 GM121696"],"award-info":[{"award-number":["R01 GM121696"]}]},{"name":"Quantifying Proteins in Plasma to Democratize Personalized Medicine for Patients","award":["1U01DK121289-01"],"award-info":[{"award-number":["1U01DK121289-01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Skyline is a Windows application for targeted mass spectrometry method creation and quantitative data analysis. Like most graphical user interface (GUI) tools, it has a complex user interface with many ways for users to edit their files which makes the task of logging user actions challenging and is the reason why audit logging of every change is not common in GUI tools. We present an object comparison-based approach to audit logging for Skyline that is extensible to other GUI tools. The new audit logging system keeps track of all document modifications made through the GUI or the command line and displays them in an interactive grid. The audit log can also be uploaded and viewed in Panorama, a web repository for Skyline documents that can be configured to only accept documents with a valid audit log, based on embedded hashes to protect log integrity. This makes workflows involving Skyline and Panorama more reproducible.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Skyline is freely available at https:\/\/skyline.ms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa547","type":"journal-article","created":{"date-parts":[[2020,5,25]],"date-time":"2020-05-25T11:08:09Z","timestamp":1590404889000},"page":"4366-4368","source":"Crossref","is-referenced-by-count":3,"title":["Audit logs to enforce document integrity in Skyline and Panorama"],"prefix":"10.1093","volume":"36","author":[{"given":"Tobias","family":"Rohde","sequence":"first","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rita","family":"Chupalov","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas","family":"Shulman","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vagisha","family":"Sharma","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Josh","family":"Eckels","sequence":"additional","affiliation":[{"name":"LabKey , San Diego, CA 92101, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian S","family":"Pratt","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael J","family":"MacCoss","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brendan X","family":"MacLean","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,5,28]]},"reference":[{"key":"2023062312041705900_btaa547-B1","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: an open source document editor for creating and analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"key":"2023062312041705900_btaa547-B2","doi-asserted-by":"crossref","first-page":"4205","DOI":"10.1021\/pr5006636","article-title":"Panorama: a targeted proteomics knowledge base","volume":"13","author":"Sharma","year":"2014","journal-title":"J. Proteome Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa547\/33651000\/btaa547.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/15\/4366\/50671663\/bioinformatics_36_15_4366.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/15\/4366\/50671663\/bioinformatics_36_15_4366.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,23]],"date-time":"2023-06-23T12:05:46Z","timestamp":1687521946000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/15\/4366\/5848405"}},"subtitle":[],"editor":[{"given":"Pier","family":"Luigi Martelli","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2020,5,28]]},"references-count":2,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2020,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa547","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,8,1]]},"published":{"date-parts":[[2020,5,28]]}}}