{"id":2975,"date":"2017-06-05T18:26:03","date_gmt":"2017-06-05T22:26:03","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/msr\/?page_id=2975"},"modified":"2018-06-01T17:00:37","modified_gmt":"2018-06-01T21:00:37","slug":"glycresoft","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/msr\/glycresoft\/","title":{"rendered":"GlycReSoft"},"content":{"rendered":"<style>.clearfix:after { visibility: hidden;display: block;font-size: 0;content: \" \";clear: both;height: 0;}.clearfix { display: inline-block; }\/* start commented backslash hack \\*\/* html .clearfix { height: 1%; }.clearfix { display: block; }\/* close commented backslash hack *\/<br \/>\n<\/style>\n<p><script type=\"text\/javascript\">\r\n    jQuery(document).ready(function () {\r\n        GetLatestReleaseInfo(\r\n           \"https:\/\/api.github.com\/repos\/BostonUniversityCBMS\/glycresoft_desktop\/releases\/latest\",\r\n           \"#glycresoft-download-container\");\r\n\r\n    });\r\n\r\n    function GetLatestReleaseInfo(url, container) {\r\n        \/\/ Use GitHub Releases API to look up the latest release on GitHub,\r\n        \/\/ and wire up the download link to point to the latest version of\r\n        \/\/ each artefact\r\n        jQuery.getJSON(url).done(function (release) {\r\n            console.log(release.assets);\r\n            var downloadContainer = jQuery(container)\r\n            for(var i = 0; i < release.assets.length; i++) { \r\n                var asset = release.assets[i];\r\n                var productName = null\r\n                if((\/GlycReSoft_.*.exe\/i).test(asset.name)) {\r\n                    productName = \"Windows Graphical Installer\"\r\n                } else if (asset.name === \"glycresoft-cli-linux.zip\") {\r\n                    productName = \"Linux CLI Executable\"\r\n                } else if (asset.name === \"glycresoft-cli-win64.zip\") {\r\n                    productName = \"Windows CLI Executable\"\r\n                } else {\r\n                    continue\r\n                }\r\n\r\n                var downloadCount = asset.download_count;\r\n                \r\n                var oneHour = 60 * 60 * 1000;\r\n                var oneDay = 24 * oneHour;\r\n                var dateDiff = new Date() - new Date(asset.updated_at);\r\n                var timeAgo;\r\n                if (dateDiff < oneDay)\r\n                {\r\n                    timeAgo = (dateDiff \/ oneHour).toFixed(1) + \" hours ago\";\r\n                }\r\n                else\r\n                {\r\n                    timeAgo = (dateDiff \/ oneDay).toFixed(1) + \" days ago\";\r\n                }\r\n                var releaseInfo = release.name + \" was updated \" + timeAgo + \" and downloaded \" + downloadCount.toLocaleString() + \" times.\";\r\n                var downloadEntry = jQuery(\"<div><\/div>\").addClass(\"glycresoft-download-entry\")\r\n                var downloadLink = jQuery('<a class=\"glycresoft-download-link\">' + productName + '<\/a>').attr(\"href\", asset.browser_download_url)\r\n                downloadEntry.append(downloadLink)\r\n                downloadEntry.append(\"<br>\")\r\n                var releaseInfo = jQuery(\"<small><\/small>\").addClass(\".release-info\").text(releaseInfo)\r\n                downloadEntry.append(releaseInfo)\r\n                downloadContainer.append(downloadEntry)\r\n            }\r\n        });\r\n    }\r\n<\/script><\/p>\n<div class=\"clearfix\">\n<div style=\"float: left; margin-top: 50px; width: 80%;\">\n<h4>Software for Glycomics and Glycoproteomics<\/h4>\n<\/div>\n<div style=\"float: right;\"><img loading=\"lazy\" src=\"\/msr\/files\/2017\/06\/GlycReSoft-Logo-300x300.png\" alt=\"GlycReSoft Logo\" width=\"120\" height=\"120\" class=\"alignnone size-medium wp-image-2983\" srcset=\"https:\/\/www.bumc.bu.edu\/msr\/files\/2017\/06\/GlycReSoft-Logo-300x300.png 300w, https:\/\/www.bumc.bu.edu\/msr\/files\/2017\/06\/GlycReSoft-Logo-150x150.png 150w, https:\/\/www.bumc.bu.edu\/msr\/files\/2017\/06\/GlycReSoft-Logo.png 417w\" sizes=\"(max-width: 120px) 100vw, 120px\" \/><\/div>\n<\/div>\n<div id=\"glycresoft-download-container\"><\/div>\n<div><a href=\"https:\/\/mobiusklein.github.io\/glycresoft\/\">Technical Manual and Documentation<\/a><\/div>\n<div><a href=\"https:\/\/groups.google.com\/forum\/#!forum\/glycresoft\">Support Forum<\/a> and <a href='mailto:glycresoft@googlegroups.com'>Mailing List<\/a><\/div>\n<p><\/p>\n<div>\nIf you&#8217;ve used this software in academic work, please cite: Klein, J., Carvalho, L., &#038; Zaia, J. (2018). Application of Network Smoothing to Glycan LC-MS Profiling. Bioinformatics <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/bty397\">https:\/\/doi.org\/10.1093\/bioinformatics\/bty397<\/a>\n<\/div>\n<p><\/p>\n<div id=\"glycresoft-content-container\">GlycReSoft implements algorithms for<\/p>\n<ul>\n<li>Generation of Glycan Composition Search Spaces using algebraic rules, the glySpace database network, or from text files<\/li>\n<li>Generation of Glycopeptide Sequence Search Spaces using protein sequences in FASTA format or Proteomics search results in PSI mzIdentML format, combined with a glycan search space. This supports <em>N<\/em>-linked, <em>O<\/em>-linked, or GAG-linker glycopeptides<\/li>\n<li>Deisotoping and charge state deconvolution of glycan and glycopeptide mass spectra<\/li>\n<li>Identification and quantification of glycans by MS and glycopeptides by MS\/MS<\/li>\n<\/ul>\n<\/div>\n<div>\n<p>GlycReSoft is able to read LC-MS data in mzML and mzXML format.Though there is currently only a Windows precompiled build, GlycReSoft is platform independent, and is usable from a remote web server, a local desktop computer, or from a terminal.<\/p>\n<\/div>\n<div>GlycReSoft is open-source and publicly available. It is made up of several components:<br \/>\n<a href=\"https:\/\/github.com\/BostonUniversityCBMS\/glycresoft\">Core Library<\/a><br \/>\n<a href=\"https:\/\/github.com\/BostonUniversityCBMS\/glycresoft_app\">Web Application Server<\/a><br \/>\n<a href=\"https:\/\/github.com\/BostonUniversityCBMS\/glycresoft_desktop\">Desktop Application<\/a><br \/>\n<a href=\"https:\/\/github.com\/BostonUniversityCBMS\/ms_deisotope\">Deconvolution Library<\/a><br \/>\n<a href=\"https:\/\/github.com\/BostonUniversityCBMS\/glypy\">Glycan Structural Library<\/a><br \/>\n<a href=\"https:\/\/github.com\/BostonUniversityCBMS\/glycopeptidepy\">Proteomics Library<\/a><br \/>\n<a href=\"https:\/\/github.com\/BostonUniversityCBMS\/psims\">PSI-HUPO XML Library<\/a><\/p>\n<p>\n<a href=\"https:\/\/www.bumc.bu.edu\/msr\/glycoproteomics-test-data\/\">Here are glycoproteomics test data sets<\/a><\/p>\n<\/div>\n<div>\n<h4>Tutorials<\/h4>\n<h5>Glycan Composition LC-MS Search Results Interpretation<\/h5>\n<div style=\"width: 1280px;\" class=\"wp-video\"><!--[if lt IE 9]><script>document.createElement('video');<\/script><![endif]-->\n<video class=\"wp-video-shortcode\" id=\"video-2975-1\" width=\"1280\" height=\"698\" preload=\"metadata\" controls=\"controls\"><source type=\"video\/mp4\" src=\"\/msr\/files\/2017\/06\/glycan-composition-search-results-tutorial.mp4?_=1\" \/><a href=\"\/msr\/files\/2017\/06\/glycan-composition-search-results-tutorial.mp4\">\/msr\/files\/2017\/06\/glycan-composition-search-results-tutorial.mp4<\/a><\/video><\/div>\n<h5>Glycopeptide LC-MS\/MS Search Results Interpretation<\/h5>\n<div style=\"width: 1280px;\" class=\"wp-video\"><video class=\"wp-video-shortcode\" id=\"video-2975-2\" width=\"1280\" height=\"698\" preload=\"metadata\" controls=\"controls\"><source type=\"video\/mp4\" src=\"\/msr\/files\/2017\/06\/glycopeptide-identification-search-results-tutorial.mp4?_=2\" \/><a href=\"\/msr\/files\/2017\/06\/glycopeptide-identification-search-results-tutorial.mp4\">\/msr\/files\/2017\/06\/glycopeptide-identification-search-results-tutorial.mp4<\/a><\/video><\/div>\n<h5>Sample Preprocessing Tutorial<\/h5>\n<p><em>Coming Soon<\/em><\/p>\n<h5>Glycan Hypothesis Tutorial<\/h5>\n<p><div style=\"width: 1920px;\" class=\"wp-video\"><video class=\"wp-video-shortcode\" id=\"video-2975-3\" width=\"1920\" height=\"1080\" preload=\"metadata\" controls=\"controls\"><source type=\"video\/mp4\" src=\"\/msr\/files\/2017\/06\/glycan-hypothesis-from-text-file.mp4?_=3\" \/><a href=\"\/msr\/files\/2017\/06\/glycan-hypothesis-from-text-file.mp4\">\/msr\/files\/2017\/06\/glycan-hypothesis-from-text-file.mp4<\/a><\/video><\/div><br \/>\n<em>More Coming Soon<\/em><\/p>\n<h5>Glycopeptide Hypothesis Tutorial<\/h5>\n<p><em>Coming Soon <\/em><\/p>\n<div id=\"experimental-version-download-container\">\n  <b>2018 Publication Version (For Review Only)<\/b><br \/>\n  <a href=\"https:\/\/github.com\/BostonUniversityCBMS\/glycresoft\/releases\/tag\/v0.3.0\">Download Options<\/a>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Software for Glycomics and Glycoproteomics Technical Manual and Documentation Support Forum and Mailing List If you&#8217;ve used this software in academic work, please cite: Klein, J., Carvalho, L., &#038; Zaia, J. (2018). Application of Network Smoothing to Glycan LC-MS Profiling. Bioinformatics https:\/\/doi.org\/10.1093\/bioinformatics\/bty397 GlycReSoft implements algorithms for Generation of Glycan Composition Search Spaces using algebraic rules, [&hellip;]<\/p>\n","protected":false},"author":12101,"featured_media":0,"parent":0,"menu_order":8,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2975"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/users\/12101"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/comments?post=2975"}],"version-history":[{"count":49,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2975\/revisions"}],"predecessor-version":[{"id":3339,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/2975\/revisions\/3339"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/media?parent=2975"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}