{"id":18,"date":"2021-04-14T14:01:49","date_gmt":"2021-04-14T14:01:45","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/template\/help-sheets\/"},"modified":"2023-02-28T16:41:15","modified_gmt":"2023-02-28T16:41:15","slug":"help-sheet","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/proteomics-bioinformatics-materials\/help-sheet\/","title":{"rendered":"Technical help sheet"},"content":{"rendered":"\n<h3 class=\"wp-block-heading\" id=\"block-ba5ec861-b630-43f6-afbf-b81ea6e3772f\">Technical requirements for data analysis<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\" id=\"block-ff390057-ad6f-4b19-abbb-8266af93d013\">You will require the following tools for executing the practicals in this course:<\/p>\n\n\n\n<h3 class=\"wp-block-heading\" id=\"block-63583c0f-3013-4649-9d19-3e1e665a76ce\"><strong>Protein Identification, from Lennart Martens, Harald Barsnes and Tine Clays<\/strong><\/h3>\n\n\n\n<ul class=\"wp-block-list\" id=\"block-dbb300cc-a2d9-4081-b6e5-1c127f981c9a\"><li>Java JRE between 1.8 and 1.15 &#8211; <a rel=\"noreferrer noopener\" href=\"https:\/\/adoptopenjdk.net\/releases.html\" target=\"_blank\">https:\/\/adoptopenjdk.net\/releases.html<\/a><\/li><li>SearchGUI &#8211; <a href=\"http:\/\/compomics.github.io\/projects\/searchgui\" target=\"_blank\" rel=\"noreferrer noopener\">http:\/\/compomics.github.io\/projects\/searchgui<\/a> <\/li><li>PeptideShaker &#8211; <a href=\"http:\/\/compomics.github.io\/projects\/peptide-shaker\" target=\"_blank\" rel=\"noreferrer noopener\">http:\/\/compomics.github.io\/projects\/peptide-shaker <\/a><\/li><li>ThermoRawFileParserGUI &#8211; <a href=\"https:\/\/github.com\/compomics\/ThermoRawFileParserGUI\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/github.com\/compomics\/ThermoRawFileParserGUI<\/a> <\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Introduction to MaxQuant, from Christoph Wichmann, Peli Kyriakidou and Daniela Ferretti<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>.NET Framework 4.7.3 or higher &#8211; <a href=\"https:\/\/dotnet.microsoft.com\/download\/dotnet-framework\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/dotnet.microsoft.com\/download\/dotnet-framework<\/a><\/li><li>MaxQuant latest version &#8211; <a href=\"https:\/\/maxquant.org\/maxquant\/\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/maxquant.org\/maxquant\/<\/a><\/li><li>Perseus latest version &#8211; <a href=\"https:\/\/maxquant.org\/perseus\/\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/maxquant.org\/perseus\/<\/a><\/li><li>.net core 2.1 &#8211; <a href=\"https:\/\/dotnet.microsoft.com\/download\/dotnet\/2.1\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/dotnet.microsoft.com\/download\/dotnet\/2.1<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Integration using Cytoscape and Network Interference, from Kalpana Panneerselvam, Birgit Meldal and Eliot Ragueneau<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Cytoscape version 3.8.2 &#8211; <a href=\"https:\/\/cytoscape.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/cytoscape.org\/<\/a><\/li><li>Apps in Cytoscape: IntAct app &#8211; <a href=\"https:\/\/apps.cytoscape.org\/apps\/intactapp\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/apps.cytoscape.org\/apps\/intactapp<\/a><\/li><li>MCODE &#8211; <a href=\"https:\/\/apps.cytoscape.org\/apps\/intactapp\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/apps.cytoscape.org\/apps\/intactapp<\/a><\/li><li>ClueGO (needs liscence) &#8211; <a href=\"https:\/\/apps.cytoscape.org\/apps\/intactapp\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/apps.cytoscape.org\/apps\/intactapp<\/a><\/li><\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Technical requirements for data analysis You will require the following tools for executing the practicals in this course: Protein Identification, from Lennart Martens, Harald Barsnes and Tine Clays Java JRE between 1.8 and 1.15 &#8211; https:\/\/adoptopenjdk.net\/releases.html SearchGUI &#8211; http:\/\/compomics.github.io\/projects\/searchgui PeptideShaker &#8211; http:\/\/compomics.github.io\/projects\/peptide-shaker ThermoRawFileParserGUI &#8211; https:\/\/github.com\/compomics\/ThermoRawFileParserGUI Introduction to MaxQuant, from Christoph Wichmann, Peli Kyriakidou and Daniela&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":6,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-18","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/proteomics-bioinformatics-materials\/wp-json\/wp\/v2\/pages\/18","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/proteomics-bioinformatics-materials\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/proteomics-bioinformatics-materials\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/proteomics-bioinformatics-materials\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/proteomics-bioinformatics-materials\/wp-json\/wp\/v2\/comments?post=18"}],"version-history":[{"count":13,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/proteomics-bioinformatics-materials\/wp-json\/wp\/v2\/pages\/18\/revisions"}],"predecessor-version":[{"id":1985,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/proteomics-bioinformatics-materials\/wp-json\/wp\/v2\/pages\/18\/revisions\/1985"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/proteomics-bioinformatics-materials\/wp-json\/wp\/v2\/media?parent=18"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}