{"id":1226,"date":"2023-10-10T15:10:23","date_gmt":"2023-10-10T22:10:23","guid":{"rendered":"https:\/\/villenlab.gs.washington.edu\/wordpress\/?page_id=1226"},"modified":"2026-03-03T14:25:19","modified_gmt":"2026-03-03T22:25:19","slug":"resources","status":"publish","type":"page","link":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"\n<div class=\"wp-block-cover alignfull is-light is-repeated has-custom-content-position is-position-top-left wp-duotone-2e2e2e-6d6d6d-1\"><div class=\"wp-block-cover__image-background wp-image-1538 is-repeated\" style=\"background-position:93% 56%;background-image:url(https:\/\/villenlab.gs.washington.edu\/wordpress\/wp-content\/uploads\/2023\/10\/PerturbationsHeatmap.png)\"><\/div><span aria-hidden=\"true\" class=\"wp-block-cover__background has-nv-light-bg-background-color has-background-dim-0 has-background-dim\"><\/span><div class=\"wp-block-cover__inner-container is-layout-constrained wp-block-cover-is-layout-constrained\">\n<div class=\"aligncenter blockart-section blockart-section-92477f9e aligncenter\"><div class=\"blockart-container\"><div class=\"blockart-section-inner\">\n<div class=\"blockart-column blockart-column-7fffbca0\"><div class=\"blockart-column-inner\">\n<p class=\"has-nv-text-dark-bg-color has-text-color has-background\" style=\"background:linear-gradient(90deg,rgba(242,246,250,0) 0%,rgba(5,5,5,0.43) 0%);font-size:40px\">Resources<\/p>\n<\/div><\/div>\n<\/div><\/div><\/div>\n<\/div><\/div>\n\n\n\n<div style=\"height:33px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p class=\"has-text-align-center has-medium-font-size\">We are providing tools and sharing data for some of our publications as web resources. Links are provided below:<\/p>\n\n\n\n<div style=\"height:69px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-buttons is-layout-flex wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button has-custom-width wp-block-button__width-100 is-style-default\"><a class=\"wp-block-button__link has-background wp-element-button\" href=\"#datasets\" style=\"background-color:#484848\">Publication Datasets<\/a><\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-buttons is-layout-flex wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button has-custom-width wp-block-button__width-100 is-style-default\"><a class=\"wp-block-button__link has-background wp-element-button\" href=\"#software\" style=\"background-color:#484848\">Software<\/a><\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-buttons is-layout-flex wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button has-custom-width wp-block-button__width-100 is-style-default\"><a class=\"wp-block-button__link has-background wp-element-button\" href=\"#protocols\" style=\"background-color:#484848\">Protocols<\/a><\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:100%\"><\/div>\n<\/div>\n\n\n\n<div style=\"height:100px\" aria-hidden=\"true\" id=\"datasets\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-align-center\">Publication Datasets<\/h2>\n\n\n\n<hr class=\"wp-block-separator has-text-color has-nv-dark-bg-color has-alpha-channel-opacity has-nv-dark-bg-background-color has-background\"\/>\n\n\n\n<div style=\"height:70px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div class=\"wp-block-media-text is-stacked-on-mobile is-vertically-aligned-center is-style-default\" style=\"grid-template-columns:39% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"7128\" height=\"1393\" src=\"https:\/\/villenlab.gs.washington.edu\/wordpress\/wp-content\/uploads\/2023\/10\/image.png\" alt=\"\" class=\"wp-image-1283 size-full\"\/><\/figure><div class=\"wp-block-media-text__content\">\n<p class=\"has-text-align-center has-medium-font-size\"><a href=\"https:\/\/phosphopedia.gs.washington.edu\/PhosphoproteomicsAssay\/\" data-type=\"link\" data-id=\"https:\/\/phosphopedia.gs.washington.edu\/PhosphoproteomicsAssay\/\"><strong>Phosphopedia<\/strong><br><\/a>targeted phosphoproteomic assays<\/p>\n<\/div><\/div>\n\n\n\n<div style=\"height:37px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<hr class=\"wp-block-separator has-text-color has-alpha-channel-opacity has-background\" style=\"background-color:#e4e4e4;color:#e4e4e4\"\/>\n\n\n\n<div class=\"wp-block-media-text is-stacked-on-mobile\" style=\"grid-template-columns:25% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"375\" height=\"375\" src=\"https:\/\/villenlab.gs.washington.edu\/wordpress\/wp-content\/uploads\/2023\/10\/1-s2.0-S2211124715003411-fx1.jpg\" alt=\"\" class=\"wp-image-1287 size-full\"\/><\/figure><div class=\"wp-block-media-text__content\">\n<p class=\"has-text-align-center has-medium-font-size\"><strong><a href=\"https:\/\/zucchini.gs.washington.edu\/BreastCancerProteome\/\" data-type=\"link\" data-id=\"https:\/\/zucchini.gs.washington.edu\/BreastCancerProteome\/\">Triple-Negative Breast Cancer Proteomes<\/a><\/strong><\/p>\n<\/div><\/div>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<hr class=\"wp-block-separator has-text-color has-alpha-channel-opacity has-background\" style=\"background-color:#e4e4e4;color:#e4e4e4\"\/>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:100%\">\n<div class=\"wp-block-media-text is-stacked-on-mobile\" style=\"grid-template-columns:39% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"834\" height=\"405\" src=\"https:\/\/villenlab.gs.washington.edu\/wordpress\/wp-content\/uploads\/2023\/10\/image-2.png\" alt=\"\" class=\"wp-image-1300 size-full\"\/><\/figure><div class=\"wp-block-media-text__content\">\n<p class=\"has-text-align-center has-medium-font-size\"><strong><a href=\"https:\/\/yeastphosphoatlas.gs.washington.edu\/\" data-type=\"link\" data-id=\"https:\/\/yeastphosphoatlas.gs.washington.edu\/\">Yeast PhosphoAtlas<\/a><\/strong><\/p>\n<\/div><\/div>\n<\/div>\n<\/div>\n\n\n\n<div style=\"height:55px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<hr class=\"wp-block-separator has-text-color has-alpha-channel-opacity has-background\" style=\"background-color:#e4e4e4;color:#e4e4e4\"\/>\n\n\n\n<div class=\"wp-block-media-text is-stacked-on-mobile\" style=\"grid-template-columns:29% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"728\" height=\"461\" src=\"https:\/\/villenlab.gs.washington.edu\/wordpress\/wp-content\/uploads\/2023\/10\/image-3.png\" alt=\"\" class=\"wp-image-1301 size-full\"\/><\/figure><div class=\"wp-block-media-text__content\">\n<p class=\"has-text-align-center has-medium-font-size\"><strong><a href=\"https:\/\/rlsproteomics.gs.washington.edu\/\" data-type=\"link\" data-id=\"https:\/\/rlsproteomics.gs.washington.edu\/\">Yeast Replicative Lifespan &#8211; Multidimensional Proteomic Atlas<\/a><\/strong><\/p>\n<\/div><\/div>\n\n\n\n<div style=\"height:130px\" aria-hidden=\"true\" id=\"software\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\"><\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<h2 class=\"wp-block-heading has-text-align-center\">Software<\/h2>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\"><div class=\"wp-block-image\">\n<figure class=\"alignleft size-full is-resized\"><a href=\"https:\/\/github.com\/Villen-Lab\"><img loading=\"lazy\" decoding=\"async\" width=\"512\" height=\"512\" src=\"https:\/\/villenlab.gs.washington.edu\/wordpress\/wp-content\/uploads\/2023\/10\/github.png\" alt=\"repository\" class=\"wp-image-1563\" style=\"object-fit:cover;width:40px;height:40px\"\/><\/a><\/figure>\n<\/div><\/div>\n<\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<div style=\"height:70px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div class=\"wp-block-media-text is-stacked-on-mobile\" style=\"grid-template-columns:29% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"1920\" height=\"576\" src=\"https:\/\/villenlab.gs.washington.edu\/wordpress\/wp-content\/uploads\/2023\/10\/pyascore.png\" alt=\"\" class=\"wp-image-1561 size-full\"\/><\/figure><div class=\"wp-block-media-text__content\">\n<p class=\"has-text-align-center has-medium-font-size\"><strong><a href=\"https:\/\/github.com\/Villen-Lab\/pyAscore\" data-type=\"link\" data-id=\"https:\/\/github.com\/Villen-Lab\/pyAscore\">pyAscore<\/a><\/strong><\/p>\n\n\n\n<p class=\"has-text-align-center has-medium-font-size\">The&nbsp;<strong>pyAscore&nbsp;<\/strong>package provides a blazingly fast implementation of the <strong>Ascore <\/strong>algorithm for localizing peptide post-translational modifications from mass spectrometry data<\/p>\n<\/div><\/div>\n\n\n\n<div style=\"height:46px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<hr class=\"wp-block-separator has-text-color has-alpha-channel-opacity has-background\" style=\"background-color:#e4e4e4;color:#e4e4e4\"\/>\n\n\n\n<div style=\"height:70px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div class=\"wp-block-media-text is-stacked-on-mobile\" style=\"grid-template-columns:29% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"469\" height=\"387\" src=\"https:\/\/villenlab.gs.washington.edu\/wordpress\/wp-content\/uploads\/2023\/10\/IsobaricQuant_Snapshot.png\" alt=\"\" class=\"wp-image-1567 size-full\"\/><\/figure><div class=\"wp-block-media-text__content\">\n<p class=\"has-text-align-center has-large-font-size\"><strong><a href=\"https:\/\/github.com\/Villen-Lab\/isobaricquant\" data-type=\"link\" data-id=\"https:\/\/github.com\/Villen-Lab\/isobaricquant\">IsobaricQuant<\/a><\/strong><\/p>\n\n\n\n<p class=\"has-text-align-center has-medium-font-size\"><strong>IsobaricQuant <\/strong>is a Java-based software tool for the quantification, visualization, and filtering of isobarically-labeled peptides. <a href=\"https:\/\/isobaricquant.readthedocs.io\/\" data-type=\"link\" data-id=\"https:\/\/isobaricquant.readthedocs.io\/\">Documentation<\/a><\/p>\n<\/div><\/div>\n\n\n\n<hr class=\"wp-block-separator has-text-color has-nv-light-bg-color has-alpha-channel-opacity has-nv-light-bg-background-color has-background\"\/>\n\n\n\n<div style=\"height:100px\" aria-hidden=\"true\" id=\"protocols\" class=\"wp-block-spacer\"><\/div>\n","protected":false},"excerpt":{"rendered":"<p>We are providing tools and sharing data for some of our publications as web resources. Links are provided below: Publication Datasets Phosphopediatargeted phosphoproteomic assays Triple-Negative Breast Cancer Proteomes Yeast PhosphoAtlas Yeast Replicative Lifespan &#8211; Multidimensional Proteomic Atlas Software pyAscore The&nbsp;pyAscore&nbsp;package provides a blazingly fast implementation of the Ascore algorithm for localizing peptide post-translational modifications from&hellip;&nbsp;<a href=\"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/resources\/\" rel=\"bookmark\">Read More &raquo;<span class=\"screen-reader-text\">Resources<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"on","footnotes":""},"class_list":["post-1226","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/pages\/1226","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/comments?post=1226"}],"version-history":[{"count":34,"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/pages\/1226\/revisions"}],"predecessor-version":[{"id":1629,"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/pages\/1226\/revisions\/1629"}],"wp:attachment":[{"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/media?parent=1226"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}