{"id":2536,"date":"2023-03-30T08:20:24","date_gmt":"2023-03-30T08:20:24","guid":{"rendered":"https:\/\/www.afroscreen.org\/?p=2536"},"modified":"2023-10-11T13:23:58","modified_gmt":"2023-10-11T13:23:58","slug":"webinar-presentation-of-gevarli-a-public-health-tool-developed-for-afroscreen-project","status":"publish","type":"post","link":"https:\/\/www.afroscreen.org\/en\/webinar-presentation-of-gevarli-a-public-health-tool-developed-for-afroscreen-project\/","title":{"rendered":"Webinar: Presentation of GeVarLi, a public health tool developed for AFROSCREEN project"},"content":{"rendered":"\n<p><\/p>\n\n\n\n<p>Nicolas Fernandez talked about the crisis of <strong>reproducibility<\/strong> affecting several scientific fields but also about several principles and good practices allowing to answer this observation. All research should follow the <strong>F.A.I<\/strong>.R. principle, presenting data as<strong>Findable<\/strong>,<strong>Accessible<\/strong>,<strong>Interoperable<\/strong> and<strong>Reusable<\/strong>, as well as the notion of<strong>Open Science<\/strong>.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"574\" src=\"https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/fair-1024x574.png\" alt=\"\" class=\"wp-image-2545\" srcset=\"https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/fair-1024x574.png 1024w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/fair-300x168.png 300w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/fair-768x431.png 768w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/fair-600x337.png 600w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/fair.png 1485w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>Nicolas Fernandez nous a rappel\u00e9 l\u2019importance d\u2019appliquer ces principes \u00e0 nos analyses bio-informatiques, avec l\u2019utilisation de divers outils, comme les gestionnaires de <strong>F.A.I.R.<\/strong> <strong>workflows<\/strong> (such as  <strong>Snakemake<\/strong>,  <strong>Nextflow<\/strong>), the<strong>environments<\/strong> (such as  <strong>Anaconda<\/strong>, <strong>Docker<\/strong>) and the need to publish and track (versioning) one&#8217;s code with tools such as <strong>Git<\/strong> (including IRD&#8217;s <strong>GitLab<\/strong> instance, <strong>IRDForge<\/strong>).<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"574\" src=\"https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/10-1024x574.png\" alt=\"\" class=\"wp-image-2547\" srcset=\"https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/10-1024x574.png 1024w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/10-300x168.png 300w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/10-768x430.png 768w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/10-600x336.png 600w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/10.png 1488w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>Nicolas Fernandez then presented an example of F.A.I.R. workflow with the &#8221; <strong>GeVarLi <\/strong>: <strong>GEnome<\/strong>assembly, <strong>VARiant<\/strong>calling and <strong>LIneage<\/strong>assignment&#8221; tool, an automated pipeline in Snakemake developed for the genomic analysis of SARS-CoV-2 and other emerging viruses He presented us its genesis, where to find it, how to install and use it as well as the results obtained and its advantages.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"575\" src=\"https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/26-1024x575.png\" alt=\"\" class=\"wp-image-2549\" srcset=\"https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/26-1024x575.png 1024w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/26-300x168.png 300w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/26-768x431.png 768w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/26-600x337.png 600w, https:\/\/www.afroscreen.org\/wp-content\/uploads\/2023\/03\/26.png 1488w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>Nicolas Fernandez insisted in particular on the fact that the workflow was <strong>open<\/strong>, <strong>free<\/strong>, <strong>scalable<\/strong>, and <strong>open to contribution<\/strong> and collaborative participation, as well as the importance of <strong>citing<\/strong> and <strong>thanking<\/strong> the <strong>authors<\/strong> of free tools created by and for the community.<\/p>\n\n\n\n<p>To learn more, watch the entire webinar:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>FR : <a href=\"https:\/\/youtu.be\/haBVJdWqNeE\">https:\/\/youtu.be\/haBVJdWqNeE<\/a><\/li>\n\n\n\n<li>EN : <a href=\"https:\/\/youtu.be\/ssEzpN2NkZc\">https:\/\/youtu.be\/ssEzpN2NkZc<\/a><\/li>\n\n\n\n<li>and more information on GeVarli:<strong> <\/strong><a href=\"https:\/\/forge.ird.fr\/transvihmi\/nfernandez\/GeVarLi\">https:\/\/forge.ird.fr\/transvihmi\/nfernandez\/GeVarLi<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Nicolas Fernandez talked about the crisis of reproducibility affecting several scientific fields but also about several principles and good practices allowing to answer this observation. All research should follow the F.A.I.R. principle, presenting data asFindable,Accessible,Interoperable andReusable, as well as the notion ofOpen Science. Nicolas Fernandez nous a rappel\u00e9 l\u2019importance d\u2019appliquer ces principes \u00e0 nos analyses [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":2576,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[53],"tags":[],"pays":[],"thematique":[38],"class_list":["post-2536","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-webinaire-en","thematique-sequencage-en"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Webinar: Presentation of GeVarLi, a public health tool developed for AFROSCREEN project - Afroscreen<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.afroscreen.org\/en\/webinar-presentation-of-gevarli-a-public-health-tool-developed-for-afroscreen-project\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Webinar: Presentation of GeVarLi, a public health tool developed for AFROSCREEN project - Afroscreen\" \/>\n<meta property=\"og:description\" content=\"Nicolas Fernandez talked about the crisis of reproducibility affecting several scientific fields but also about several principles and good practices allowing to answer this observation. 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