{"id":2857,"date":"2024-12-23T16:53:18","date_gmt":"2024-12-23T15:53:18","guid":{"rendered":"https:\/\/spgoo.org\/?page_id=2857"},"modified":"2025-04-30T11:51:40","modified_gmt":"2025-04-30T09:51:40","slug":"rhodb","status":"publish","type":"page","link":"https:\/\/spgoo.org\/?page_id=2857","title":{"rendered":"RhoDB"},"content":{"rendered":"\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<link rel='stylesheet' id='2931-css'  href='https:\/\/spgoo.org\/wp-content\/uploads\/winp-css-js\/2931.css?ver=1735226507' type='text\/css' media='all' \/>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-align-center\">CDA RhoDb : resp M. Boudvillain CBM<\/h2>\n\n\n\n<p class=\"has-text-align-center has-vivid-green-cyan-color has-text-color has-link-color has-medium-font-size wp-elements-d28b228304061cc540ceae6f47aba105\">Ressources : Eric Eveno, Yvan Stroppa (D\u00e9c 2024 &#8211; )<\/p>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\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<p class=\"has-text-align-right has-medium-font-size\"><strong>Projet RhoDB avec <\/strong><\/p>\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 img_logo wp-duotone-unset-1\">\n<figure class=\"alignleft size-large is-resized\"><a href=\"https:\/\/jbrowse.org\/jb2\/\" target=\"_blank\" rel=\" noreferrer noopener\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"512\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/78e8ba6f-bbfb-4fbe-80e2-4ca2a3148b62-1024x512.png\" alt=\"\" class=\"wp-image-2860\" style=\"width:167px;height:auto\" srcset=\"https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/78e8ba6f-bbfb-4fbe-80e2-4ca2a3148b62-1024x512.png 1024w, https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/78e8ba6f-bbfb-4fbe-80e2-4ca2a3148b62-300x150.png 300w, https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/78e8ba6f-bbfb-4fbe-80e2-4ca2a3148b62-768x384.png 768w, https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/78e8ba6f-bbfb-4fbe-80e2-4ca2a3148b62-1536x768.png 1536w, https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/78e8ba6f-bbfb-4fbe-80e2-4ca2a3148b62-2048x1024.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/a><\/figure>\n<\/div><\/div>\n<\/div>\n\n\n\n<p class=\"has-medium-font-size\"><strong>Construction d&#8217;une base de connaissances sur la terminaison Rho-d\u00e9pendante chez les bact\u00e9ries \u00e0 l&#8217;aide de JBrowse 2<\/strong><\/p>\n\n\n\n<p>La terminaison Rho-d\u00e9pendante est un m\u00e9canisme cl\u00e9 dans la r\u00e9gulation transcriptionnelle des bact\u00e9ries, reposant sur l&#8217;interaction de la prot\u00e9ine Rho avec l&#8217;ARN. Afin de mieux comprendre et caract\u00e9riser les sites d&#8217;interaction potentiels de cette prot\u00e9ine, nous avons men\u00e9 une approche SELEX (Systematic Evolution of Ligands by EXponential enrichment). Ce travail a permis d\u2019identifier des s\u00e9quences susceptibles de jouer un r\u00f4le crucial dans ce processus biologique.<br>Pour rendre ces donn\u00e9es accessibles et exploitables par la communaut\u00e9 scientifique, nous avons comme objectif de construit une base de connaissances en ligne bas\u00e9e sur&nbsp;<strong>JBrowse 2<\/strong>, un navigateur g\u00e9nomique moderne et interactif. Cet outil permet une exploration intuitive des donn\u00e9es g\u00e9nomiques et offre une plateforme id\u00e9ale pour visualiser les r\u00e9sultats de nos analyses.<\/p>\n\n\n\n<p><strong>Objectifs de la base de connaissances :<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><\/li>\n<\/ul>\n\n\n\n<ol start=\"1\" class=\"wp-block-list\">\n<li><strong>Centralisation des donn\u00e9es<\/strong>&nbsp;:\n<ul class=\"wp-block-list\">\n<li>R\u00e9unir les s\u00e9quences identifi\u00e9es par SELEX en les annotant comme sites potentiels d&#8217;interaction de Rho.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Visualisation intuitive<\/strong>&nbsp;:\n<ul class=\"wp-block-list\">\n<li>Offrir une repr\u00e9sentation claire et interactive des sites d&#8217;interaction sur diff\u00e9rents g\u00e9nomes bact\u00e9riens.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Accessibilit\u00e9 en ligne<\/strong>&nbsp;:\n<ul class=\"wp-block-list\">\n<li>Fournir un acc\u00e8s web universel, permettant aux chercheurs d&#8217;explorer les donn\u00e9es sans n\u00e9cessiter d&#8217;installation locale.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Extension des analyses<\/strong>&nbsp;:\n<ul class=\"wp-block-list\">\n<li>Int\u00e9grer des informations suppl\u00e9mentaires telles que les r\u00e9gions conserv\u00e9es, les motifs sp\u00e9cifiques et les annotations fonctionnelles associ\u00e9es.<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n\n\n\n<p><strong>Fonctionnalit\u00e9s offertes par JBrowse 2 :<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Exploration des sites identifi\u00e9s<\/strong>&nbsp;:\n<ul class=\"wp-block-list\">\n<li>Les s\u00e9quences enrichies par SELEX sont affich\u00e9es comme des pistes sp\u00e9cifiques sur les g\u00e9nomes bact\u00e9riens correspondants.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Comparaison multi-g\u00e9nomique<\/strong>&nbsp;:\n<ul class=\"wp-block-list\">\n<li>Les utilisateurs peuvent visualiser la conservation de ces sites entre diff\u00e9rentes esp\u00e8ces bact\u00e9riennes.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Annotations dynamiques<\/strong>&nbsp;:\n<ul class=\"wp-block-list\">\n<li>Chaque site est associ\u00e9 \u00e0 des m\u00e9tadonn\u00e9es, incluant les scores SELEX, les pr\u00e9dictions fonctionnelles et des donn\u00e9es exp\u00e9rimentales compl\u00e9mentaires.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>Compatibilit\u00e9 des formats<\/strong>&nbsp;:\n<ul class=\"wp-block-list\">\n<li>JBrowse 2 prend en charge des formats standard tels que GFF3, BED, ou FASTA, permettant une int\u00e9gration transparente de nos r\u00e9sultats.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p><strong>Perspectives :<\/strong><\/p>\n\n\n\n<p>Cette base de connaissances a pour ambition de servir de ressource pour :<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Explorer les m\u00e9canismes de terminaison transcriptionnelle Rho-d\u00e9pendante.<\/li>\n\n\n\n<li>Identifier des cibles potentielles pour des applications biotechnologiques ou th\u00e9rapeutiques.<\/li>\n\n\n\n<li>Encourager la collaboration et l\u2019\u00e9change d\u2019informations entre chercheurs en g\u00e9nomique bact\u00e9rienne.<\/li>\n<\/ul>\n\n\n\n<p>Gr\u00e2ce \u00e0 JBrowse 2, nous mettons \u00e0 disposition un outil performant et \u00e9volutif, capable d\u2019accompagner les avanc\u00e9es dans ce domaine crucial de la biologie mol\u00e9culaire.<\/p>\n\n\n\n<p class=\"has-pale-cyan-blue-color has-text-color has-link-color has-medium-font-size wp-elements-5323c16c3f15fb4968658c7942d35aee\">Proc\u00e9dure d&#8217;installation de JBrowse2 sous Linux : <\/p>\n\n\n\n<p>Cette page d\u00e9crit les diff\u00e9rentes op\u00e9rations \u00e0 mener pour effectuer cette installation et le d\u00e9ploiement sur une des machines de SPGoO.<\/p>\n\n\n\n<p class=\"title_parag has-pale-cyan-blue-color has-text-color has-link-color has-medium-font-size wp-elements-422a659d8c609eead95e9200f8954db5\">Pr\u00e9paration de l&#8217;image docker<\/p>\n\n\n\n<p>Se connecter sous le github suivant : <a href=\"https:\/\/github.com\/biocorecrg\/jbrowse_docker\/tree\/master\">https:\/\/github.com\/biocorecrg\/jbrowse_docker\/tree\/master<\/a> et r\u00e9cup\u00e9rer l&#8217;ensemble du github via la commande <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code><strong>git clone https:\/\/github.com\/biocorecrg\/jbrowse_docker.git<\/strong><\/code><\/pre>\n\n\n\n<p>Construction de l&#8217;image \u00e0 l&#8217;aide de la commande <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code><strong>docker build -t jbrowse2 .<\/strong><\/code><\/pre>\n\n\n\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-constrained wp-block-group-is-layout-constrained\">\n<details class=\"wp-block-details has-pale-cyan-blue-color has-text-color has-link-color wp-elements-baf8c5805334408aecc11e169cb4bc32 is-layout-flow wp-block-details-is-layout-flow\"><summary>Contenu du Dockerfile<\/summary>\n<p># from node image<br>FROM node:16-buster<br>LABEL org.opencontainers.image.authors=&#8221;toni.hermoso@crg.eu&#8221;<br>ARG JBROWSE_VERSION=1.7.9<br>ARG SAMTOOLS_VERSION=1.15.1<br>ARG HTSLIB_VERSION=1.15.1<br>#&nbsp;Handle dependencies<br>RUN apt-get update &amp;&amp; apt-get -y upgrade &amp;&amp; apt-get -y install build-essential git zlib1g-dev \\<br>genometools &amp;&amp; \\<br>apt-get clean &amp;&amp; echo -n &gt; \/var\/lib\/apt\/extended_states<br>RUN mkdir -p \/soft\/bin<br>RUN wget -q https:\/\/github.com\/samtools\/samtools\/releases\/download\/${SAMTOOLS_VERSION}\/samtools-${SAMTOOLS_VERSION}.tar.bz2 &amp;&amp; \\<br>tar jxf samtools-${SAMTOOLS_VERSION}.tar.bz2 &amp;&amp; \\<br>cd samtools-${SAMTOOLS_VERSION} &amp;&amp; \\<br>make prefix=\/soft\/samtools install &amp;&amp; \\<br>cd \/soft\/bin &amp;&amp; ln -s \/soft\/samtools\/bin\/* . &amp;&amp; cd \/soft &amp;&amp; \\<br>rm -rf *tar.bz2<br>RUN wget -q https:\/\/github.com\/samtools\/htslib\/releases\/download\/${HTSLIB_VERSION}\/htslib-${HTSLIB_VERSION}.tar.bz2 &amp;&amp; \\<br>tar jxf htslib-${HTSLIB_VERSION}.tar.bz2 &amp;&amp; \\<br>cd htslib-${HTSLIB_VERSION} &amp;&amp; \\<br>make prefix=\/soft\/htslib install &amp;&amp; \\<br>cd \/soft\/bin &amp;&amp; ln -s \/soft\/htslib\/bin\/* . &amp;&amp; cd \/soft &amp;&amp; \\<br>rm -rf *tar.bz2<br># PATH<br>ENV PATH $PATH:\/soft\/bin<br>RUN mkdir -p \/srv<br>WORKDIR \/srv<br>COPY index.js .<br>COPY package.json .<br>RUN npm install -g forever<br>RUN npm install -g @jbrowse\/cli@${JBROWSE_VERSION}<br>RUN npm install<br># Volumes<br>VOLUME \/var\/www<br>VOLUME \/data<br>EXPOSE 8080<br>CMD NODE_ENV=production forever index.js<\/p>\n<\/details>\n<\/div><\/div>\n\n\n\n<p>Une fois le script de cr\u00e9ation de l&#8217;image termin\u00e9, vous devez visualiser dans votre d\u00e9p\u00f4t local l&#8217;image \u00e0 l&#8217;aide de la commande <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code><strong>docker images<\/strong>\nubuntu@vps:~\/CBM\/jbrowse_docker$ docker images\nREPOSITORY       TAG     IMAGE ID    CREATED       SIZE\njbrowse2       latest 94fb0b13e9c1   16 hours ago 1.38GB\n<\/code><\/pre>\n\n\n\n<p>Pr\u00e9-requis: cr\u00e9ation des r\u00e9pertoires pour les deux volumes <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code><strong>mkdir www &amp;&amp; mkdir  data <\/strong><\/code><\/pre>\n\n\n\n<p>D\u00e9marrage de l&#8217;image<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code><strong>docker run -d --user $(id -u):$(id -g) --name mybrowser -v \/my\/var\/www:\/var\/www -v \/my\/data:\/data -p 8081:8080 jbrowse2<\/strong>\n<\/code><\/pre>\n\n\n\n<p class=\"title_parag has-pale-cyan-blue-color has-text-color has-link-color has-medium-font-size wp-elements-f24d2d096168c2817ec1a5748ec9481b\">Param\u00e9trage de l&#8217;instance :<\/p>\n\n\n\n<p>Installation des donn\u00e9es issues d&#8217;Ecoli <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>docker exec mybrowser samtools faidx \/data\/GCF_000005845.2_ASM584v2_genomic.fna<br>docker exec mybrowser bash -c 'jbrowse add-assembly \/data\/GCF_000005845.2_ASM584v2_genomic.fna --out \/var\/www\/ecoli --load symlink'<br>docker exec mybrowser bash -c 'jbrowse add-track \/data\/H4R0_StrandMinus.bw --name H4R0_StrandMinus --out \/var\/www\/ecoli --load symlink'<br>docker exec mybrowser bash -c 'jbrowse add-track \/data\/H4R0_StrandPlus.bw --name H4R0_StrandPlus --out \/var\/www\/ecoli --load symlink'<br>docker exec mybrowser bash -c 'jbrowse text-index --out \/var\/www\/ecoli'<\/code><\/pre>\n\n\n\n<p class=\"title_parag has-pale-cyan-blue-color has-text-color has-link-color has-medium-font-size wp-elements-c7a5049ae9d0e03120604e33541270ed\">S\u00e9curisation <\/p>\n\n\n\n<p>Modification des param\u00e8tres du reverse proxy pour prendre en compte une authentification simple pour le moment.<\/p>\n\n\n\n<p class=\"title_parag has-pale-cyan-blue-color has-text-color has-link-color has-medium-font-size wp-elements-9befa768bf1a13e629fcfc196d00c29b\">Exploitation :<\/p>\n\n\n\n<p>Acc\u00e8s via l&#8217;url https:\/\/rhodb.educandgames.org\/ecoli <br>(12\/02\/2025 neutralis\u00e9 en attendant l&#8217;h\u00e9bergement CBM)<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"353\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/rhodb_images1-1024x353.png\" alt=\"\" class=\"wp-image-2902\" srcset=\"https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/rhodb_images1-1024x353.png 1024w, https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/rhodb_images1-300x104.png 300w, https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/rhodb_images1-768x265.png 768w, https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/rhodb_images1-1536x530.png 1536w, https:\/\/spgoo.org\/wp-content\/uploads\/2024\/12\/rhodb_images1.png 1973w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p class=\"title_parag has-pale-cyan-blue-color has-text-color has-link-color has-medium-font-size wp-elements-31386f1b6198535abf566f6bb747c831\">Int\u00e9gration dans  Jupyter NoteBook<\/p>\n\n\n\n<p>Comment utiliser JBrowse2 \u00e0 partir de  Jupyter Notebook.<\/p>\n\n\n\n<p>voir doc : <a href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC9887080\/\">https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC9887080\/<\/a> <\/p>\n\n\n\n<p class=\"title_parag has-pale-cyan-blue-color has-text-color has-link-color has-medium-font-size wp-elements-0a0ed8fb33be1bf3ef6c212ccaaca13f\">Extension : <\/p>\n\n\n\n<p>A pr\u00e9voir une authentification via annuaire LDAP (int\u00e9gration dans nginx)<br>Voir <a href=\"https:\/\/jbrowse.org\/docs\/authentication.html\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/jbrowse.org\/docs\/authentication.html<\/a><\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>CDA RhoDb : resp M. Boudvillain CBM Ressources : Eric Eveno, Yvan Stroppa (D\u00e9c 2024 &#8211; ) Projet RhoDB avec Construction d&#8217;une base de connaissances sur la terminaison Rho-d\u00e9pendante chez les bact\u00e9ries \u00e0 l&#8217;aide de JBrowse 2 La terminaison Rho-d\u00e9pendante est un m\u00e9canisme cl\u00e9 dans la r\u00e9gulation transcriptionnelle des bact\u00e9ries, reposant sur l&#8217;interaction de la [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2857","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/pages\/2857","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/spgoo.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2857"}],"version-history":[{"count":90,"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/pages\/2857\/revisions"}],"predecessor-version":[{"id":6258,"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/pages\/2857\/revisions\/6258"}],"wp:attachment":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2857"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}