{"id":11919,"date":"2026-02-17T13:50:07","date_gmt":"2026-02-17T12:50:07","guid":{"rendered":"https:\/\/spgoo.org\/?page_id=11919"},"modified":"2026-02-17T14:35:46","modified_gmt":"2026-02-17T13:35:46","slug":"cad-valbiocosm","status":"publish","type":"page","link":"https:\/\/spgoo.org\/?page_id=11919","title":{"rendered":"CAD Valbiocosm"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">CDA Valbiocosm : P. Baril (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-9207aa81b94f28f9d55cea3fffd34029\">Ressources SPGoO : YS (Janv 2026 \u2013 juin 2026)<\/p>\n\n\n\n<link rel='stylesheet' id='4485-css'  href='https:\/\/spgoo.org\/wp-content\/uploads\/winp-css-js\/4485.css?ver=1747039442' type='text\/css' media='all' \/>\n\n\n\n<p>Objectifs : dans le cadre de la collaboration CBM et SPGoO pour l&#8217;appel \u00e0 projet APR-IR 2025, ce CDA a pour objectif de reconstruire les traitements et analyses effectu\u00e9s au cours de la premi\u00e8re campagne qui a donn\u00e9 lieu une publication  et de les revisiter. Il se d\u00e9roulera en plusieurs \u00e9tapes :<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Reprise de l&#8217;existant et inventaire : donn\u00e9es et traitements <\/li>\n\n\n\n<li>Compr\u00e9hension du contexte et des r\u00e9sultats <\/li>\n\n\n\n<li>Elaboration d&#8217;un site web de manipulation de ces donn\u00e9es et traitements<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<p class=\"has-pale-cyan-blue-color has-text-color has-link-color has-medium-font-size wp-elements-d9e2413e3013a7ef2cb8f80734cd9af6\">D\u00e9roulement des op\u00e9rations : <\/p>\n\n\n\n<p>Reprise des analyses de donn\u00e9es issues de la premi\u00e8re campagne de collecte. <\/p>\n\n\n\n<p>Inventaire des donn\u00e9es existantes <\/p>\n\n\n\n<p>Etat des traitements associ\u00e9s <\/p>\n\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Script d&#8217;alimentation de la base <span class='tooltipsall tooltipsincontent classtoolTips3'>MongoDB<\/span><\/summary>\n<pre class=\"wp-block-code\"><code># -------------------------------------------------------------------------------------------\n# SPGoO    Mars 2025 \n# Projet valbiocosm\n#\n# -------------------------------------------------------------------------------------------\nimport pymongo\nimport re\nimport os\nimport string\nimport sys\nimport getopt\nimport csv\nimport collections\nimport glob\n\n# -----------------------------------------\n# Connexion a la base de donnees\n# -----------------------------------------\nmyclient = pymongo.MongoClient(\"mongodb:\/\/localhost:27087\/\",username=\"spgoo\",password=\"toto&amp;tata\",authSource=\"valbiocosm\",authMechanism='SCRAM-SHA-1')\nmydb = myclient&#91;\"valbiocosm\"]\nmycol = mydb&#91;\"data\"]\n# on le lit ligne par ligne et on interprete \nattributs=&#91;\"ID\",\"Name\",\"baseMean\",\"log2FoldChange\",\"padj\",\"TGF_rep1\",\"TGF_rep2\",\"TGF_rep3\",\"TGF_SM31_rep1\",\"TGF_SM31_rep2\",\"TGF_SM31_rep3\"]\n\nwith open('ANALYSIS_TGF-SM31_vs_TGF_DESeq_results_geneName.csv', 'r') as file:\n    reader = csv.reader(file, delimiter=\";\")\n    for row in reader:\n        struc={}\n        indice=0\n        for element in row:\n           struc&#91;attributs&#91;indice]]=element\n           indice+=1\n        print(struc)\n        mycol.insert_one(struc)\n<\/code><\/pre>\n<\/details>\n\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Repr\u00e9sentation d&#8217;une donn\u00e9e sur 57281 au total<\/summary>\n<pre class=\"wp-block-code\"><code>{\n    \"_id\" : ObjectId(\"67c95492fcd9f3b2f67e8631\"),\n    \"ID\" : \"ENSG00000226777,3\",\n    \"Name\" : \"KIAA0125\",\n    \"baseMean\" : \"8.86271877039942\",\n    \"log2FoldChange\" : \"4.77052727744133\",\n    \"padj\" : \"0.000266037476676622\",\n    \"TGF_rep1\" : \"0\",\n    \"TGF_rep2\" : \"0\",\n    \"TGF_rep3\" : \"2.0227232449272\",\n    \"TGF_SM31_rep1\" : \"16.4122278619582\",\n    \"TGF_SM31_rep2\" : \"16.5666702377195\",\n    \"TGF_SM31_rep3\" : \"18.1746912777916\"\n}<\/code><\/pre>\n<\/details>\n\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Statistiques pour les valeurs non NA (18679)<\/summary>\n<pre class=\"wp-block-code\"><code>&gt;&gt;&gt; df2.describe()\n            baseMean  log2FoldChange          padj       TGF,rep1       TGF,rep2       TGF,rep3  TGF,SM31,rep1  TGF,SM31,rep2  TGF,SM31,rep3\ncount   18679.000000    18679.000000  18679.000000   18679.000000   18679.000000   18679.000000   1.867900e+04   1.867900e+04   1.867900e+04\nmean     1400.981008       -0.032196      0.419208    1419.357753    1408.611267    1404.150946   1.391443e+03   1.380072e+03   1.402251e+03\nstd      9234.981940        0.512314      0.351076    9057.133664    9010.878394    8729.792399   9.656131e+03   9.648963e+03   9.549623e+03\nmin         5.256422       -5.894301      0.000000       0.000000       0.000000       0.000000   0.000000e+00   0.000000e+00   0.000000e+00\n25%        39.028457       -0.203786      0.039928      38.896284      39.872183      39.443103   3.829520e+01   3.823078e+01   3.808031e+01\n50%       311.902495        0.005739      0.393300     310.286263     309.915606     310.488018   3.063616e+02   3.020231e+02   3.055079e+02\n75%      1225.563792        0.189984      0.759990    1230.536976    1223.351078    1230.827095   1.221617e+03   1.218287e+03   1.229821e+03\nmax    986302.417185        4.770527      0.999992  935041.908875  937074.238843  898936.641787   1.052831e+06   1.067114e+06   1.026816e+06\n<\/code><\/pre>\n<\/details>\n\n\n\n<p>Repr\u00e9sentation graphique Graphe1<\/p>\n\n\n<script type=\"text\/javascript\" src=\"https:\/\/fastly.jsdelivr.net\/npm\/echarts@5\/dist\/echarts.min.js\"><\/script>\r\n<script type=\"text\/javascript\" src=\"https:\/\/fastly.jsdelivr.net\/npm\/echarts@5\/dist\/extension\/dataTool.min.js\"><\/script>\r\n<script type=\"text\/javascript\" src=\"https:\/\/echarts.apache.org\/en\/js\/vendors\/echarts-gl@2\/dist\/echarts-gl.min.js\"><\/script>\r\n\r\n<script type=\"text\/javascript\" src=\"https:\/\/string-db.org\/javascript\/combined_embedded_network_v2.0.6.js\"><\/script>\r\n\r\n<style>\r\n.dg.main {\r\n\twidth : 200px;\r\n    transition: opacity .1s linear;\r\n}\r\n.dg {\r\n    color: #eee;\r\n    font: 11px Lucida Grande, sans-serif;\r\n    text-shadow: 0 -1px 0 #111;\r\n}\r\n\t\r\n.dg .closed li:not(.title), .dg .closed ul li, .dg .closed ul li>* {\r\n    height: 0;\r\n    overflow: hidden;\r\n    border: 0;\r\n}\r\n\t\r\n.dg .cr.string {\r\n    border-left: 3px solid #1ed36f;\r\n\tdisplay:flex;\r\n}\r\n\r\n.dg li:not(.folder) {\r\n    background: #1a1a1a;\r\n    border-bottom: 1px solid #2c2c2c;\r\n}\r\n\r\n.dg li:not(.folder) {\r\n    cursor: auto;\r\n    height: 27px;\r\n    line-height: 27px;\r\n    padding: 0 4px 0 5px;\r\n}\r\n\r\n.dg .cr {\r\n    clear: both;\r\n    padding-left: 3px;\r\n    height: 27px;\r\n    overflow: hidden;\r\n}\r\n.dg.main * {\r\n    box-sizing: content-box;\r\n}\r\n\r\n.dg li {\r\n    transition: height .1s ease-out;\r\n    transition: overflow .1s linear;\r\n}\r\n\r\n.dg ul {\r\n    list-style: none;\r\n    margin: 0;\r\n    padding: 0;\r\n    width: 100%;\r\n    clear: both;\r\n}\r\n\t\r\n.dg.main .close-button.close-bottom {\r\n    position: absolute;\r\n}\r\n\r\n\r\n.dg.main .close-button {\r\n    transition: opacity .1s linear;\r\n    border: 1px;\r\n    line-height: 19px;\r\n    height: 20px;\r\n\twidth: 200px;\r\n    cursor: pointer;\r\n    text-align: center;\r\n    background-color: #000;\r\n}\r\n\t#mydivString {\r\n  position: fixed;\r\n  top: 150px;\r\n  left: 200px;\r\n  z-index: 9;\r\n  background-color: #f1f1f1;\r\n  border: 1px solid #d3d3d3;\r\n  text-align:left;\r\n}\r\n\r\n#mydivStringheader {\r\n  padding: 10px;\r\n  cursor: move;\r\n  z-index: 10;\r\n  font-size:16px;\r\n  background-color: #130b8c;\r\n  color: #fff;\r\n}\t\r\n\t\r\n\t\r\n.fen_arrondie {\r\n  border-bottom: 1px solid #ddd;\r\n  -webkit-border-top-left-radius: 10px;\r\n  -moz-border-radius-topleft: 10px;\r\n  -ms-border-radius-topleft: 10px;\r\n  border-top-left-radius: 10px;   \r\n\t\r\n  -webkit-border-top-right-radius: 10px;\r\n  -ms-border-top-right-radius: 10px;\r\n  -moz-border-radius-topright: 10px;\r\n  border-top-right-radius: 10px;\t\r\n\t\r\n  -webkit-border-bottom-right-radius: 10px;\r\n  -ms-border-bottom-right-radius: 10px;\r\n  -moz-border-radius-bottomright: 10px;\r\n  border-bottom-right-radius: 10px;\t\r\n\t\r\n  -webkit-border-bottom-left-radius: 10px;\r\n  -ms-border-bottom-left-radius: 10px;\r\n  -moz-border-radius-bottomleft: 10px;\r\n  border-bottom-left-radius: 10px;\t\t\t\r\n}\t\t\r\n\t\r\n\t\r\n\t\r\n<\/style>\r\n\r\n<div id=\"mydivString\" class=\"fen_arrondie\" style=\"width:500px;margin-bottom:10px;display:none\" >\r\n\t<div id=\"mydivStringtheader\"  class=\"fen_arrondie\" style=\"display:flex;justify-content:space-between;\">\r\n\t\tOrigine STRING https:\/\/string-db.org\/\r\n\t\t<h4 id=\"title_string\" ><\/h4>\r\n\t\t<button type=\"button\" onclick=\"close_fen('mydivString');\">\r\n\t\t\t<span style=\"color:white;opacity:0.5\">\u00d7<\/span>\r\n        <\/button>\r\n\t<\/div>\r\n\t<div id=\"div_corps_String\" \r\n\t\t style=\"width:500px;height:500px;background-color:rgb(91, 192, 222);color:#130b8c;padding:10px 10px 10px 10px;overflow:auto\" class=\"fen_arrondie\">\r\n\t\t<!-- <img decoding=\"async\" id=\"image_string\" src=\"#\" style=\"width:400px;height:400px\" \/> -->\r\n\t\t<div id=\"stringEmbedded\" style=\"width:400px;height:400px\" ><\/div>\r\n\t<\/div>\r\n<\/div>\r\n\r\n<div style=\"display:block;width:100%; height:740px;\">\r\n\t<div class=\"dg main\" id=\"box_controls\"  style=\"color:green;width: 200px; z-index: 1000;\">\r\n\t\t<ul>\r\n\t\t\t<li class=\"cr string\">\r\n\t\t\t\t<div style=\"width:250px; display:flex;justify-content:space-around;\">\r\n\t\t\t\t\t<span class=\"property-name\">xAxisLeft<\/span>\r\n\t\t\t\t\t<div class=\"45\">\r\n\t\t\t\t\t\t<select id=\"select_axisX\" onchange=\"reactualise_config();\" >\r\n\t\t\t\t\t\t\t<option value=\"baseMean\">BaseMean<\/option>\r\n\t\t\t\t\t\t\t<option value=\"log2FoldChange\" selected>log2FoldChange<\/option>\r\n\t\t\t\t\t\t\t<option value=\"padj\">padj<\/option>\r\n\t\t\t\t\t\t\t<option value=\"padjlog10\">padjlog10<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_rep1\">TGF_rep1<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_rep2\" >TGF_rep2<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_rep3\">TGF_rep3<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_SM31_rep1\">TGF_SM31_rep1<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_SM31_rep2\">TGF_SM31_rep2<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_SM31_rep2\">TGF_SM31_rep3<\/option>\r\n\t\t\t\t\t\t<\/select>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t<\/div>\r\n\t\t\t<\/li>\r\n\t\t\t<li class=\"cr string\">\r\n\t\t\t\t<div  style=\"width:250px; display:flex;justify-content:space-around;\">\r\n\t\t\t\t\t<span class=\"property-name\">yAxisTop<\/span>\r\n\t\t\t\t\t<div class=\"c\">\r\n\t\t\t\t\t\t<select id=\"select_axisY\" onchange=\"reactualise_config();\" >\r\n\t\t\t\t\t\t\t<option value=\"baseMean\">BaseMean<\/option>\r\n\t\t\t\t\t\t\t<option value=\"log2FoldChange\" >log2FoldChange<\/option>\r\n\t\t\t\t\t\t\t<option value=\"padj\">padj<\/option>\r\n\t\t\t\t\t\t\t<option value=\"padjlog10\" selected>padjlog10<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_rep1\">TGF_rep1<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_rep2\" >TGF_rep2<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_rep3\">TGF_rep3<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_SM31_rep1\">TGF_SM31_rep1<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_SM31_rep2\">TGF_SM31_rep2<\/option>\r\n\t\t\t\t\t\t\t<option value=\"tgf_SM31_rep2\">TGF_SM31_rep3<\/option>\r\n\t\t\t\t\t\t<\/select>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t<\/div>\r\n\t\t\t<\/li>\r\n\t\t<\/ul>\r\n\t\t<div class=\"close-button close-bottom\"  id=\"btn_controls\" onclick=\"fermeture_controls();\">Close Controls<\/div>\r\n\t<\/div>\r\n\t<div id=\"container_nuage\" style=\"height: 700px\"><\/div>\r\n\t<\/div>\t\r\n\r\n\t<div style=\"margin:50px;\">\r\n\t\t<ul>\r\n\t\t\t<li style=\"color:yellow;\" >padj > 0.01 &#038; Log2FoldChange < 1 &#038; Log2FoldChange > -1 <\/li>\r\n\t\t\t<li style=\"color:green;\">padj > 0.01 &#038; Log2FoldChange > 1 &#038; Log2FoldChange < -1 <\/li>\r\n\t\t\t<li style=\"color:lightblue;\">padj < 0.01 &#038; Log2FoldChange < -1 <\/li>\r\n\t\t\t<li style=\"color:red;\">padj < 0.01 &#038; Log2FoldChange > 1  <\/li>\r\n\t\t<\/ul>\r\n\t<\/div>\r\n\r\n\r\n<script>\r\n\tconst fermeture_controls=function() {\r\n\t\t\/\/ document.getElementById(\"box_controls\").style.height=\"40px\";\r\n\t\tdocument.querySelectorAll(\".dg ul\").forEach((elem)=> elem.classList.toggle(\"closed\"))\t\r\n\t\t\r\n\t\tif (document.getElementById(\"btn_controls\").innerHTML==\"Close Controls\") {\r\n\t\t\tdocument.getElementById(\"btn_controls\").innerHTML=\"Open Controls\";\r\n\t\t} else {\r\n\t\t\tdocument.getElementById(\"btn_controls\").innerHTML=\"Close Controls\";\r\n\t\t}\r\n\t}\r\ndragElement(document.getElementById(\"mydivString\"));\r\n\r\n\r\nfunction dragElement(elmnt) {\r\n  var pos1 = 0, pos2 = 0, pos3 = 0, pos4 = 0;\r\n  if (document.getElementById(elmnt.id + \"header\")) {\r\n    \/\/ if present, the header is where you move the DIV from:\r\n    document.getElementById(elmnt.id + \"header\").onmousedown = dragMouseDown;\r\n  } else {\r\n    \/\/ otherwise, move the DIV from anywhere inside the DIV:\r\n   elmnt.onmousedown = dragMouseDown;\r\n  }\r\n\r\n  function dragMouseDown(e) {\r\n    e = e || window.event;\r\n    e.preventDefault();\r\n    \/\/ get the mouse cursor position at startup:\r\n    pos3 = e.clientX;\r\n    pos4 = e.clientY;\r\n    document.onmouseup = closeDragElement;\r\n    \/\/ call a function whenever the cursor moves:\r\n    document.onmousemove = elementDrag;\r\n  }\r\n\r\n  function elementDrag(e) {\r\n    e = e || window.event;\r\n    e.preventDefault();\r\n    \/\/ calculate the new cursor position:\r\n    pos1 = pos3 - e.clientX;\r\n    pos2 = pos4 - e.clientY;\r\n    pos3 = e.clientX;\r\n    pos4 = e.clientY;\r\n    \/\/ set the element's new position:\r\n    elmnt.style.top = (elmnt.offsetTop - pos2) + \"px\";\r\n    elmnt.style.left = (elmnt.offsetLeft - pos1) + \"px\";\r\n  }\r\n\r\n  function closeDragElement() {\r\n    \/\/ stop moving when mouse button is released:\r\n    document.onmouseup = null;\r\n    document.onmousemove = null;\r\n  }\r\n}\t\t\r\n<\/script>\n\n<script type='text\/javascript'>\nvar id = \"11926\";<\/script>\n<script type='text\/javascript' src='https:\/\/spgoo.org\/wp-content\/uploads\/winp-css-js\/11926.js?ver=1771346736'><\/script>\n<script type=\"text\/javascript\"> toolTips('.classtoolTips3','<a style=\"text-decoration: none;\" href=\"https:\/\/www.mongodb.com\/fr-fr\"><img style=\"width: 180px; height: 50px;\" src=\"\/wp-content\/uploads\/2025\/01\/mongodb-logo-rgb-scaled.jpg\" \/><\/a>'); <\/script>","protected":false},"excerpt":{"rendered":"<p>CDA Valbiocosm : P. Baril (CBM) Ressources SPGoO : YS (Janv 2026 \u2013 juin 2026) Objectifs : dans le cadre de la collaboration CBM et SPGoO pour l&#8217;appel \u00e0 projet APR-IR 2025, ce CDA a pour objectif de reconstruire les traitements et analyses effectu\u00e9s au cours de la premi\u00e8re campagne qui a donn\u00e9 lieu une [&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-11919","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/pages\/11919","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=11919"}],"version-history":[{"count":4,"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/pages\/11919\/revisions"}],"predecessor-version":[{"id":11928,"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/pages\/11919\/revisions\/11928"}],"wp:attachment":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=11919"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}