{"id":594,"date":"2018-05-31T17:34:46","date_gmt":"2018-05-31T15:34:46","guid":{"rendered":"https:\/\/www.sys2diag.cnrs.fr\/?page_id=594"},"modified":"2020-04-24T14:17:51","modified_gmt":"2020-04-24T12:17:51","slug":"softwares","status":"publish","type":"page","link":"https:\/\/www.sys2diag.cnrs.fr\/en\/softwares\/","title":{"rendered":"Softwares"},"content":{"rendered":"<div class='white' style='background:rgba(0,0,0,0); border:solid 0px rgba(0,0,0,0); border-radius:0px; padding:0px 0px 0px 0px;'>\n<div id='slider_research' class='owl-carousel sa_owl_theme ' data-slider-id='slider_research' style='visibility:hidden;'>\n<div id='slider_research_slide01' class='sa_hover_container' style='padding:0% 0%; margin:0px 0%; min-height:0px; '><p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-407\" style=\"margin-top: 0px; margin-bottom: 0px; border-radius: 6px;\" src=\"https:\/\/www.sys2diag.cnrs.fr\/wp-content\/uploads\/2018\/05\/PERRIN_IMG7-copie-2-e1492521950757.jpg\" alt=\"\" width=\"1799\" height=\"387\" \/><\/p><\/div>\n<div id='slider_research_slide03' class='sa_hover_container' style='padding:0% 0%; margin:0px 0%; min-height:0px; '><p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-407\" style=\"margin-top: 0px; margin-bottom: 0px; border-radius: 6px;\" src=\"https:\/\/www.sys2diag.cnrs.fr\/wp-content\/uploads\/2020\/04\/PERRIN_IMG2.jpg\" alt=\"\" width=\"1800\" height=\"387\" \/><\/p><\/div>\n<div id='slider_research_slide02' class='sa_hover_container' style='padding:0% 0%; margin:0px 0%; min-height:0px; '><p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-407\" style=\"margin-top: 0px; margin-bottom: 0px; border-radius: 6px;\" src=\"https:\/\/www.sys2diag.cnrs.fr\/wp-content\/uploads\/2020\/04\/IMG_4504-1.jpg\" alt=\"\" width=\"1800\" height=\"387\" \/><\/p><\/div>\n<\/div>\n<\/div>\n<script type='text\/javascript'>\n\tjQuery(document).ready(function() {\n\t\tjQuery('#slider_research').owlCarousel({\n\t\t\titems : 1,\n\t\t\tanimateOut : 'fadeOut',\n\t\t\tsmartSpeed : 3000,\n\t\t\tautoplay : true,\n\t\t\tautoplayTimeout : 7000,\n\t\t\tautoplayHoverPause : false,\n\t\t\tsmartSpeed : 3000,\n\t\t\tfluidSpeed : 3000,\n\t\t\tautoplaySpeed : 3000,\n\t\t\tnavSpeed : 3000,\n\t\t\tdotsSpeed : 3000,\n\t\t\tloop : true,\n\t\t\tnav : false,\n\t\t\tnavText : ['Previous','Next'],\n\t\t\tdots : false,\n\t\t\tresponsiveRefreshRate : 200,\n\t\t\tslideBy : 1,\n\t\t\tmergeFit : true,\n\t\t\tautoHeight : false,\n\t\t\tmouseDrag : false,\n\t\t\ttouchDrag : false\n\t\t});\n\t\tjQuery('#slider_research').css('visibility', 'visible');\n\t\tvar owl_goto = jQuery('#slider_research');\n\t\tjQuery('.slider_research_goto1').click(function(event){\n\t\t\towl_goto.trigger('to.owl.carousel', 0);\n\t\t});\n\t\tjQuery('.slider_research_goto2').click(function(event){\n\t\t\towl_goto.trigger('to.owl.carousel', 1);\n\t\t});\n\t\tjQuery('.slider_research_goto3').click(function(event){\n\t\t\towl_goto.trigger('to.owl.carousel', 2);\n\t\t});\n\t\tvar resize_965 = jQuery('.owl-carousel');\n\t\tresize_965.on('initialized.owl.carousel', function(e) {\n\t\t\tif (typeof(Event) === 'function') {\n\t\t\t\twindow.dispatchEvent(new Event('resize'));\n\t\t\t} else {\n\t\t\t\tvar evt = window.document.createEvent('UIEvents');\n\t\t\t\tevt.initUIEvent('resize', true, false, window, 0);\n\t\t\t\twindow.dispatchEvent(evt);\n\t\t\t}\n\t\t});\n\t});\n<\/script>\n\n<h1 class=\"bigtitleHOne\">The Sys2Diag unit has developed various computer tools that it makes available for non-commercial use.<\/h1>\n<hr>\n<h3 style=\"color: #b550b1;\"><a href=\"https:\/\/www.sys2diag.cnrs.fr\/pepop\/\"> <span class=\"label label-primary \">By clicking here<\/span><\/a> &gt; access to PEPOP<\/h3>\n<p>Prediction of antigenic and \/ or immunogenic peptides (PEPOP Moreau et al., 2008)): representative peptides of the protein of interest are predicted from its 3D structure. These peptides can be used to localize an epitope, obtain Acs targeting a particular area of the protein, obtain antibody pairs targeting two distinct areas of a molecule to develop a sandwich immunoassay, etc.<\/p>\n<hr>\n<h3 style=\"color: #b550b1;\"><a href=\"https:\/\/www.sys2diag.cnrs.fr\/dup\/\"> <span class=\"label label-primary \">By clicking here<\/span><\/a> &gt; access to DUP<\/h3>\n<p><span id=\"result_box\" class=\"\" tabindex=\"-1\" lang=\"en\"><span title=\"DUP est une base de donn\u00e9es qui r\u00e9f\u00e9rence l\u2019ensemble des prot\u00e9ines urinaires normales d\u00e9crites dans les articles d\u2019analyse prot\u00e9omique.\">DUP is a database that references all of the normal urinary proteins described in the proteomic analysis articles. <\/span><span title=\"Actuellement DUP contient plus de 1800 prot\u00e9ines non redondantes observ\u00e9es dans au moins 1 des 12 publications \u00e9tudi\u00e9es.\">Currently DUP contains more than 1800 non-redundant proteins observed in at least 1 of the 12 publications studied. <\/span><span title=\"DUP contient des informations g\u00e9n\u00e9rales comme le nom de la prot\u00e9ine ou sa masse mol\u00e9culaire, des informations sur la description la prot\u00e9ine ainsi que sur sa s\u00e9quence;\">DUP contains general information such as the name of the protein or its molecular weight, information on the description of the protein as well as its sequence; <\/span><span title=\"le lien avec les articles cit\u00e9s est \u00e9galement disponible interactivement.\">the link with the quoted articles is also available interactively. <\/span><span title=\"La liste des prot\u00e9ines urinaires normales peut \u00eatre visualis\u00e9e \u00e0 l\u2019aide d\u2019une interface web facile d\u2019utilisation.\">The list of normal urinary proteins can be viewed using an easy-to-use web interface. <\/span><span title=\"Plusieurs outils facilitent l\u2019interrogation de la base de donn\u00e9es : deux outils permettent de rechercher une prot\u00e9ine \u00e0 partir de son num\u00e9ro d\u2019accession SwissProt\/IPI, de mot-cl\u00e9 ou par similarit\u00e9 de s\u00e9quence.\">Several tools make it easy to query the database: two tools make it possible to search for a protein from its SwissProt \/ IPI accession number, keyword or by sequence similarity. <\/span><span title=\"L\u2019ensemble des prot\u00e9ines peut \u00eatre repr\u00e9sent\u00e9 sous la forme d\u2019un gel 2D virtuel \u00e0 l\u2019aide d\u2019un outil graphique interactif.\">The set of proteins can be represented in the form of a virtual 2D gel using an interactive graphical tool. <\/span><span title=\"La base de donn\u00e9es DUP est aujourd\u2019hui, la seule base de donn\u00e9es permettant une vision globale du prot\u00e9ome urinaire et pourrait servir de r\u00e9f\u00e9rence pour l\u2019identification de biomarqueurs urinaires dans diverses maladies r\u00e9nales.\">Today, the DUP database is the only database allowing a global vision of the urinary proteome and could serve as a reference for the identification of urinary biomarkers in various renal diseases.<\/span><\/span><\/p>\n<hr>\n<h3 style=\"color: #b550b1;\"><a href=\"https:\/\/www.sys2diag.cnrs.fr\/en\/softwares\/sili2dgel\/\"><span class=\"label label-primary \">By clicking here<\/span><\/a> &gt; Access to Sili2DGel page<\/h3>\n<p><b style=\"color: #346db0;\">Sili2DGel <\/b> is an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. It is based on graph theory in which the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). To run Sili2DGel, you have to install JRE. Sili2DGel needs a recursive alignment result file (tabular file of this form) and spot coordinate file (tabular file of this form). Gamma is comprised between 0 and 1; strengh is comprised between 0 and 2.<\/p>\n<hr>\n<h3 style=\"color: #b550b1;\"><a href=\"https:\/\/www.sys2diag.cnrs.fr\/en\/softwares\/bionetcad\/\"><span class=\"label label-primary \">By clicking here<\/span><\/a> &gt; Access to BioNetCAD page<\/h3>\n<p><b style=\"color: #346db0;\">BioNetCAD<\/b> is a CellDesigner (http:\/\/www.celldesigner.org\/) plug-in, is a computer assisted design tool for synthetic biology. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The Sys2Diag unit has developed various computer tools that it makes available for non-commercial use. By clicking here &gt; access to PEPOP Prediction of antigenic and \/ or immunogenic peptides &#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":19,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-594","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.sys2diag.cnrs.fr\/en\/wp-json\/wp\/v2\/pages\/594","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.sys2diag.cnrs.fr\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.sys2diag.cnrs.fr\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.sys2diag.cnrs.fr\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.sys2diag.cnrs.fr\/en\/wp-json\/wp\/v2\/comments?post=594"}],"version-history":[{"count":6,"href":"https:\/\/www.sys2diag.cnrs.fr\/en\/wp-json\/wp\/v2\/pages\/594\/revisions"}],"predecessor-version":[{"id":1037,"href":"https:\/\/www.sys2diag.cnrs.fr\/en\/wp-json\/wp\/v2\/pages\/594\/revisions\/1037"}],"wp:attachment":[{"href":"https:\/\/www.sys2diag.cnrs.fr\/en\/wp-json\/wp\/v2\/media?parent=594"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}