{"id":24,"date":"2018-04-12T14:56:58","date_gmt":"2018-04-12T14:56:58","guid":{"rendered":"http:\/\/serranolab.crg.eu\/?page_id=24"},"modified":"2023-02-20T09:02:25","modified_gmt":"2023-02-20T09:02:25","slug":"resources","status":"publish","type":"page","link":"http:\/\/serranolab.crg.eu\/index.php\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"<h3>Software<\/h3>\n<p><strong>Sequencing technologies<\/strong><\/p>\n<p><figure id=\"attachment_765\" aria-describedby=\"caption-attachment-765\" style=\"width: 200px\" class=\"wp-caption alignleft\"><a href=\"https:\/\/github.com\/lionking0000\/ELMSeq\"><img loading=\"lazy\" class=\"size-full wp-image-765\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/Screenshot-from-2018-07-26-13-04-18.png\" alt=\"\" width=\"200\" height=\"68\" \/><\/a><figcaption id=\"caption-attachment-765\" class=\"wp-caption-text\">Transform ELMSeq sequencing files into sequence-specific DAMRatios [<a href=\"https:\/\/github.com\/lionking0000\/ELMSeq\">link<\/a>]<\/figcaption><\/figure><br \/>\n<figure id=\"attachment_763\" aria-describedby=\"caption-attachment-763\" style=\"width: 180px\" class=\"wp-caption alignleft\"><a href=\"https:\/\/github.com\/lionking0000\/recYnH\"><img loading=\"lazy\" class=\"size-full wp-image-763\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/Screenshot-from-2018-07-26-13-01-48.png\" alt=\"\" width=\"180\" height=\"46\" \/><\/a><figcaption id=\"caption-attachment-763\" class=\"wp-caption-text\">Generate recYnH interaction score matrix [<a href=\"https:\/\/github.com\/lionking0000\/recYnH\">link<\/a>]<\/figcaption><\/figure><br \/>\n<figure id=\"attachment_763\" aria-describedby=\"caption-attachment-763\" style=\"width: 250px\" class=\"wp-caption alignleft\"><a href=\"https:\/\/github.com\/CRG-CNAG\/fastqins\"><img loading=\"lazy\" class=\"size-full wp-image-763\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2020\/09\/fastqins.png\" alt=\"\" width=\"250\" height=\"46\" \/><\/a><figcaption id=\"caption-attachment-763\" class=\"wp-caption-text\">Generate transposon insertion profiles from Tn-Seq sequencing files [<a href=\"https:\/\/github.com\/CRG-CNAG\/fastqins\">link<\/a>]<\/figcaption><\/figure><\/p>\n<hr \/>\n<p><strong>Analysis frameworks<\/strong><\/p>\n<p><figure id=\"attachment_722\" aria-describedby=\"caption-attachment-722\" style=\"width: 300px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/ranseps.crg.es\/about\"><img loading=\"lazy\" class=\"size-medium wp-image-722\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/logo_ranseps-300x107.png\" alt=\"\" width=\"300\" height=\"107\" srcset=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/logo_ranseps-300x107.png 300w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/logo_ranseps-480x172.png 480w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/logo_ranseps.png 481w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/a><figcaption id=\"caption-attachment-722\" class=\"wp-caption-text\">Framework for bacterial genome re-annotation and novel small proteins prediction [<a href=\"http:\/\/ranseps.crg.es\/about\">link<\/a>]<\/figcaption><\/figure><br \/>\n<figure id=\"attachment_763\" aria-describedby=\"caption-attachment-763\" style=\"width: 250px\" class=\"wp-caption alignleft\"><a href=\"https:\/\/github.com\/CRG-CNAG\/anubis\"><img loading=\"lazy\" class=\"size-full wp-image-763\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2020\/09\/anubis.png\" alt=\"\" width=\"250\" height=\"46\" \/><\/a><figcaption id=\"caption-attachment-763\" class=\"wp-caption-text\">Analysis framework to explore essentiality from Tn-Seq [<a href=\"https:\/\/github.com\/CRG-CNAG\/anubis\">link<\/a>]<\/figcaption><\/figure><br \/>\n<figure id=\"attachment_10952\" aria-describedby=\"caption-attachment-10952\" style=\"width: 300px\" class=\"wp-caption alignleft\"><img loading=\"lazy\" class=\"wp-image-10952 size-medium\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_custom-300x160.png\" alt=\"\" width=\"300\" height=\"160\" srcset=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_custom-300x160.png 300w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_custom-1024x545.png 1024w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_custom-768x409.png 768w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_custom-1536x817.png 1536w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_custom-649x345.png 649w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_custom.png 1667w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><figcaption id=\"caption-attachment-10952\" class=\"wp-caption-text\">Codon optimization tool for tissue-specific gene design. [<a href=\"https:\/\/custom.crg.eu\/\">link<\/a>]<\/figcaption><\/figure><\/p>\n<figure id=\"attachment_10977\" aria-describedby=\"caption-attachment-10977\" style=\"width: 194px\" class=\"wp-caption alignleft\"><img loading=\"lazy\" class=\"wp-image-10977 size-full\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_robustica.png\" alt=\"\" width=\"194\" height=\"194\" srcset=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_robustica.png 194w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2023\/01\/logo_robustica-150x150.png 150w\" sizes=\"(max-width: 194px) 100vw, 194px\" \/><figcaption id=\"caption-attachment-10977\" class=\"wp-caption-text\">Fully customizable robust Independent Component Analysis (ICA). [<a href=\"https:\/\/github.com\/CRG-CNAG\/robustica\">link<\/a>]<\/figcaption><\/figure>\n<hr \/>\n<p><strong>Structural bioinformatics<\/strong><\/p>\n<p><figure id=\"attachment_732\" aria-describedby=\"caption-attachment-732\" style=\"width: 250px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/foldxsuite.crg.eu\/\"><img loading=\"lazy\" class=\"size-full wp-image-732\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/FoldX.png\" alt=\"\" width=\"250\" height=\"114\" \/><\/a><figcaption id=\"caption-attachment-732\" class=\"wp-caption-text\">Fast and quantitative estimation of interactions and stability between molecular species [<a href=\"http:\/\/foldxsuite.crg.eu\/\">link<\/a>]<\/figcaption><\/figure><br \/>\n<figure id=\"attachment_775\" aria-describedby=\"caption-attachment-775\" style=\"width: 300px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/agadir.crg.es\/\"><img loading=\"lazy\" class=\"size-medium wp-image-775\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/Screenshot-from-2018-07-30-10-48-18-300x127.png\" alt=\"\" width=\"300\" height=\"127\" srcset=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/Screenshot-from-2018-07-30-10-48-18-300x127.png 300w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/Screenshot-from-2018-07-30-10-48-18.png 301w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/a><figcaption id=\"caption-attachment-775\" class=\"wp-caption-text\">Predict the helical behaviour of monomeric peptides [<a href=\"http:\/\/agadir.crg.es\/\">link<\/a>]<\/figcaption><\/figure><br \/>\n<figure id=\"attachment_777\" aria-describedby=\"caption-attachment-777\" style=\"width: 260px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/tango.crg.es\/\"><img loading=\"lazy\" class=\"size-full wp-image-777\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/Screenshot-from-2018-07-30-10-50-36.png\" alt=\"\" width=\"260\" height=\"103\" \/><\/a><figcaption id=\"caption-attachment-777\" class=\"wp-caption-text\">Algorithm to predict aggregation nucleating regions in proteins [<a href=\"http:\/\/tango.crg.es\/\">link<\/a>]<\/figcaption><\/figure><\/p>\n<hr \/>\n<h3>Databases<\/h3>\n<figure id=\"attachment_735\" aria-describedby=\"caption-attachment-735\" style=\"width: 300px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/mycowiki.uni-goettingen.de\/v1\/\"><img loading=\"lazy\" class=\"size-medium wp-image-735\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/mycowiki-300x96.png\" alt=\"\" width=\"300\" height=\"96\" srcset=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/mycowiki-300x96.png 300w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/mycowiki-768x244.png 768w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/mycowiki-649x207.png 649w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/mycowiki-800x255.png 800w, http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/mycowiki.png 801w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/a><figcaption id=\"caption-attachment-735\" class=\"wp-caption-text\"><em>Mycoplasma pneumoniae<\/em> functional database. Joined effort with <a href=\"http:\/\/www.uni-goettingen.de\/en\/577601.html\">Dpt. of General Microbiology<\/a>, University of G\u00f6ttingen (Germany) [<a href=\"http:\/\/mycowiki.uni-goettingen.de\/v1\/\">link<\/a>]<\/figcaption><\/figure>\n<hr \/>\n<h3>Courses<\/h3>\n<p><strong>FoldX In silico protein engineering: From modeling to docking<\/strong><br \/>\nI edition (2018) [<a href=\"http:\/\/www.crg.eu\/en\/event\/coursescrg-foldx-silico-protein-engineering-modeling-docking\">link<\/a>]<\/p>\n<p><strong>Tissue Engineering Course: From Stem Cells to Organoids<\/strong><br \/>\nII edition (2018) [<a href=\"2018: http:\/\/www.crg.eu\/en\/event\/coursescrg-tissue-engineering-course-stem-cells-organoids-0\">link<\/a>]<br \/>\nI edition (2017) [<a href=\"http:\/\/www.crg.eu\/en\/event\/coursescrg-tissue-engineering-course-stem-cells-organoids\">link<\/a>]<\/p>\n<p><strong>Whole-cell modeling<\/strong><br \/>\nIII edition, EMBO course (2019) [<a href=\"https:\/\/meetings.embo.org\/event\/19-whole-cell-modelling\">link<\/a>]<br \/>\nII edition (2017) [<a href=\"http:\/\/www.crg.eu\/en\/event\/coursescrg-whole-cell-modeling-0\">link 1<\/a>] [<a href=\"http:\/\/www.wholecell.org\/v2\/school-2016\/\">link2<\/a>]<br \/>\nI edition (2016) [<a href=\"http:\/\/www.crg.eu\/en\/event\/coursescrg-whole-cell-modeling\">link 1<\/a>] [<a href=\"http:\/\/www.wholecell.org\/v2\/school-2017\/\">link2<\/a>]<\/p>\n<hr \/>\n<h3>Other Resources<\/h3>\n<p><figure id=\"attachment_743\" aria-describedby=\"caption-attachment-743\" style=\"width: 143px\" class=\"wp-caption alignleft\"><a href=\"https:\/\/www.wholecell.org\/\"><img loading=\"lazy\" class=\"size-thumbnail wp-image-743\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/07\/Screenshot-from-2018-07-24-19-05-40.png\" alt=\"\" width=\"143\" height=\"150\" \/><\/a><figcaption id=\"caption-attachment-743\" class=\"wp-caption-text\">Whole-cell model web of reference. By <a href=\"http:\/\/www.karrlab.org\/\">Jonathan Karr&#8217;s group<\/a> at Mt. Sinai School of Medicine (US) [<a href=\"https:\/\/www.wholecell.org\/\">link<\/a>]<\/figcaption><\/figure><br \/>\n<figure id=\"attachment_784\" aria-describedby=\"caption-attachment-784\" style=\"width: 250px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/www.systemtb.crg.eu\/the-project\/\"><img loading=\"lazy\" class=\"size-full wp-image-784\" src=\"http:\/\/serranolab.crg.eu\/wp-content\/uploads\/2018\/08\/Screenshot-from-2018-08-14-10-50-08.png\" alt=\"\" width=\"250\" height=\"91\" \/><\/a><figcaption id=\"caption-attachment-784\" class=\"wp-caption-text\">Collaborative Project for the establishment of a Systems Biology framework to understand key features of Mycobacterium tuberculosis [<a href=\"http:\/\/www.systemtb.crg.eu\/\">link<\/a>]<\/figcaption><\/figure><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Software Sequencing technologies Analysis frameworks Structural bioinformatics Databases Courses FoldX In silico protein engineering: From modeling to docking I edition (2018) [link] Tissue Engineering Course: From Stem Cells to Organoids II edition (2018) [link] I edition (2017) [link] Whole-cell modeling III edition, EMBO course (2019) [link] II edition (2017) [link &hellip;<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_mi_skip_tracking":false},"_links":{"self":[{"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/pages\/24"}],"collection":[{"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/comments?post=24"}],"version-history":[{"count":65,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/pages\/24\/revisions"}],"predecessor-version":[{"id":11024,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/pages\/24\/revisions\/11024"}],"wp:attachment":[{"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/media?parent=24"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}