{"id":1966,"date":"2025-09-23T11:54:17","date_gmt":"2025-09-23T09:54:17","guid":{"rendered":"https:\/\/www.gemma-project.eu\/?page_id=1966"},"modified":"2026-03-24T09:05:25","modified_gmt":"2026-03-24T08:05:25","slug":"toolbox","status":"publish","type":"page","link":"https:\/\/www.gemma-project.eu\/it\/toolbox\/","title":{"rendered":"Gemma &#8211; Multi-Omics Toolbox Approach"},"content":{"rendered":"<div data-elementor-type=\"wp-page\" data-elementor-id=\"1966\" class=\"elementor elementor-1966\" data-elementor-post-type=\"page\">\n\t\t\t\t<div class=\"elementor-element elementor-element-74275d5 e-flex e-con-boxed e-con e-parent\" data-id=\"74275d5\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-969e5df elementor-widget elementor-widget-heading\" data-id=\"969e5df\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">GEMMA Multi-Omics Toolbox<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-671af20 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"671af20\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b636fc4 elementor-widget elementor-widget-text-editor\" data-id=\"b636fc4\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\tThe GEMMA multi-omics toolbox includes tools and pipeline modules developed and used during the GEMMA project. The toolbox includes dedicated pipelines for the analysis of individual omics layers, quality control (QC) routines, and integrative multi-omics workflows.\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-fb0deca e-flex e-con-boxed e-con e-parent\" data-id=\"fb0deca\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-bca87b4 elementor-widget elementor-widget-heading\" data-id=\"bca87b4\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Quick Start<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fa8332f elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"fa8332f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-425ec0a elementor-icon-list--layout-traditional elementor-list-item-link-full_width elementor-widget elementor-widget-icon-list\" data-id=\"425ec0a\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-list.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul class=\"elementor-icon-list-items\">\n\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Tools include scripts, containers, workflow modules, and links to two software tools used in GEMMA omics analyses.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Requirements and dependencies are documented in each tool\u2019s README.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Tools can be combined based on available omics layers and research aims.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Example datasets and usage examples are included.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-536daf1 e-flex e-con-boxed e-con e-parent\" data-id=\"536daf1\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-187767a elementor-widget elementor-widget-heading\" data-id=\"187767a\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Available Tools<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3dbf30e elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"3dbf30e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-afb7f42 elementor-widget elementor-widget-basic-table\" data-id=\"afb7f42\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"basic-table.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<div id='tablentor-bt-afb7f42' class='ct-basic-table-container'><div class='tablentor-bt-search'><input class='tablentor-bt-search-input' placeholder='Search' \/><\/div><table class='ct-basic-table' ><tr><th><p>TOOL TYPE<\/p><\/th> <th><p>TITLE<\/p><\/th> <th><p>LEAD PARTNER<\/p><\/th><\/tr><tr><td><p>Data analysis, Script<\/p><\/td> <td><p><a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/omics-integration-for-preclinical-gemma-data\/\">OMICS INTEGRATION FOR PRECLINICAL GEMMA DATA<\/a><\/p><\/td> <td><p>Tampere University, INRAE<\/p><\/td><\/tr><tr><td><p>Data analysis, Script<\/p><\/td> <td><p><a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/gemma-whole-genome-sequencing-data-processing\/\">GEMMA WHOLE GENOME SEQUENCING DATA PROCESSING<br \/><\/a><\/p><\/td> <td><p>Tampere University, CNR-ITB<\/p><\/td><\/tr><tr><td><p>Data analysis, Script<\/p><\/td> <td><p><a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/biomarker-based-polygenic-risk-score-for-gemma-genomes\/\">BIOMARKER-BASED POLYGENIC RISK SCORE FOR GEMMA GENOMES\u200b<br \/><\/a><\/p><\/td> <td><p>Tampere University, CNR-ITB<\/p><\/td><\/tr><tr><td><p>Dataset<\/p><\/td> <td><p><a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/a-network-of-molecular-and-functional-interactions-to-analyse-gemma-omics-datasets\/\">A NETWORK OF MOLECULAR AND FUNCTIONAL INTERACTIONS TO ANALYSE GEMMA OMICS DATASETS<br \/><\/a><\/p><\/td> <td><p>CNR-ITB<\/p><\/td><\/tr><tr><td><p>Data analysis, Script<\/p><\/td> <td><p><a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/network-based-multi-omics-integration-to-prioritize-features-in-gemma-omics-datasets\/\">NETWORK-BASED MULTI-OMICS INTEGRATION TO PRIORITIZE FEATURES IN GEMMA OMICS DATASETS<br \/><\/a><\/p><\/td> <td><p>CNR-ITB<\/p><\/td><\/tr><tr><td><p>Data analysis, Script<\/p><\/td> <td><p><a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/assessment-of-functional-similarity-among-biomarkers\/\">ASSESSMENT OF FUNCTIONAL SIMILARITY AMONG BIOMARKERS<br \/><\/a><\/p><\/td> <td><p>CNR-ITB<\/p><\/td><\/tr><tr><td><p>Data analysis, Script<\/p><\/td> <td><p><a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/assessment-of-functional-similarity-among-biomarkers\/\" target=\"_blank\" rel=\"noopener\">ASSESSMENT OF CLASSIFICATION PERFORMANCE OF BIOMARKERS<\/a><\/p><\/td> <td><p>CNR-ITB<\/p><\/td><\/tr><tr><td><p>Data analysis, Script<\/p><\/td> <td><p><a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/graph-based-multi-omics-integration\/\">GRAPH-BASED MULTI-OMICS INTEGRATION<\/a><\/p><\/td> <td><p>Medinok, Italy<\/p><\/td><\/tr><tr><td>Automated full clinical NGS data quality control and validation<\/td> <td><p><a href=\"https:\/\/www.euformatics.com\/products\/sample-quality-control\" target=\"_blank\" rel=\"noopener\">omnomicsQ<\/a><\/p><\/td> <td>Euformatics<\/td><\/tr><tr><td>Agnostic clinical variant annotation and interpretation for gene panels, WES, and WGS<\/td> <td><p><a href=\"https:\/\/www.euformatics.com\/products\/variant-interpretation\" target=\"_blank\" rel=\"noopener\">omnomicsNGS<\/a><\/p><\/td> <td>Euformatics<\/td><\/tr><\/table>\t\t<script>\n\t\t\tjQuery(document).ready(function($){\n\t\t\t\tvar container_id = '#tablentor-bt-afb7f42';\n\t\t\t\t$( container_id + \" .tablentor-bt-search-input\").on(\"keyup\", function() {\n\t\t\t\t\tvar value = $(this).val().toLowerCase();\n\t\t\t\t\t$( container_id + \" .ct-basic-table tr\").filter(function() {\n\t\t\t\t\t\t$(this).toggle($(this).text().toLowerCase().indexOf(value) > -1)\n\t\t\t\t\t\t});\n\t\t\t\t});\n\t\t\t});\n\t\t<\/script>\n\t\t<\/div>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-4e1fb59 e-flex e-con-boxed e-con e-parent\" data-id=\"4e1fb59\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-4c73376 elementor-widget elementor-widget-heading\" data-id=\"4c73376\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Toolbox Approach<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-bcc13bb elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"bcc13bb\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7daae01 elementor-icon-list--layout-traditional elementor-list-item-link-full_width elementor-widget elementor-widget-icon-list\" data-id=\"7daae01\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-list.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul class=\"elementor-icon-list-items\">\n\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Reproducibility: scripts, containers, and workflow managers ensure that analyses can be replicated across environments.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Data security: sensitive data is not shared and thus do not need to be uploaded to external servers.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Resource efficiency: avoids maintaining an online platform while still allowing scalable computations on institutional systems.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Ease of maintenance: pipelines can be updated and released through version control (e.g., GitHub), with changelogs and environment specifications. <\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Analysing data: The data will be linked to the toolbox once the results are published in scientific articles. The data will be shared via dedicated data repositories (e.g., ENA, SRA, GEO, EGA, MGnify) designed for this purpose.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">User support: documentation, and examples facilitate the further use of the tools.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-40ae518 e-flex e-con-boxed e-con e-parent\" data-id=\"40ae518\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-7cdc3be elementor-widget elementor-widget-heading\" data-id=\"7cdc3be\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Integration Strategies within the Toolbox<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1dbe704 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"1dbe704\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a99bf19 elementor-widget elementor-widget-text-editor\" data-id=\"a99bf19\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>The toolbox will support multiple integration strategies depending on the research question and data availability. <b>Late integration<\/b> is implemented by processing each omics layer independently (e.g., calling variants, detecting differentially methylated regions, profiling microbial differences) and combining the <b>results<\/b> at the interpretation stage, through pathway enrichment, network analyses, or meta-analyses. This approach is straightforward, robust to technical differences across datasets, and provides biologically interpretable outcomes.<\/p>\n<p><\/p>\n<p>Another option for integration is <b>mid integration<\/b>, which is achieved by feeding the different omics layers into a <b>joint statistical or machine learning model <\/b>, which identifies shared latent factors across data types while preserving their specific structures. This approach is more powerful for uncovering cross-omics interactions and mechanistic links.<\/p>\n<p><\/p>\n<p>With both late and mid integration modules, the toolbox ensures flexibility: researchers can choose simpler workflows when appropriate, but also apply state-of-the-art integrative modeling for comprehensive analyses.<\/p>\n<p><\/p>\n<p>Last option in the toolbox is a graph-based integration model. It is an integration strategy based on logical connections among nodes that represent omics data. Reactome Pathways database is then used to glue different omics domains according to their participation in biological reactions.<\/p>\n<p><\/p>\n<p>In GEMMA project the mid integration strategy for is used for integrating microbiome, methylation and genome data, and further late integration strategy for associating metabolomics, immunoprofiling and proteome data with the other omics measurements.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-03fdad4 e-flex e-con-boxed e-con e-parent\" data-id=\"03fdad4\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-35e57a4 elementor-widget elementor-widget-heading\" data-id=\"35e57a4\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Risk Mitigation<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4c2b70f elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"4c2b70f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8bcac51 elementor-widget elementor-widget-text-editor\" data-id=\"8bcac51\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\tPotential concerns and our solutions:\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-445fa27 elementor-icon-list--layout-traditional elementor-list-item-link-full_width elementor-widget elementor-widget-icon-list\" data-id=\"445fa27\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-list.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul class=\"elementor-icon-list-items\">\n\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Usability: clear README,  and  instructions.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Dependencies: will be given in instructions.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Computation needs: documented resource requirements.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Integration methods:  toolbox includes modules for both mid-integration (combined modeling) and late-integration (result combination), depending on the scientific question.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-circle\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Sustainability: reproducibility supported via version control, documented updates, and maintained environments.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>","protected":false},"excerpt":{"rendered":"<p>GEMMA Multi-Omics Toolbox The GEMMA multi-omics toolbox includes tools and pipeline modules developed and used during the GEMMA project. The toolbox includes dedicated pipelines for the analysis of individual omics layers, quality control (QC) routines, and integrative multi-omics workflows. Quick Start Tools include scripts, containers, workflow modules, and links to two software tools used in&hellip;&nbsp;<a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/\" rel=\"bookmark\">Leggi tutto &raquo;<span class=\"screen-reader-text\">Gemma &#8211; Multi-Omics Toolbox Approach<\/span><\/a><\/p>","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/template-pagebuilder-full-width.php","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"","footnotes":""},"class_list":["post-1966","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1966","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/comments?post=1966"}],"version-history":[{"count":64,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1966\/revisions"}],"predecessor-version":[{"id":2168,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1966\/revisions\/2168"}],"wp:attachment":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/media?parent=1966"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}