{"id":5261,"date":"2024-07-28T23:36:59","date_gmt":"2024-07-28T21:36:59","guid":{"rendered":"https:\/\/nwww.crs4.it\/?p=5261"},"modified":"2025-04-29T15:49:09","modified_gmt":"2025-04-29T13:49:09","slug":"omero-biobank","status":"publish","type":"post","link":"https:\/\/www.crs4.it\/en\/technology-catalogue\/omero-biobank\/","title":{"rendered":"OMERO Biobank"},"content":{"rendered":"<p><script src=\"\/crs4_js\/people-details.js\"><\/script><\/p>\n<h3>OMERO Biobank<\/h3>\n<h3>Large scale biomedical computation on OMERO<\/h3>\n<div class=\"sm_hr\"><\/div>\n<h4>Contacts<\/h4>\n<div><a href=\"javascript:PeopleDetails.showAuthorDetails('219')\">Luca Lianas<\/a>,\u00a0<a href=\"javascript:PeopleDetails.showAuthorDetails('31')\">Simone Leo<\/a>,\u00a0<a href=\"javascript:PeopleDetails.showAuthorDetails('148')\">Luca Pireddu<\/a>, Gianluigi Zanetti. E-mail\u00a0<a class=\"linkurl\" href=\"mailto:valorisation@crs4.it\">valorisation@crs4.it<\/a><\/div>\n<h4>Challenge<\/h4>\n<p>The number of domains affected by the big data phenomenon is constantly increasing, both in science and industry, with high-throughput DNA sequencers being among the most massive data producers. Building analysis frameworks that can keep up with such a high production rate, however, is only part of the problem: current challenges include dealing with articulated data repositories where objects are connected by multiple relationships, managing complex processing pipelines where each step depends on a large number of configuration parameters and ensuring reproducibility, error control and usability by non technical staff.<\/p>\n<h4>Overview<\/h4>\n<p>OMERO.biobank is a robust, extensible and scalable traceability framework developed to support large-scale experiments in data-intensive biology. The data management system is built on top of the core services of OME Remote Objects (OMERO), an open source software platform that includes a number of storage mechanisms, remoting middleware, an API and client applications.<\/p>\n<h4>Innovative features<\/h4>\n<ul>\n<li>OMERO.biobank\u2019s kernel is complemented with an indexing system that maintains a persistent version of the traceability structure by mapping entities to nodes and actions to edges in a graph database;<\/li>\n<li>it is implemented with Neo4j;<\/li>\n<li>the indexing system can manage a large number of items.<\/li>\n<\/ul>\n<h4>Potential users<\/h4>\n<p>Researchers, developers<\/p>\n<h4>Impact sectors<\/h4>\n<p>Health &#8211; ICT<\/p>\n<h4>Other resources<\/h4>\n<ol>\n<li><a href=\"https:\/\/github.com\/crs4\/omero.biobank\">https:\/\/github.com\/crs4\/omero.biobank<\/a><\/li>\n<li><a href=\"http:\/\/publications.crs4.it\/pubdocs\/2014\/CLLMPPUAFZ14\/hpcs_2014_bologna_global_view_automation.pdf\">G. Cuccuru, S. Leo, L. Lianas, M. Muggiri, A. Pinna, L. Pireddu, P. Uva, A. Angius, G. Fotia, G. Zanetti, &#8220;An automated infrastructure to support high-throughput bioinformatics&#8221;, 2014 International Conference on High Performance Computing Simulation (HPCS), pp. 600-607, July 2014.<\/a><\/li>\n<li><a href=\"http:\/\/publications.crs4.it\/pubdocs\/2015\/CUOALLOPACZF15\/\">G. Cuccuru, P. Uva, S. Onano, R. Atzeni, S. Leo, L.Lianas, Manuela Oppo, Luca Pireddu, Andrea Angius, Laura Crisponi, Gianluigi Zanetti, Giorgio Fotia, Exploiting a large scale biodata management system to support NGS variant detection studies. Poster presentation at ISMB\/ECCB, 10-14 July 2015, Dublin &#8211; 2015.<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>OMERO Biobank Large scale biomedical computation on OMERO Contacts Luca Lianas,\u00a0Simone Leo,\u00a0Luca Pireddu, Gianluigi Zanetti. E-mail\u00a0valorisation@crs4.it Challenge The number of domains affected by the big data phenomenon is constantly increasing, both in science and industry, with high-throughput DNA sequencers being among the most massive data producers. Building analysis frameworks that can keep up with such [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[93,90],"tags":[],"class_list":["post-5261","post","type-post","status-publish","format-standard","hentry","category-life-sciences","category-technology-catalogue"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v25.9 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>OMERO Biobank - CRS4<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.crs4.it\/en\/technology-catalogue\/omero-biobank\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"OMERO Biobank - CRS4\" \/>\n<meta property=\"og:description\" content=\"OMERO Biobank Large scale biomedical computation on OMERO Contacts Luca Lianas,\u00a0Simone Leo,\u00a0Luca Pireddu, Gianluigi Zanetti. 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