{"id":187,"date":"2020-10-08T12:46:06","date_gmt":"2020-10-08T12:46:06","guid":{"rendered":"https:\/\/website.prod.unilu.spikeseed.cloud\/lcsb-fr\/news\/permedcoe-hpc-exascale-centre-of-excellence-in-personalised-medicine\/"},"modified":"2020-10-08T12:46:06","modified_gmt":"2020-10-08T12:46:06","slug":"permedcoe-hpc-exascale-centre-of-excellence-in-personalised-medicine","status":"publish","type":"news","link":"https:\/\/www.uni.lu\/lcsb-fr\/news\/permedcoe-hpc-exascale-centre-of-excellence-in-personalised-medicine\/","title":{"rendered":"PerMedCoE: HPC\/Exascale Centre of Excellence in Personalised Medicine"},"content":{"rendered":"<section class=\"wp-block-unilux-blocks-free-section section\"><div class=\"container xl:max-w-screen-xl\"><p>Coordinated by the Barcelona Supercomputing Center (BSC) and funded by the European Commission, this recently launched HPC centre of excellence will optimise codes for cell-level simulations in HPC\/Exascale and bridge the gap between organ and molecular\u00a0 simulations, thus contributing to the European Personalised Medicine Roadmap.<\/p><p>The next generation of Exascale supercomputers will become a necessary tool to treat diseases on an individual level and make one step forward in personalised medicine. The recently launched European HPC\/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE) will provide an efficient and sustainable infrastructure to support the development of personalised medicine by showcasing HPC\/Exascale-upgraded use cases such as translating the consequences of single cell omics information into actionable molecular disease models.<\/p><figure class=\"wp-block-dev4-reusable-blocks-image  object-fit--contain\">\n    \n<img decoding=\"async\" class=\"wp-block-image unilux-custom-image-block\"\n                alt=\"\"\n            src=\"https:\/\/www.uni.lu\/wp-content\/uploads\/sites\/22\/2023\/07\/permedcoe.png\"\n                srcset=\"https:\/\/www.uni.lu\/wp-content\/uploads\/sites\/22\/2023\/07\/permedcoe-300x196.png 300w, https:\/\/www.uni.lu\/wp-content\/uploads\/sites\/22\/2023\/07\/permedcoe.png 550w\"\n                style=\"object-position: 50.00% 50.00%; font-family: &quot;object-fit: contain; object-position: 50.00% 50.00%;&quot;; aspect-ratio: 3\/2; object-fit: contain; width: 100%;\"\n        loading=\"lazy\"\n\/>    <\/figure>\n<h7 class=\"has-text-align-left wp-block-unilux-blocks-heading\"        id=\"example-of-the-framework-that-enables-multiscale-simulations-permedcoe-will-allow-the-scaling-up-of-multiscale-simulations-that-combine-boolean-models-that-capture-intracellular-behaviours-and-agent\"\n    >\nExample of the framework that enables multiscale simulations. PerMedCoE will allow the scaling-up of multiscale simulations that combine Boolean models that capture intracellular behaviours and agent-based models that study population dynamics. Image by Miguel Ponce de Le\u00f3n (PerMedCoE)<\/h7>\n<p><\/p><p>One of the most significant contributions of PerMedCoE will be to scale-up cell-level simulations to HPC\/Exascale level, which will fill the gap between the molecular-and organ-level simulations provided by other Centres of Excellence (CoEs) such as <a href=\"https:\/\/www.compbiomed.eu\/\" target=\"_blank\" title=\"\" rel=\"noopener\">CompBioMed<\/a> and <a href=\"https:\/\/bioexcel.eu\/\" target=\"_blank\" title=\"\" rel=\"noopener\">BioExcel<\/a>.<\/p><p>\u201cPerMedCoE will boost the competitiveness of European personalised medicine and aims to become the community hub for Exascale-ready software in this domain\u201d, says <a href=\"https:\/\/www.bsc.es\/valencia-alfonso\" target=\"_blank\" title=\"\" rel=\"noopener\">Alfonso Valencia<\/a>, ICREA Research Professor, BSC Life Sciences Department Director and PerMedCoE Coordinator.<\/p><p>Personalised medicine opens unexplored\u00a0 frontiers to treating diseases at the\u00a0 individual level combining clinical and omics information. However, the performance of the current simulation software is still insufficient to tackle medical problems such as tumour evolution and response to treatment at the single-cell level or patient-specific treatments. For this reason, this European centre of excellence pursues the following main objectives:<\/p><ul class=\"ulux-list\"><li class=\"ulux-list-item\">To optimise key software for cell-level simulations to the new pre-exascale platforms to contribute to the European Personalised Medicine Roadmap.<\/li><li class=\"ulux-list-item\">To integrate personalised medicine into the new European HPC\/Exascale ecosystem, by offering access to HPC\/Exascale-adapted and optimised software.<\/li><li class=\"ulux-list-item\">To design and complete a comprehensive set of personalised medicine use cases to drive the development of cell-level simulations.<\/li><li class=\"ulux-list-item\">To build the basis for its sustainability by coordinating personalised medicine and HPC communities, and reaching out to industrial and academic end-users with use cases, training, expertise and best practices.<\/li><\/ul><p>The LCSB will be in charge of developing and optimising a pre exascale cell level simulation software and lead the tasks of developing guidelines for data protection and privacy preservation in an exascale HPC environment. \u00ab\u00a0This project is in line with our future vision of the <a href=\"https:\/\/wwwfr.uni.lu\/lcsb\/research\/bioinformatics_core\" target=\"_self\" title=\"\" rel=\"noopener\">Bioinformatics Core<\/a> at the LCSB\u00a0\u00bb, says <a href=\"https:\/\/wwwfr.uni.lu\/lcsb\/people\/reinhard_schneider\" target=\"_self\" title=\"\" rel=\"noopener\">Prof. Dr. Reinhard Schneider<\/a>, \u00ab\u00a0and works in synergy with the national strategy of HPC.\u00a0\u00bb<\/p><p>The centre will become the entry point to Exascale-ready cell-level simulation software, able to transform personal omics data into actionable mechanistic\u00a0 models\u00a0 of medical relevance, supporting developers and end-users with know-how and best practices. It will also connect simulation software developers with HPC, HTC and HPDA experts at the CoEs <a href=\"https:\/\/pop-coe.eu\/\" target=\"_blank\" title=\"\" rel=\"noopener\">POP<\/a> and <a href=\"https:\/\/hidalgo-project.eu\/\" target=\"_blank\" title=\"\" rel=\"noopener\">HiDALGO<\/a>, and work with other biomedical consortia such as <a href=\"https:\/\/elixir-europe.org\/\" target=\"_blank\" title=\"\" rel=\"noopener\">ELIXIR<\/a> and <a href=\"https:\/\/lifetime-fetflagship.eu\/\" target=\"_blank\" title=\"\" rel=\"noopener\">LifeTime<\/a>, also connecting pre-exascale infrastructures hosted by supercomputing centres such as the <a href=\"https:\/\/www.bsc.es\/news\/bsc-news\/eurohpc-selects-barcelona-supercomputing-center-entity-host-one-the-largest-european-supercomputers\" target=\"_blank\" title=\"\" rel=\"noopener\">BSC<\/a> and <a href=\"https:\/\/www.csc.fi\/en\/modern-datacenter-environment\" target=\"_blank\" title=\"\" rel=\"noopener\">CSC\u2013IT Center for Science<\/a>.<\/p>\n<h3 class=\"has-text-align-left wp-block-unilux-blocks-heading\"        id=\"about-permedcoe\"\n    >\nAbout PerMedCoE<\/h3>\n<p>PerMedCoE is the HPC\/ExascaleCentreof Excellence for Personalised Medicine in Europe and aims\u00a0 to\u00a0 provide\u00a0 an\u00a0 efficient\u00a0 and\u00a0 sustainable\u00a0 entry\u00a0 point\u00a0 to\u00a0 the\u00a0 HPC\/Exascale-upgraded methodology\u00a0 to\u00a0 translate\u00a0 omics information into \u00a0actionable\u00a0 models\u00a0 of\u00a0 cellular\u00a0 functions\u00a0 of medical\u00a0 relevance. Coordinated\u00a0 by\u00a0 the\u00a0 Barcelona\u00a0 Supercomputing\u00a0 Center\u00a0 (BSC), this CoE has been awarded \u20ac5million in funding from the European Commission and will run from 1 October 2020 to 30\u00a0 September\u00a0 2023. A range of 12 world-class\u00a0 academic and industry partners from across Europe are participating in the CoE: <a href=\"https:\/\/www.bsc.es\/\" target=\"_blank\" title=\"\" rel=\"noopener\">Barcelona Supercomputing\u00a0 Center<\/a>(BSC), <a href=\"https:\/\/www.csc.fi\/en\/csc\" target=\"_blank\" title=\"\" rel=\"noopener\">CSC\u2013IT Center for Science<\/a>, University of Luxembourg, <a href=\"https:\/\/institut-curie.org\/\" target=\"_blank\" title=\"\" rel=\"noopener\">Institut Curie<\/a>, <a href=\"https:\/\/www.klinikum.uni-heidelberg.de\/\" target=\"_blank\" title=\"\" rel=\"noopener\">University Hospital Heidelberg<\/a>, <a href=\"https:\/\/atos.net\/es\/spain\" target=\"_blank\" title=\"\" rel=\"noopener\">Atos Spain<\/a>, <a href=\"https:\/\/www.kth.se\/en\" target=\"_blank\" title=\"\" rel=\"noopener\">KTH Royal Institute of Technology<\/a>, <a href=\"https:\/\/www.embl.de\/\" target=\"_self\" title=\"\" rel=\"noopener\">European Molecular Biology Laboratory (EMBL)<\/a>, <a href=\"https:\/\/www.crg.eu\/\" target=\"_blank\" title=\"\" rel=\"noopener\">Centre for Genomic Regulation (CRG)<\/a>, <a href=\"https:\/\/www.mdc-berlin.de\/\" target=\"_blank\" title=\"\" rel=\"noopener\">Max Delbr\u00fcck Center for Molecular Medicine (MDC)<\/a>, <a href=\"https:\/\/www.uni-lj.si\/eng\/\" target=\"_blank\" title=\"\" rel=\"noopener\">University of Ljubljana<\/a> and <a href=\"https:\/\/elem.bio\/\" target=\"_blank\" title=\"\" rel=\"noopener\">ELEM Biotech<\/a>.<\/p><p>Further information: <a href=\"http:\/\/www.permedcoe.eu\" target=\"_self\" title=\"\" rel=\"noopener\">www.permedcoe.eu<\/a> \/ @PerMedCoE \/ #PerMedCoE<\/p><p>The\u00a0 PerMedCoE\u00a0 project\u00a0 has received funding from the European Union\u2019s Horizon 2020research\u00a0 and innovation programme under the grant agreement N\u00ba 951773.<\/p><\/div><\/section>","protected":false},"excerpt":{"rendered":"<p>Coordinated by the Barcelona Supercomputing Center (BSC) and funded by the European Commission, this recently launched HPC centre of excellence will optimise codes for cell-level simulations in HPC\/Exascale and bridge the gap between organ and molecular\u00a0 simulations, thus contributing to the European Personalised Medicine Roadmap.<\/p>\n","protected":false},"author":0,"featured_media":188,"template":"","format":"standard","meta":{"featured_image_focal_point":[],"show_featured_caption":false,"ulux_newsletter_groups":"","uluxPostTitle":"","uluxPrePostTitle":"","_trash_the_other_posts":false,"_price":"","_stock":"","_tribe_ticket_header":"","_tribe_default_ticket_provider":"","_tribe_ticket_capacity":"0","_ticket_start_date":"","_ticket_end_date":"","_tribe_ticket_show_description":"","_tribe_ticket_show_not_going":false,"_tribe_ticket_use_global_stock":"","_tribe_ticket_global_stock_level":"","_global_stock_mode":"","_global_stock_cap":"","_tribe_rsvp_for_event":"","_tribe_ticket_going_count":"","_tribe_ticket_not_going_count":"","_tribe_tickets_list":"[]","_tribe_ticket_has_attendee_info_fields":false},"news-category":[],"news-topic":[18],"organisation":[],"authorship":[],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v22.3 (Yoast SEO v22.3) - 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