{"id":240,"date":"2023-09-12T11:45:21","date_gmt":"2023-09-12T08:45:21","guid":{"rendered":"https:\/\/sites.uef.fi\/bioinformatics\/?page_id=240"},"modified":"2026-01-22T15:37:20","modified_gmt":"2026-01-22T13:37:20","slug":"infrastructure","status":"publish","type":"page","link":"https:\/\/sites.uef.fi\/bioinformatics\/infrastructure\/","title":{"rendered":"Computing Environment"},"content":{"rendered":"\n<p>The Bioinformatics Center operates an environment designed to meet the computational demands of bioinformatics research while ensuring the security and integrity of sensitive data. It includes Linux computing environments for interactive and batch jobs, optimized for diverse bioinformatics workloads, with remote access available.<\/p>\n\n\n\n<p>Among the pre-installed tools and applications, users will find, for example, R, MATLAB, Python, Nextflow, Apptainer, and CellBender. For added flexibility, users are permitted to install customized versions of these applications as needed to meet specific research requirements.<\/p>\n\n\n\n<p>Only <a href=\"https:\/\/asiointi.uef.fi\/ssc\/app#\/order\/1924199\/\">registered<\/a> UEF researchers and students are eligible to gain access to the server infrastructure. Authorization is granted for a period of two years, after which users are required to submit a renewal application to maintain access privileges.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Usage Agreement<\/h3>\n\n\n\n<p>When using the computing environment and the services provided by the Bioinformatics Center, users agree to the following rules and regulations:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>The computing environment should be used for research and educational purposes only.<\/li>\n\n\n\n<li>The Bioinformatics Center does not guarantee that your data will be backed up or recoverable. Therefore, the user should keep external copies of their important data.<\/li>\n\n\n\n<li>The user should acknowledge the use of the computing environment, for example in publications or course materials. See further details <a href=\"https:\/\/sites.uef.fi\/bioinformatics\/acknowledge\/\">here<\/a>.<\/li>\n\n\n\n<li>Access is granted for two years at a time and the user should renew it by submitting a new application.<\/li>\n<\/ul>\n\n\n\n<p><strong><a href=\"https:\/\/link.webropolsurveys.com\/S\/5732DDB4FCEBF473\" target=\"_blank\" rel=\"noreferrer noopener\">Apply for Server Access<\/a><\/strong>.<\/p>\n\n\n\t<div id=\"accordion-block_a02b983f747aaf38187fc1c8a411cff8\" class=\"accordions\">\n\t\t\t\t\t<div class=\"accordion accordion-js\">\n\t\t\t\t<button class=\"accordion__button\" aria-controls=\"content-4750\" aria-expanded=\"false\" id=\"accordion-control-4750\">\n\t\t\t\t\t<h3 class=\"accordion__heading\" >\n\t\t\t\t\t\ttuma.uef.fi\t\t\t\t\t<\/h3>\n\t\t\t\t<\/button>\n\t\t\t\t<div class=\"accordion__content\" role=\"region\" aria-labelledby=\"accordion-control-4750\" aria-hidden=\"true\" id=\"content-4750\">\n\t\t\t\t\t<p><!-- wp:paragraph --><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\" wp-image-1208 alignnone\" src=\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/tools-300x188.png\" alt=\"\" width=\"199\" height=\"125\" srcset=\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/tools-300x188.png 300w, https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/tools.png 600w\" sizes=\"auto, (max-width: 199px) 100vw, 199px\" \/><\/p>\n<p>The Tuma computing server is meant for interactive computing workloads. In addition to traditional <a href=\"https:\/\/en.wikipedia.org\/wiki\/Secure_Shell\">SSH<\/a> terminal access, the server provides a graphical desktop environment that can be used with the <a href=\"https:\/\/en.wikipedia.org\/wiki\/Remote_Desktop_Protocol\">Remote Desktop Connection Protocol<\/a>.<\/p>\n<p>Computing resources are limited to 10 CPUs and 200 GB of RAM per user.<\/p>\n<p>More information can be found <a href=\"https:\/\/studentuef.sharepoint.com\/sites\/BIC\/SitePages\/tuma.uef.fi.aspx\">here<\/a>.<\/p>\n<p>Server address: <strong>tuma.uef.fi<\/strong><\/p>\n<p><!-- \/wp:paragraph --> <!-- wp:heading --><\/p>\n<h4 id=\"system_specs\" class=\"wp-block-heading\">System specs<\/h4>\n<p><!-- \/wp:heading --> <!-- wp:list --><\/p>\n<ul class=\"wp-block-list\">\n<li style=\"list-style-type: none\">\n<ul class=\"wp-block-list\"><!-- wp:list-item --><\/p>\n<li>CPU: 2x AMD EPYC 7302 \/ 64 threads<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><!-- \/wp:list-item --> <!-- wp:list-item --><\/p>\n<ul class=\"wp-block-list\">\n<li style=\"list-style-type: none\">\n<ul class=\"wp-block-list\">\n<li>RAM: 1024 GB<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><!-- \/wp:list-item --> <!-- wp:list-item --><\/p>\n<ul class=\"wp-block-list\">\n<li style=\"list-style-type: none\">\n<ul class=\"wp-block-list\">\n<li>OS: Rocky Linux 8<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><!-- \/wp:list-item --><\/p>\n<p><!-- \/wp:list --> <!-- wp:heading --><\/p>\n<h4 id=\"storage\" class=\"wp-block-heading\">Storage<\/h4>\n<p><!-- \/wp:heading --> <!-- wp:paragraph --><\/p>\n<p>Storage space for the server is provided by <a href=\"https:\/\/www.uef.fi\/en\/digital-services\">UEF Digital Services.<\/a><\/p>\n<!-- \/wp:paragraph -->\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t<div class=\"accordion accordion-js\">\n\t\t\t\t<button class=\"accordion__button\" aria-controls=\"content-6265\" aria-expanded=\"false\" id=\"accordion-control-6265\">\n\t\t\t\t\t<h3 class=\"accordion__heading\" >\n\t\t\t\t\t\tkudos.uef.fi\t\t\t\t\t<\/h3>\n\t\t\t\t<\/button>\n\t\t\t\t<div class=\"accordion__content\" role=\"region\" aria-labelledby=\"accordion-control-6265\" aria-hidden=\"true\" id=\"content-6265\">\n\t\t\t\t\t<p><img loading=\"lazy\" decoding=\"async\" class=\" wp-image-1214 alignnone\" src=\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/infra-300x159.png\" alt=\"\" width=\"199\" height=\"105\" srcset=\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/infra-300x159.png 300w, https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/infra.png 632w\" sizes=\"auto, (max-width: 199px) 100vw, 199px\" \/><\/p>\n<p>For demanding computing tasks, we have a high-performance computing (HPC) environment powered by the <a href=\"https:\/\/slurm.schedmd.com\/\">SLURM<\/a> job scheduler.<\/p>\n<p>More information can be found <a href=\"https:\/\/studentuef.sharepoint.com\/sites\/BIC\/SitePages\/kudos.uef.fi.aspx\">here<\/a>.<\/p>\n<p>Server address: <strong>kudos.uef.fi<\/strong><\/p>\n<p><!-- \/wp:paragraph --> <!-- wp:heading --><\/p>\n<h4 id=\"system_specs\" class=\"wp-block-heading\">System specs<\/h4>\n<p>The cluster has various CPU and GPU computing nodes. The operating system is Rocky Linux 9.<\/p>\n<p><strong><em>8 x CPU nodes<\/em><\/strong><\/p>\n<ul>\n<li>CPU: 2 x Intel Xeon Gold 5418Y<\/li>\n<li>512 GB RAM<\/li>\n<\/ul>\n<p><strong><em>1x CPU node<\/em><\/strong><\/p>\n<ul>\n<li>CPU: 2 x AMD Ryzen Threadripper PRO 3995WX<\/li>\n<li>512 GB RAM<\/li>\n<\/ul>\n<p><strong><em>2 x GPU nodes<\/em><\/strong><\/p>\n<ul>\n<li>CPU: 2 x Intel Xeon Gold 6326<\/li>\n<li>512 GB RAM<\/li>\n<li>4 x NVIDIA A100 40 GB<\/li>\n<\/ul>\n<h4 id=\"storage\" class=\"wp-block-heading\">Storage<\/h4>\n<p><!-- \/wp:heading --> <!-- wp:paragraph --><\/p>\n<p>Storage space for the server is provided by <a href=\"https:\/\/www.uef.fi\/en\/digital-services\">UEF Digital Services.<\/a><\/p>\n<p><!-- \/wp:paragraph --><\/p>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t<div class=\"accordion accordion-js\">\n\t\t\t\t<button class=\"accordion__button\" aria-controls=\"content-1320\" aria-expanded=\"false\" id=\"accordion-control-1320\">\n\t\t\t\t\t<h3 class=\"accordion__heading\" >\n\t\t\t\t\t\tRemote access\t\t\t\t\t<\/h3>\n\t\t\t\t<\/button>\n\t\t\t\t<div class=\"accordion__content\" role=\"region\" aria-labelledby=\"accordion-control-1320\" aria-hidden=\"true\" id=\"content-1320\">\n\t\t\t\t\t<p>You can connect to our services remotely using three different methods.<\/p>\n<p>1) If you have a university laptop, you can use the built-in VPN service.<\/p>\n<p>2) If you do not have a university laptop, you can connect via <a href=\"https:\/\/studentuef.sharepoint.com\/sites\/heimo_en\/services\/software-and-licenses\/Pages\/Software-for-home-computers.aspx\">Azure Virtual Desktop<\/a>.<\/p>\n<p>3) The UEF SSH Gateway server is another way to access our services. More information about the service can be found <a href=\"https:\/\/studentuef.sharepoint.com\/sites\/BIC\/SitePages\/sshgw.uef.fi.aspx\">here<\/a>.<\/p>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t<\/div>\n\t","protected":false},"excerpt":{"rendered":"<p>The Bioinformatics Center operates an environment designed to meet the computational demands of bioinformatics research while ensuring the security and integrity of sensitive data. It includes Linux computing environments for interactive and batch jobs, optimized for diverse bioinformatics workloads, with remote access available. Among the pre-installed tools and applications, users will find, for example, R, [&hellip;]<\/p>\n","protected":false},"author":990,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-240","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Computing Environment - UEF Bioinformatics Center<\/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:\/\/sites.uef.fi\/bioinformatics\/infrastructure\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Computing Environment - UEF Bioinformatics Center\" \/>\n<meta property=\"og:description\" content=\"The Bioinformatics Center operates an environment designed to meet the computational demands of bioinformatics research while ensuring the security and integrity of sensitive data. 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