{"id":875,"date":"2012-12-12T14:37:35","date_gmt":"2012-12-12T12:37:35","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2012\/12\/12\/computational-biology-course-on-icts-hpc"},"modified":"2015-08-14T11:49:51","modified_gmt":"2015-08-14T09:49:51","slug":"computational-biology-course-on-icts-hpc","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2012\/12\/12\/computational-biology-course-on-icts-hpc\/","title":{"rendered":"Computational Biology course on ICTS HPC"},"content":{"rendered":"<em>Some feedback from Gerrit Botha at\u00a0<a href=\"http:\/\/www.cbio.uct.ac.za\/\">UCT CBIO<\/a>:<\/em>\r\n\r\nA hands-on course in 16S microbial composition analysis recently held at\r\nUCT and the HPC cluster was used as a training platform. Participants\r\nreceived a temporary account and most of the exercises were done using\r\nan interactive qsub session. The QIIME (<a href=\"http:\/\/qiime.org\/\">Quantitative Insights Into\r\nMicrobial Ecology<\/a>) tool set was used for data cleaning and preliminary\r\nanalysis while the\u00a0<a href=\"https:\/\/github.com\/joey711\/phyloseq\">R phyloseq package<\/a>\u00a0was used for final statistical\r\nanalysis.\r\n\r\nThe 200 series was sufficient for processing the small test\r\ndatasets, however real datasets are larger and will have memory\r\nrequirements in the range of the 400 series. The overall course feedback\r\nwas positive and the UCT participants plan to register for permanent\r\naccounts to start processing their own data.\u00a0 The only part that proved\r\nchallenging was to get the participants accustomed to the Linux\r\nenvironment. Many of the them had no or limited exposure to Linux so\r\nfuture courses will definitely need to keep it in mind and give a\r\nthorough introduction to the environment.","protected":false},"excerpt":{"rendered":"<p>    Some feedback from Gerrit Botha at&nbsp;UCT CBIO:A hands-on course in 16S microbial composition analysis recently held at<br \/>\nUCT and the HPC cluster was used as a training platform. Participants<br \/>\nreceived a temporary account and most of the exercise&#8230;<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[9,4],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Computational Biology course on ICTS HPC - UCT HPC<\/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:\/\/ucthpc.uct.ac.za\/index.php\/2012\/12\/12\/computational-biology-course-on-icts-hpc\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Computational Biology course on ICTS HPC - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"Some feedback from Gerrit Botha at&nbsp;UCT CBIO:A hands-on course in 16S microbial composition analysis recently held at  UCT and the HPC cluster was used as a training platform. 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