{"id":4154,"date":"2023-03-09T15:35:06","date_gmt":"2023-03-09T07:35:06","guid":{"rendered":"https:\/\/medicine.nus.edu.sg\/bch\/?page_id=4154"},"modified":"2026-05-05T12:20:11","modified_gmt":"2026-05-05T04:20:11","slug":"phm5004","status":"publish","type":"page","link":"https:\/\/medicine.nus.edu.sg\/bch\/phm5004\/","title":{"rendered":"PHM5004 &#8211; High Performance Computing for Precision Medicine"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"4154\" class=\"elementor elementor-4154\" data-elementor-post-type=\"page\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-1a7af21 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"1a7af21\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-1f1c220\" data-id=\"1f1c220\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-946348f elementor-widget elementor-widget-spacer\" data-id=\"946348f\" data-element_type=\"widget\" data-widget_type=\"spacer.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-spacer\">\n\t\t\t<div class=\"elementor-spacer-inner\"><\/div>\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-6d4c434 elementor-widget elementor-widget-heading\" data-id=\"6d4c434\" data-element_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\">Course Overview<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-43faf36 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"43faf36\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-85384c6\" data-id=\"85384c6\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-f96a0ef elementor-widget elementor-widget-text-editor\" data-id=\"f96a0ef\" data-element_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><span lang=\"EN-SG\" style=\"font-size: 14pt; color: #000000;\">Healthcare is becoming more data-driven with the advent of \u2018omics technologies and the ability to profile multi-dimensional parameters. High-performance or supercomputing systems are increasingly being used to accelerate data-intensive pipelines used in precision medicine that take advantage of multiple nodes and high-speed interconnected systems for parallel computing.<\/span><\/p><p><span lang=\"EN-GB\" style=\"font-size: 14pt; color: #000000;\">This course provides the foundational knowledge and skills for big data processing by leveraging on high performance computing resources. Students will be introduced to the theory and application of high performance systems covering HPC architecture and workflows as well as approaches to accelerate analytical pipelines.<\/span><\/p>\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-8bc5c98 elementor-widget elementor-widget-spacer\" data-id=\"8bc5c98\" data-element_type=\"widget\" data-widget_type=\"spacer.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-spacer\">\n\t\t\t<div class=\"elementor-spacer-inner\"><\/div>\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-89981aa elementor-widget elementor-widget-heading\" data-id=\"89981aa\" data-element_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\">Learning Outcomes<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ded01ca elementor-widget elementor-widget-text-editor\" data-id=\"ded01ca\" data-element_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><span lang=\"EN-SG\" style=\"font-size: 14pt; color: #000000;\">At the end of the module, students will be able to<\/span><\/p><ul style=\"list-style-type: disc;\"><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Evaluate and explain the runtime complexity of algorithms used in analysing data for precision medicine<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Describe the architecture of high-performance systems and relate it to the latencies in processing data<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Evaluate data processing workflows and identify bottlenecks using profiling methods<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Explain the different models of parallel computing<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Evaluate and identify suitable applications that utilize parallel computing for accelerating workflows<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Parallelize a high-throughput workflow and optimize the bottlenecks where necessary<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Containerize applications and binaries for reproducible computing in a shared HPC environment<\/span><\/span><\/li><\/ul>\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-4c49a3c elementor-widget elementor-widget-spacer\" data-id=\"4c49a3c\" data-element_type=\"widget\" data-widget_type=\"spacer.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-spacer\">\n\t\t\t<div class=\"elementor-spacer-inner\"><\/div>\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-1797eb7 elementor-widget elementor-widget-heading\" data-id=\"1797eb7\" data-element_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\">Course Outline<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9a0e2f5 elementor-widget elementor-widget-text-editor\" data-id=\"9a0e2f5\" data-element_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<ul style=\"list-style-type: disc;\"><li><span style=\"font-size: 14pt;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\" style=\"color: #000000;\">Runtime complexity<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Approaches to speeding up analysis<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Overview of HPC architecture<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Measuring performance<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Types of parallel computing models<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">High throughput computing for workflows<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Reproducible computing in shared environment<\/span><\/span><\/li><li><span style=\"font-size: 14pt; color: #000000;\"><span lang=\"EN-SG\"> <\/span><span lang=\"EN-SG\">Case studies of parallelization<\/span><\/span><ul><\/ul><\/li><\/ul>\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-4ffbe37 elementor-widget elementor-widget-spacer\" data-id=\"4ffbe37\" data-element_type=\"widget\" data-widget_type=\"spacer.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-spacer\">\n\t\t\t<div class=\"elementor-spacer-inner\"><\/div>\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-54b6f3d elementor-widget elementor-widget-heading\" data-id=\"54b6f3d\" data-element_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\">Course Requirements<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-587fb2e elementor-widget elementor-widget-text-editor\" data-id=\"587fb2e\" data-element_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><span style=\"font-family: tahoma, arial, helvetica, sans-serif; font-size: 14pt; color: #000000;\">Familiarity with Linux environment<\/span><\/p>\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-bdf22c5 elementor-widget elementor-widget-spacer\" data-id=\"bdf22c5\" data-element_type=\"widget\" data-widget_type=\"spacer.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-spacer\">\n\t\t\t<div class=\"elementor-spacer-inner\"><\/div>\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-b49c198 elementor-widget elementor-widget-heading\" data-id=\"b49c198\" data-element_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\">Course Coordinators<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<section class=\"elementor-section elementor-inner-section elementor-element elementor-element-2794ccc elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"2794ccc\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-inner-column elementor-element elementor-element-beec95b\" data-id=\"beec95b\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-7dad186 elementor-cta--layout-image-left elementor-cta--skin-classic elementor-animated-content elementor-widget elementor-widget-call-to-action\" data-id=\"7dad186\" data-element_type=\"widget\" data-widget_type=\"call-to-action.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<a class=\"elementor-cta\" href=\"https:\/\/medicine.nus.edu.sg\/bch\/faculty\/ban-hon-kim-kenneth\/\" target=\"_blank\">\n\t\t\t\t\t<div class=\"elementor-cta__bg-wrapper\">\n\t\t\t\t<div class=\"elementor-cta__bg elementor-bg\" style=\"background-image: url(https:\/\/medicine.nus.edu.sg\/bch\/wp-content\/uploads\/sites\/13\/2020\/01\/team-1-1.jpg);\" role=\"img\" aria-label=\"team-1\"><\/div>\n\t\t\t\t<div class=\"elementor-cta__bg-overlay\"><\/div>\n\t\t\t<\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-cta__content\">\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<h2 class=\"elementor-cta__title elementor-cta__content-item elementor-content-item\">\n\t\t\t\t\t\tDr Kenneth Ban\t\t\t\t\t<\/h2>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-cta__description elementor-cta__content-item elementor-content-item\">\n\t\t\t\t\t\tCo-Director, MSc in Precision Health &amp; Medicine, NUS<br><br>Programme Director, National Supercomputing Cluster Singapore (NSCC)\t\t\t\t\t<\/div>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-cta__button-wrapper elementor-cta__content-item elementor-content-item \">\n\t\t\t\t\t<span class=\"elementor-cta__button elementor-button elementor-size-\">\n\t\t\t\t\t\tProfile\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-inner-column elementor-element elementor-element-b7d65af\" data-id=\"b7d65af\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-06d0084 elementor-cta--layout-image-left elementor-cta--skin-classic elementor-animated-content elementor-widget elementor-widget-call-to-action\" data-id=\"06d0084\" data-element_type=\"widget\" data-widget_type=\"call-to-action.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<a class=\"elementor-cta\" href=\"https:\/\/medicine.nus.edu.sg\/bch\/faculty\/tan-tin-wee\/\" target=\"_blank\">\n\t\t\t\t\t<div class=\"elementor-cta__bg-wrapper\">\n\t\t\t\t<div class=\"elementor-cta__bg elementor-bg\" style=\"background-image: url(https:\/\/medicine.nus.edu.sg\/bch\/wp-content\/uploads\/sites\/13\/2020\/01\/bchtantw.jpg);\" role=\"img\" aria-label=\"bchtantw\"><\/div>\n\t\t\t\t<div class=\"elementor-cta__bg-overlay\"><\/div>\n\t\t\t<\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-cta__content\">\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<h2 class=\"elementor-cta__title elementor-cta__content-item elementor-content-item\">\n\t\t\t\t\t\tA\/Prof Tan Tin Wee\t\t\t\t\t<\/h2>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-cta__description elementor-cta__content-item elementor-content-item\">\n\t\t\t\t\t\tCo-Director, MSc in Precision Health &amp; Medicine, NUS <br><br> Della Lee Professor in Mental Health and Digital Science, Mind Science Centre, NUS and NUHS\t\t\t\t\t<\/div>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-cta__button-wrapper elementor-cta__content-item elementor-content-item \">\n\t\t\t\t\t<span class=\"elementor-cta__button elementor-button elementor-size-\">\n\t\t\t\t\t\tProfile\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Course Overview Healthcare is becoming more data-driven with the advent of \u2018omics technologies and the ability to profile multi-dimensional parameters&#8230;.<\/p>\n","protected":false},"author":8259,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-4154","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>PHM5004 - High Performance Computing for Precision Medicine - Department of Biochemistry \u2013 School of Medicine, National University of Singapore<\/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:\/\/medicine.nus.edu.sg\/bch\/phm5004\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"PHM5004 - High Performance Computing for Precision Medicine - Department of Biochemistry \u2013 School of Medicine, National University of Singapore\" \/>\n<meta property=\"og:description\" content=\"Course Overview Healthcare is becoming more data-driven with the advent of \u2018omics technologies and the ability to profile multi-dimensional parameters....\" \/>\n<meta property=\"og:url\" content=\"https:\/\/medicine.nus.edu.sg\/bch\/phm5004\/\" \/>\n<meta property=\"og:site_name\" content=\"Department of Biochemistry \u2013 School of Medicine, National University of Singapore\" \/>\n<meta property=\"article:modified_time\" content=\"2026-05-05T04:20:11+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/medicine.nus.edu.sg\/bch\/phm5004\/\",\"url\":\"https:\/\/medicine.nus.edu.sg\/bch\/phm5004\/\",\"name\":\"PHM5004 - High Performance Computing for Precision Medicine - Department of Biochemistry \u2013 School of Medicine, National University of Singapore\",\"isPartOf\":{\"@id\":\"https:\/\/medicine.nus.edu.sg\/bch\/#website\"},\"datePublished\":\"2023-03-09T07:35:06+00:00\",\"dateModified\":\"2026-05-05T04:20:11+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/medicine.nus.edu.sg\/bch\/phm5004\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/medicine.nus.edu.sg\/bch\/phm5004\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/medicine.nus.edu.sg\/bch\/phm5004\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/medicine.nus.edu.sg\/bch\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"PHM5004 &#8211; 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