{"id":8910,"date":"2022-05-16T11:44:43","date_gmt":"2022-05-16T04:44:43","guid":{"rendered":"https:\/\/gcloudvn.com\/?p=8910"},"modified":"2023-03-23T13:18:46","modified_gmt":"2023-03-23T06:18:46","slug":"broad-institue-tang-toc-do-nghien-cuu-khoa-hoc-voi-google-cloud-sql","status":"publish","type":"post","link":"https:\/\/gcloudvn.com\/en\/kienthuc\/broad-institue-tang-toc-do-nghien-cuu-khoa-hoc-voi-google-cloud-sql\/","title":{"rendered":"Broad Institute speeds scientific research with Cloud SQL"},"content":{"rendered":"<p style=\"text-align: justify;\"><b><i>Editor\u2019s note:<\/i><\/b><i><span style=\"font-weight: 400;\">The Broad Institute of MIT and Harvard, a nonprofit biomedical research organization that develops genomics software, needs to keep pace with the latest scientific discoveries. Here\u2019s how they use managed database services from Google Cloud to move fast and stay on the cutting edge.<\/span><\/i><\/p>\n<p><strong>&gt; Reference:<\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/gcloudvn.com\/en\/kienthuc\/mysql-8-da-san-sang-cho-doanh-nghiep-voi-cloud-sql\/\">MySQL 8 is enterprise-ready with Cloud SQL<\/a><\/li>\n<li><a href=\"https:\/\/gcloudvn.com\/en\/kienthuc\/google-cloud-sql-nay-da-ho-tro-postgresql-13\/\">Google Cloud SQL now supports PostgreSQL 13<\/a><\/li>\n<li><a href=\"https:\/\/gcloudvn.com\/en\/kienthuc\/chuyen-dich-co-so-du-lieu-len-google-cloud-tang-bung-no-trong-nam-2020\/\">Database migration to Google Cloud increases explosively in 2020<\/a><\/li>\n<\/ul>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">The <\/span><a href=\"https:\/\/www.broadinstitute.org\/\" rel=\"nofollow noopener\" target=\"_blank\"><span style=\"font-weight: 400;\">Broad Institute of MIT and Harvard<\/span><\/a><span style=\"font-weight: 400;\"> is a nonprofit biomedical research organization that focuses on advancing the understanding and treatment of human disease. One of our major initiatives is developing genomics tools and making them available across the scientific ecosystem. The rapid pace of discovery means our data sciences team has to keep pace so that our software products enable the best research. Our ability to move fast is critical. And when we decided to pivot our focus during the pandemic to develop and process tens of millions of COVID-19 tests, speed was a driving factor. Fully managed database services and analytics solutions from Google Cloud helped Google accelerate their pace of development.<\/span><\/p>\n<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_80 counter-hierarchy ez-toc-counter ez-toc-grey ez-toc-container-direction\">\n<div class=\"ez-toc-title-container\">\n<p class=\"ez-toc-title\" style=\"cursor:inherit\">Table of contents<\/p>\n<span class=\"ez-toc-title-toggle\"><a href=\"#\" class=\"ez-toc-pull-right ez-toc-btn ez-toc-btn-xs ez-toc-btn-default ez-toc-toggle\" aria-label=\"Toggle Table of Content\"><span class=\"ez-toc-js-icon-con\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #999;color:#999\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewbox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #999;color:#999\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewbox=\"0 0 24 24\" version=\"1.2\" baseprofile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/span><\/a><\/span><\/div>\n<nav><ul class='ez-toc-list ez-toc-list-level-1' ><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/gcloudvn.com\/en\/kienthuc\/broad-institue-tang-toc-do-nghien-cuu-khoa-hoc-voi-google-cloud-sql\/#Tang_toc_thong_tin_chi_tiet_ve_gen_voi_Cloud_SQL\" >Accelerating genomics insights with Cloud SQL<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/gcloudvn.com\/en\/kienthuc\/broad-institue-tang-toc-do-nghien-cuu-khoa-hoc-voi-google-cloud-sql\/#Toi_uu_hoa_chi_tieu_tren_dam_may_voi_phan_tich_BigQuery\" >Optimizing cloud spend with BigQuery analytics\u00a0<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/gcloudvn.com\/en\/kienthuc\/broad-institue-tang-toc-do-nghien-cuu-khoa-hoc-voi-google-cloud-sql\/#Xoay_vong_de_xu_ly_cac_xet_nghiem_COVID-19\" >Pivoting to process COVID-19 tests<\/a><\/li><\/ul><\/nav><\/div>\n<h2 style=\"text-align: justify;\"><span class=\"ez-toc-section\" id=\"Tang_toc_thong_tin_chi_tiet_ve_gen_voi_Cloud_SQL\"><\/span><strong>Accelerating genomics insights with Cloud SQL<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">One of Google main products that uses Google Cloud services is <\/span><a href=\"https:\/\/terra.bio\/\" rel=\"nofollow noopener\" target=\"_blank\"><span style=\"font-weight: 400;\">Terra<\/span><\/a><span style=\"font-weight: 400;\"> \u2014a secure, scalable, open source platform for biomedical research. We co-developed it with Microsoft and Verily to help researchers access public data files, manage private data, organize research, and collaborate with others. After working with Google Cloud for a long time, we will naturally use its services <a href=\"https:\/\/gcloudvn.com\/en\/google-cloud-platform\/\">Google Cloud Platform<\/a> for Terra&#039;s dashboard.\u00a0<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">For the backend, we use a number of cloud services including <\/span><a href=\"https:\/\/gcloudvn.com\/en\/cloud-sql\/\"><span style=\"font-weight: 400;\">Cloud SQL<\/span><\/a><span style=\"font-weight: 400;\"> for PostgreSQL and MySQL, as well as <\/span><span style=\"font-weight: 400;\">.<\/span><span style=\"font-weight: 400;\">, to allow users to track their different data assets, methods, and research results, and to power the Terra control plane. Cloud SQL helps us accelerate development in two key areas. First, our developers can get these database services up and running quickly, without going through some centralized system that might become a bottleneck. And secondly, using Cloud SQL lowers our operational burden. We can keep managed services running and performing well using fewer of our own developers. Instead, these teams can focus on developing new features for users.<\/span><\/p>\n<h2 style=\"text-align: justify;\"><span class=\"ez-toc-section\" id=\"Toi_uu_hoa_chi_tieu_tren_dam_may_voi_phan_tich_BigQuery\"><\/span><strong>Optimizing cloud spend with BigQuery analytics\u00a0<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">For much of Google's genomics analysis, they use <\/span><a href=\"https:\/\/gcloudvn.com\/en\/bigquery\/\"><span style=\"font-weight: 400;\">BigQuery,<\/span><\/a> <a href=\"https:\/\/gcloudvn.com\/en\/compute-engine\/\"><span style=\"font-weight: 400;\">Compute Engine<\/span><\/a><span style=\"font-weight: 400;\"> and <\/span><span style=\"font-weight: 400;\">Dataproc (<a href=\"https:\/\/cloud.google.com\/dataproc\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/cloud.google.com\/dataproc<\/a>)<\/span><span style=\"font-weight: 400;\">, but understanding the detailed costs of that research has been challenging.   Billing data can be exported into BigQuery, but the costs wouldn't be attributed to the specific analyses being performed.  However, by adding billing labels to each cloud resource used and joining that information with detailed metadata in our relational Cloud SQL databases we can provide extremely fine grained cost information.  As a result, for example, we\u2019re able to tell a researcher that their virtual machine spent 17 cents as part of a certain analysis, research project, or sample. With these insights, our researchers have visibility into their costs, and are able to  decide where to focus their optimizations.<\/span><\/p>\n<h2 style=\"text-align: justify;\"><span class=\"ez-toc-section\" id=\"Xoay_vong_de_xu_ly_cac_xet_nghiem_COVID-19\"><\/span><strong>Pivoting to process COVID-19 tests<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">When the global pandemic hit, the Broad Institute volunteered to make our clinical testing and diagnostics facilities available to serve public health needs. We created a novel automation system for COVID-19 test processing that is scalable, modular, and high-throughput, in service of the public health needs of the Commonwealth of Massachusetts and surrounding areas. In the first several months of the pandemic, Broad processed more than 10 percent of all PCR tests in the United States, and today has processed <\/span><a href=\"https:\/\/covid19-testing.broadinstitute.org\/\" rel=\"nofollow noopener\" target=\"_blank\"><span style=\"font-weight: 400;\">more than 30 million tests<\/span><\/a><span style=\"font-weight: 400;\">, with turnaround times of less than 24 hours. Using serverless components with a Cloud SQL for PostgreSQL database at its core, we built a testing solution\u2014going from an idea to launching our large-scale COVID-19 operation in just two weeks. On our first day, we delivered 140 tests. But a year later we were delivering up to 150,000 tests<\/span><span style=\"font-weight: 400;\"> a day. That\u2019s in part because our database solution was able to scale up really quickly.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">With a few <\/span><span style=\"font-weight: 400;\">.<\/span><span style=\"font-weight: 400;\"> CLI commands, we enabled high availability and read replicas for our database, while backups and maintenance upgrades were handled automatically. This scalability made a big difference to us considering we were a small team working on very tight timelines.<\/span><\/p>\n<p style=\"text-align: right;\"><strong>Source: <a href=\"https:\/\/gcloudvn.com\/en\/\">Gimasys<\/a><\/strong><\/p>","protected":false},"excerpt":{"rendered":"<p>L\u01b0u \u00fd c\u1ee7a Bi\u00ean t\u1eadp vi\u00ean: Vi\u1ec7n Broad c\u1ee7a MIT v\u00e0 Harvard, m\u1ed9t t\u1ed5 ch\u1ee9c nghi\u00ean c\u1ee9u y sinh phi l\u1ee3i nhu\u1eadn ph\u00e1t tri\u1ec3n ph\u1ea7n m\u1ec1m gen, c\u1ea7n b\u1eaft k\u1ecbp v\u1edbi nh\u1eefng kh\u00e1m ph\u00e1 khoa h\u1ecdc m\u1edbi nh\u1ea5t. \u0110\u00e2y l\u00e0&hellip;<\/p>","protected":false},"author":2,"featured_media":8911,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"inline_featured_image":false,"footnotes":""},"categories":[1],"tags":[],"class_list":["post-8910","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-kienthuc","entry","has-media"],"_links":{"self":[{"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/posts\/8910","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/comments?post=8910"}],"version-history":[{"count":0,"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/posts\/8910\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/media\/8911"}],"wp:attachment":[{"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/media?parent=8910"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/categories?post=8910"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/gcloudvn.com\/en\/wp-json\/wp\/v2\/tags?post=8910"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}