{"id":298,"date":"2021-03-11T21:49:47","date_gmt":"2021-03-11T21:49:47","guid":{"rendered":"https:\/\/terrabioappdev.wpenginepowered.com\/a-year-in-lockdown-6-minutes-of-feature-highlights\/"},"modified":"2023-12-27T04:54:35","modified_gmt":"2023-12-27T04:54:35","slug":"a-year-in-lockdown-6-minutes-of-feature-highlights","status":"publish","type":"post","link":"https:\/\/terra.bio\/a-year-in-lockdown-6-minutes-of-feature-highlights\/","title":{"rendered":"A year in lockdown; 6 minutes of feature highlights"},"content":{"rendered":"<p><span style=\"font-weight: 400;\">We&#8217;re seeing a lot of news features this week about the anniversary of the first coronavirus lockdowns in the US, from lighthearted takes on quarantine trends like hoarding toilet paper, baking sourdough, and sea shanties on TikTok, to much more serious reckonings of the dramatic and deeply unequal toll that this disaster has levied on our nation and the world.\u00a0<\/span><\/p>\n<p><span style=\"font-weight: 400;\">For those of us in the Broad Institute Data Sciences Platform, this is a time to take stock, but also to step away and allow ourselves to breathe. The Broad Institute has declared tomorrow, Friday 3\/12, an Institute-wide holiday, which I expect will be particularly appreciated by our many team members and collaborators who have worked tirelessly both on the front lines and behind the scenes of COVID-19 response efforts.<\/span><\/p>\n<p><span style=\"font-weight: 400;\">For my part, the ambient retrospective mood inspired me to take a trip down memory lane, i.e. trawl through the <\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/sections\/360003424251-Release-Notes\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">release notes<\/span><\/a><span style=\"font-weight: 400;\">, to get a sense of how much functionality has been added in Terra since we formally switched to remote work a year ago. Turns out, there was a lot \u2014 including some things I wasn&#8217;t even aware of. This motivated me to compile a list of &#8220;actionable highlights&#8221;, focusing specifically on new options and capabilities that you would interact with in the user interface.<\/span><\/p>\n<p><span style=\"font-weight: 400;\">Assuming the last thing anyone wants is another slide deck to scroll through, I turned my list into two bite-size videos (3 mins each) dedicated to Interactive Analysis and Workflow Execution, respectively. You can find both videos embedded below and in the <a href=\"https:\/\/youtube.com\/playlist?list=PLh_zJaZ9uQ7PbyNZHOWf7GAceIz22axb7\">TerraBites playlist<\/a> of the <a href=\"https:\/\/www.youtube.com\/channel\/UCkXAqpR5Hk1ZmNd2-1K2l5Q\">Terra YouTube channel<\/a>, as well as a list of resources for learning more about the features they cover at the end of this post.<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><iframe title=\"Lockdown Roundup \u2014 Interactive Analysis\" width=\"800\" height=\"450\" src=\"https:\/\/www.youtube.com\/embed\/BhA82NsZ2fM?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" allowfullscreen><\/iframe><\/p>\n<p>&nbsp;<\/p>\n<p><iframe title=\"Lockdown Roundup \u2014 Workflow Execution\" width=\"800\" height=\"450\" src=\"https:\/\/www.youtube.com\/embed\/TPop5zaebcM?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" allowfullscreen><\/iframe><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"font-weight: 400;\">W<\/span><span style=\"font-weight: 400;\">e&#8217;d love to hear your thoughts on whether this kind of feature roundup is helpful; if there&#8217;s enough demand we could do this on a more regular basis, perhaps quarterly. In the meantime, consider subscribing to this blog, the newsletter (which is a monthly digest of the blog content), or the <a href=\"https:\/\/www.youtube.com\/channel\/UCkXAqpR5Hk1ZmNd2-1K2l5Q\" target=\"_blank\" rel=\"noopener\">Terra YouTube channel<\/a>\u00a0to get regular updates delivered to your inbox.\u00a0<\/span><\/p>\n<p>&nbsp;<\/p>\n<hr \/>\n<h3><span style=\"color: #008000;\"><b>Resources<\/b><\/span><\/h3>\n<p>&nbsp;<\/p>\n<h4><span style=\"color: #008000;\"><b>Interactive Analysis\u00a0<\/b><\/span><b><\/b><\/h4>\n<ul>\n<li aria-level=\"1\"><b>Available applications<\/b><\/li>\n<\/ul>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Added RStudio (alpha) (<\/span><a href=\"https:\/\/terra.bio\/try-rstudio-in-terra\"><span style=\"font-weight: 400;\">blog<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Added Galaxy (alpha) (<\/span><a href=\"https:\/\/terra.bio\/try-out-galaxy-in-terra\"><span style=\"font-weight: 400;\">blog<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Notebooks: added Playground Mode (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360034505132\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">doc<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li aria-level=\"1\"><b>Cloud environments <\/b>(<a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360057425291\" target=\"_blank\" rel=\"noopener\">faq<\/a>)<\/li>\n<\/ul>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Persistent disks (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360047318551\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">doc<\/span><\/a><span style=\"font-weight: 400;\">)\u00a0<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Built-in &amp; custom cloud environments (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360038125912\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">doc<\/span><\/a><span style=\"font-weight: 400;\">)<\/span>\n<ul>\n<li style=\"font-weight: 400;\" aria-level=\"3\"><span style=\"font-weight: 400;\">Community-contributed environments (<\/span><a href=\"https:\/\/terra.bio\/community-maintained-notebook-environments-in-terra\/\"><span style=\"font-weight: 400;\">blog<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"3\"><span style=\"font-weight: 400;\">Roll your own (via Terra base container) (<\/span><a href=\"https:\/\/github.com\/DataBiosphere\/terra-app\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">github<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<\/ul>\n<\/li>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Top 3 new packages pre-installed in built-in environments<\/span>\n<ul>\n<li style=\"font-weight: 400;\" aria-level=\"3\"><span style=\"font-weight: 400;\">Bioconductor (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360037749912\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">doc<\/span><\/a><span style=\"font-weight: 400;\">)\u00a0<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"3\"><span style=\"font-weight: 400;\">AnVIL package (<\/span><a href=\"https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/AnVIL.html\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">doc<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"3\"><span style=\"font-weight: 400;\">Seurat pre-installed in all R images (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360057158031\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">release note<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<h4><span style=\"color: #008000;\"><b>Workflow Execution\u00a0<\/b><\/span><b><\/b><\/h4>\n<ul>\n<li aria-level=\"1\"><b>Cromwell capabilities<\/b><\/li>\n<\/ul>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Deleting intermediate files (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360039681632\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">doc<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Task-level checkpointing (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360056897032\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">doc<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li aria-level=\"1\"><b>Data sources\u00a0<\/b><\/li>\n<\/ul>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Broad reference bundle on persistent disk (<\/span><a href=\"https:\/\/terra.bio\/coming-soon-faster-cheaper-workflows\/\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">blog<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Creating entity sets on the fly (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360047611871\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">doc<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">DRS integration (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360039330211\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">doc<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li aria-level=\"1\"><b>Third-party\u00a0<\/b><\/li>\n<\/ul>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">Dockstore support for relative import paths (<\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/community\/posts\/360073538432\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">forum<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"2\"><span style=\"font-weight: 400;\">New WDL 1.1 features (<\/span><a href=\"https:\/\/github.com\/openwdl\/wdl\/blob\/main\/versions\/1.1\/SPEC.md\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">specification<\/span><\/a><span style=\"font-weight: 400;\">)\u00a0<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>A list of Terra highlights from this past year, focusing specifically on new options and capabilities for interactive analysis and workflow execution that you would interact within the user interface.<\/p>\n","protected":false},"author":4,"featured_media":299,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[12,18,31,43,44,45,39,32],"tags":[],"class_list":["post-298","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-analysis","category-data","category-ecosystem","category-features","category-interactive-analysis","category-notebooks","category-videos","category-workflows"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.0 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>A year in lockdown; 6 minutes of feature highlights - Terra<\/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:\/\/terra.bio\/a-year-in-lockdown-6-minutes-of-feature-highlights\/\" \/>\n<meta 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