Product updates, announcements and stories from the trenches.

Update to Jupyter Notebook environment in Terra : Persistent Disk storage now available This week, we released one of those changes that looks small on the face of it but is actually a really big deal. Specifically, we upgraded the cloud environment (previously called "runtime") that we provide in Terra for running Jupyter Notebooks ...

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Terra videos on YouTube What do the Teen Titans and a German docu-series called Terra X have in common? That's right, they're the top hits you get on Google when you search for "Terra intro videos YouTube". So, you might have already searched for Terra videos and come up...

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Coming Soon - Faster, cheaper workflows Whether you’re processing ten data files or ten thousand, making your workflows run faster and cost less is always a goal. The Terra Workflow (aka “Batch”) team has been working on some cost and performance improvements. These aren’t available qui...

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COVID-19 viral genomics: Updated public workspace and Boston outbreak preprint in medRxiv As we have discussed previously, our collaborators in the Sabeti Lab at the Broad Institute have been analyzing SARS-CoV-2 viral genomes from COVID-19 cases in the Boston area, in partnership with the MA Department of Public Health and Massachuset...

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Making large-scale single-cell RNASeq analysis scalable and cost-effective with Cumulus In this guest blog post, Bo Li, Principal Investigator at Massachusetts General Hospital and Assistant Professor of Medicine at Harvard Medical School, explains how using Terra enabled his group to develop a new single-cell transcriptomic analysi...

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“Delete intermediates” option now available for Workflows in Terra Summary: Intermediate files generated by your workflow may be an unexpected source of storage costs. Fortunately, you now have an easy option to delete these files immediately after your workflow runs. Just select the new “delete intermediate outp...

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Faster creation of Notebook environments with Google Compute Engine VMs Summary: We know that the 4 minutes it takes to create a cloud environment to perform a Jupyter Notebook analysis can feel like a long time. To reduce this time and save you cost, Terra has added support for using standard Google Compute Engine Vi...

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Single-cell transcriptome atlas of COVID-19 in primates arms scientists in the fight against SARS-CoV-2 In this guest blog post, Longqi Liu from Beijing Genomics Institute-Research and Miguel A. Esteban from the Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), discuss their efforts in developing a better understanding of...

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Announcing the NCI Cancer Data Aggregator (CDA) - A new collaboration led by Broad Institute in partnership with NCI, SBG, and ISB In the last decade, we’ve seen exponential growth in the amount and breadth of cancer research data. We’ve harnessed the power of cloud repositories to host large oncology datasets, including genomics, proteomics, imaging, and more! Although this ...

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Successes (and stumbles) in cloud-based research: Why we moved to Terra and what we learned along the way In this guest blog post, Timothy Majarian, a Computational Associate from the Manning lab is giving us a glimpse to the lab's journey with transitioning to cloud computing using Terra from the lab's local high-performance compute cluster. Back in ...

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COVID-19 Genomic Surveillance in the Boston Area - Powered by Terra As the global battle against COVID-19 continues, researchers in the viral genomics group at the Broad Institute have been hard at work using viral sequencing and genomic epidemiology to understand the spread of SARS-CoV-2 close to home, yielding n...

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COVID-19 Integrated Analyses using Single Cell Data Recently, we’ve been writing here about the work of the Viral Genomics group at Broad and how they’re using Terra to support their workflows for genome assembly and phylogenomic analysis of novel coronavirus (SARS-CoV-2) genomes recovered from pat...

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A textbook for life sciences in the cloud I remember when I originally started hearing about Docker containers; I didn't really understand what they were and anything I googled on the topic seemed awfully complicated. And I'll admit, getting used to working with cloud storage was rough to...

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Workflow updates to the COVID-19 workspace: Better viral assembly and phylogenetics with NextStrain In our last blog post, we featured a public workspace containing best-practices workflows for viral genome analysis developed by Dr. Danny Park's Viral Genomics group, and used to process COVID-19 research data. We have been working with the viral...

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Broad scientists release COVID-19 best-practices workflows and analysis tools in Terra Like you, we are adapting to a different way of living and working as the 2019 novel coronavirus (COVID-19) spreads, claiming many lives, sickening many more, and upending daily life around the world. We are heartened to see that the scientific co...

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Funding opportunity: Analyze TOPMed and GTEx datasets with support from NHLBI BioData Catalyst It’s the holidays, which means the season of giving is here. And we’re excited to hear that our Data Biosphere partners over at the National Heart, Lung, and Blood Institute (NHLBI) are leading the way with a timely offering. No, it’s not the late...

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Single Cell Portal for collaborations In this post, Amanda Kedaigle, a computational scientist from the Stanley Center for Psychiatric Research is describing her experience with the Single-Cell Portal (SCP), a data visualization portal built on top of Terra. As a computational biologi...

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Ontology and automation: a powerful DUO for streamlining data access Life as a biomedical researcher is a rollercoaster of emotions. One moment you're marvelling at how technology has revolutionized the field -- SO. MUCH. DATA. -- and the next, you're tearing your hair out at how antiquated some of our processes st...

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Improving Job Manager functionality on Terra We can probably all agree that the main point of running analyses in the form of workflows is to automate as much of it as you can. So when something goes wrong, you want to be able to identify the nature of the problem as quickly and easily as po...

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Workflow worries to working WDLs in under a week How insightful feedback about the GATK showcase led to a flurry of updates and the creation of a suite of format conversion tools Last June, just as we were putting the final touches on the teaching materials for a 4-day GATK workshop that we were...

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Upgrade to the workflow system coming soon: heads up on possible side effects When you launch a workflow in Terra, there's a lot that happens behind the scenes to get the work done. Usually you don't need to care about any of it, but we're about to release a system upgrade that may cause some of your workflows to fail where...

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The most Terra-fic features for FireCloud veterans In case you haven't met us yet, Beri and I (Sushma) are part of the Frontline Support Team here, aka the real humans behind the FireCloud and Terra forums and helpdesk. We're on deck every day answering questions and helping troubleshoot problems,...

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New file paths for TARGET and TCGA workspaces Heads up if you use the TARGET and/or TCGA data workspaces: we're planning an update that will change the paths to the data files. This will disable access to the original files in any clones of the original workspaces that retain the old paths, a...

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Testimonials from FireCloud and Terra users The following testimonials have been freely provided by researchers working in Terra or its earlier incarnation, FireCloud. Read on to see how how specific features of the platform enabled their work. Teaching and code sharing in a common env...

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FireCloud to Terra transition coming May 1st Last month we were excited to announce that FireCloud is getting a big upgrade, including a new and improved user interface called Terra. As a reminder, going forward we'll use the name "Terra" to refer to the overall platform that you use to get ...

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Terra's support for scientific projects The vision of Terra is to enable the next generation of collaborative biomedical research. To that end, there are several projects that exist independently on the platform - AnVIL, BioData Catalyst, and FIreCloud, for example. Each project on Terr...

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CRDC and other cloud resources Below is a summary of Cancer Research Data Commons (CRDC) and National Cancer Institute (NCI) cloud resources, and how they meld together to advance cancer research. For more comprehensive information, see the CRDC website. Terms and helpful lin...

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