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Product updates, announcements and stories from the trenches.

• Introducing WARP: A collection of cloud-optimized workflows for biological data processing and analysis

  Guest blog post by Kylee Degatano, Product Manager for the Lantern Pipelines team in the Data Sciences Platform at the Broad Institute. I'm very excited to announce the recent release of WDL Analysis Research Pipelines (WARP), a brand new, public ...
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• The freedom of portable workflows

  One of the foundational principles of Terra is that it's designed to be an open ecosystem, not a walled garden -- there are no lock-in mechanisms. If after a while you decide to leave, you can take all the analysis tooling you've been using here a...
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• Terra at ASHG 2020: Workshop plans and a video preview

  Every year we run a workshop at the annual meeting of the American Society for Human Genetics, and it's a highlight of our year for many reasons. My favorite aspect of it is that we use the ASHG workshop to drive development of brand new education...
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• Synthetic phenotypes for 1000 Genomes: Updated dataset for testing, training, and learning

  One of the challenges we face in human genomic research is that there is a lot of data that we can't freely share with one another, for legal and ethical reasons. This can be particularly vexing for tool developers who need data for testing, and f...
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• Community-maintained Notebook environments in Terra

  Ever since we introduced Jupyter Notebooks in Terra, we've sought to provide default environments pre-loaded with software packages that are likely to interest you, to minimize the amount of setup necessary to get your work going. However, we've f...
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• GA4GH Interoperability standards in action

  Today is the second day of the 8th plenary meeting of GA4GH, aka the Global Alliance for Genomics & Health, an international collaborative effort that has been driving the development of standards for infrastructure, policy, and security in the ge...
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• Behind the scenes: Bringing the analysis of COVID-19 data from greater Boston into the cloud

  Christine Loreth is a project manager in the Data Sciences Platform at the Broad Institute. In this guest blog post, she tells the story of how she and colleagues in the DSP helped members of the Sabeti Lab, a leading infectious diseases research ...
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• 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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