Being Productive during COVID-19 Quarantine

A new Linus Group study finds that many life science practitioners have had their work disrupted, with their labs and offices largely shut down due to COVID-19. However, many are taking advantage of working from home, to dive into writing, data analysis, planning for future work, even launching “in silico” studies.“1 

One of the biggest challenges people face while working from home is accessing the data, applications, and compute resources they need. For organizations where remote work is the exception rather than the rule, network bottlenecks and slow download times can quickly become a chronic problem, when the majority of employees are all using the  VPN every day. Moreover, not all applications may work properly and some data and resources may simply not be accessible to users who aren’t on-premise.

We’ve heard from many of our customers that they’re grateful that access to the DNAnexus Platform is efficient and straightforward. They’ve been able to shift to working from home without hiccups. Unlike most on-prem analytics setups, the DNAnexus Platform allows them to leverage any of a wide range of compute resources, provides cost-effective storage options, and enables secure, fluid collaboration and sharing with partners and peers around the globe. 

And thanks to the DNAnexus Cloud Workstation App, those working from home are able to keep working at speed. Accessible via SSH, it gives you the ability to explore and analyze your data, directly on the DNAnexus cloud platform, just as you would in a local Linux environment. There’s nothing to download, so your work won’t be slowed by network bandwidth constraints. Note as well that when accessing the app, your connection is secure, and encrypted end-to-end, and the DNAnexus environment ensures the right access controls and permissions, along with the strong compliance.  So you can work safely and efficiently at home, like you do in the office.

Everyone hopes that life – and work – will return soon, to something akin to normal. That will bring life science practitioners back to their labs and office.

1 – “How Scientific Research Progresses Amidst a Global Pandemic,” Linus Group, https://www.thelinusgroup.com/coronavirus-report-summary

A New Way to Play in May: Brush Up On Bioinformatics From Home

Bioinformatics from Home

You told us what you wanted to learn, and we listened. Thanks to everyone who participated in our poll to determine our new online bioinformatics curriculum. We’re happy to announce four free courses available to users of varying experience levels. The online classes will expand the knowledge and skills of biomedical researchers and bioinformaticians alike.

Drug Discovery

How can you nearly double the chance of a drug’s clinical success? Incorporate genomics data from the start. This promising strategy does not come without its challenges, however.

This half-day course, which is designed for all levels of expertise, will provide hands-on experience of the DNAnexus Titan Platform and show you how to bridge the gaps between expression datasets, drug effectiveness, and genetic variation. You will be able to explore secondary RNAseq analysis of cancer cell lines exposed to various levels of certain drugs, as well as variant calling and tertiary analysis in those cell lines. We will also share some prototype custom workflows with Jupyter Notebooks.

For an introduction to incorporating both genomic and detailed clinical data for drug discovery, check out this previous virtual webinar from our Bio-IT World series.

Tuesday, May 12, 2020
10 a.m. – 1 p.m. PT
Register here

How to Efficiently Build Apps/Workflows and Run Analyses on DNAnexus Titan

Curious about best practices for app(let) and workflow building on the DNAnexus Titan Platform? This workshop will walk you through how to implement apps and workflows on Titan, as well as how to optimize them in the cloud. You will learn best practices, patterns to avoid, and be provided with useful templates and code snippets to kickstart your app development.  By the end of the workshop, you will have built an optimized executable that runs a complex pipeline efficiently and securely. We will also teach you how to use the Smart Reuse feature to accelerate development and iterations.

Friday, May 15, 2020
10 a.m.  – 11:30 a.m.  PT
Register here

Complex Genotype/Phenotype Analysis

Combining large cohorts of deeply phenotyped individuals with their genomic data is useful in a wide range of applications, including the development of companion diagnostics, patient stratification, and clinical trial recruitment. But finding those links between genetic markers and the end phenotype can be difficult.

Our second half-day course designed for all levels of expertise will teach you to ‘slice and dice’ cohorts for rapid hypothesis testing — no coding required. It will take you from Graphical User Interface exercises to more technical Command Line applications, and cover mutation analysis on WGS data, generating clusters of SNPs that are drug responsive, and validating hypotheses with pre-existing RNAseq analysis on Jupyter Notebooks.

NOTE: Attendees will need to preregister for a DNAnexus account and login to the appropriate org/project prior to entering the course. Instructions will be sent ahead of time.

Tuesday, May 19th, 2020
10 a.m. – 1 p.m. PT 
Register here

Using Docker and WDL for App and Workflow Development

Do you have a library of existing tools produced and maintained by internal teams or third party groups that you’d like to run on our platform?  DNAnexus supports Docker containers and WDL, allowing the easy import of existing tools and workflows into DNAnexus Titan or Apollo Platforms, and this course will show you how to do so.  Learn how to use public Docker containers as part of your apps and how to run WDL workflows, with hands-on time for an exploration of the DNAnexus Apollo Platform. We will provide some sample .wdl workflows that can be modified, or simply deployed onto DNAnexus Apollo, and you will be able to work with DNAnexus staff to efficiently deploy your pipelines.

NOTE: Attendees will need to preregister for a DNAnexus Apollo account ahead of the workshop and basic exposure to Docker and WDL and/or watch DNAnexus Docker/WDL webinars, including  ‘Using WDL to Develop Locally and Scale to the Cloud’ 

Thursday, May 21, 2020
10 a.m. – 11:30 a.m. PT
Register here

Self-Servicing Archiving Now Available for DNAnexus on Azure

Self-Service Archiving

Whether you’re running DNAnexus on Amazon Web Services (AWS) or on Microsoft Azure, you can take advantage of tiered storage pricing to get control of storage costs, while keeping quick access to the data you need most

And now, DNAnexus on Azure users can take advantage of self-service archiving, to move files, folders, and entire projects easily and quickly between storage states. 

For data you use less frequently, use economical archive storage. Whenever you need archived data for an analysis, you can unarchive one or more files or folders, or entire projects, at reasonable cost.  Storing data in “live” state costs more, but you can use it right away. And as soon as you no longer have immediate need of it, you can archive it to keep expenses in line.

Note also that in all storage states, your data will be stored in accord with your organization’s data-retention policies, while maintaining security, file provenance, meta-data searchability, and other core features of the DNAnexus platform.

The DNAnexus Archive/Unarchive Service is accessible via API to licensed users.  For more details, including pricing information for different storage states, please see this FAQ.