Update to Ubuntu 14.04

Ubuntu 12.04 has reached end-of-life, and the DNAnexus team is taking  steps to ensure that customer applications and DNAnexus backend systems migrate away from this version of the software. We recommend any customers who develop and maintain DNAnexus applications update your applications and applets to Ubuntu 14.04 as soon as possible to identify any issues that may arise. We are currently using Canonical’s Extended Security Maintenance feature to help ensure the ongoing security and integrity of Ubuntu 12.04 systems, however, support for 12.04 DNAnexus applications and applets on all instance types will officially end on April 28th, 2018.

Tips for Updating to Ubuntu 14.04: 

  • If your application uses assets, ‘execDepends’, or installs from ‘apt’ directly within the application, it is recommended that you ensure any version changes in these packages when using Ubuntu 14.04 are compatible with your application. It may be helpful to use a Cloud Workstation to test out these differences.
  • Instead of using ‘execDepends’ for installing packages, consider using DNAnexus assets or Docker images. Your application will incur less runtime dependency on the network availability of Canonical packages, and by using Docker, you can choose different runtime environments, including Ubuntu 16.04, to encapsulate the core functionality of the application.

Beginning October 15th, 2017, the DNAnexus Platform will also require the ‘distribution’ and ‘release’ fields to be specified within the application’s ‘runSpec’ when building an applet. Please ensure that any applications you build from source contain those fields. Note that if you use ‘dx-app-wizard’ to generate an application template, these fields are populated for you. Please ensure you are using a recent version of the dx-toolkit when using ‘dx-app-wizard’ or performing a build. You can obtain the latest version of the toolkit from our wiki or by using the ‘dx upgrade‘ command.

Please do not hesitate to contact support@dnanexus.com with any questions or concerns regarding this software update.

The New UI: Sleeker. Modern. Intuitive.

We are pleased to announce a design refresh of the DNAnexus web user interface! The new, modern interface incorporates visual enhancements that make the most common tasks and interactions intuitive and delightful, without changing the underlying functions that power your biomedical research. Explore some of the updates below, highlighted in yellow.

Project List

Your list of projects and files has a sleeker layout and more intuitive filtering system. Looking for your Bookmarks? The Bookmarks tab has been renamed to Saved Filters so you can quickly find and access the projects you’re looking for.

Project Page

Managing workflows has never been easier. The main actions are listed using clear, modernized icons to help you know exactly which steps to take next. Each file also has a context menu. Clicking on these three dots will help you accomplish actions such as view, copy, delete, and download one item at a time. You can still apply bulk action to all the files by clicking the icons at the top of the page.

App Library

The available apps are displayed in a simplified and visually appealing manner. The inputs and outputs of each tool are clearly shown, and finding the appropriate app for your analysis is now easier than ever. 

Billing Information

Your user settings have been reorganized to show your billing information in one distinct location. This will help you easily review your budget, spend, and remaining funds.

We hope these changes make using the DNAnexus web interface an intuitive and seamless experience. If you have any questions about the updates, let us know at support@dnanexus.com.

DNAnexus: Powering AZ’s 2-Million Genome Translational Vision

AstraZenecaThe volume of biomedical data available for analysis is increasing at an exponential rate, yet translating this information into insight remains both a formidable challenge and a remarkable opportunity. The demonstrable success already achieved by the Regeneron Genetics Center (RGC) and Geisinger Health System in integrating genetic and phenotypic data to inform drug development and benefit patients points to the potential of this approach, and highlights what impassioned champions with a good plan and the right platform can accomplish. (RGC/Geisinger publications, powered by DNAnexus, are discussed here and here.)

The success and promise of the RGC/Geisinger collaboration has prompted an expansion of this vision – including at Regeneron itself, which, in partnership with GSK and the UK Biobank, has announced plans to analyze the genetic data of another 500,000 individuals, powered again by the DNAnexus Platform.

These studies, aimed to catalyze the discovery and development of consequential new medicines, are motivated in part by what translational scientist Robert Plenge (formerly of Merck, now at Celgene) has termed “causal human biology” – the ability to use rare, highly informative genetic variants to better understand the staggering complexity of human biology and human disease. (Plenge has discussed this concept in Science Translational Medicine, in a fantastic Timmerman Report post reprinted in his must-read Plenge Gen blog, and on the Tech Tonics podcast.)

Plenge – and the industry, more generally – is hopeful that leveraging causal human biology can help pharma companies select better targets and more intelligently prosecute them, hopefully resulting in dramatically improved success in phase 2/3 trials; the high failure rates in these expensive mid- and late-stage studies are one of the main reasons drug development is so costly.

In this context, DNAnexus is especially excited to announce today its partnership with Astrazeneca in a particularly ambitious genetics project, the AstraZeneca Centre for Genomic Research, which was established by AZ in 2016 “to transform drug discovery and development across its entire research and development pipeline.

The vision, has been nicely articulated by Menelas Pangalos, Executive Vice President, Innovative Medicines & Early Development at AstraZeneca:

“Using the power of genomics is the foundation of our ambition to develop the most innovative and impactful treatments for patients. With the advent of next generation sequencing and the increased sophistication of data analysis, the time is now right to immerse ourselves fully in the international genomics community through these pioneering collaborations and through the creation of our own genome centre. We will leverage information from up to 2 million genome sequences, including over 500,000 from our own clinical trials, to drive drug discovery and development across all our therapeutic areas. Genomics will be fundamental to our laboratory research, our clinical trials and the launch of our medicines for patients.”

The requirements of this project – including, in particular, the ability to (a) manage high volumes of genomic data in a secure and compliant fashion; (b) facilitate the integration of genetic data with other data types, and (c) enable global collaboration around these data – were a natural fit for the DNAnexus translational informatics platform.

The DNAnexus team is tremendously exciting by the opportunity to power the efforts of visionary industry leaders such as Regeneron and AstraZeneca in translating the promise of precision medicine and data analytics into discrete novel medicines that can meaningfully improve the lives of patients.