DNAnexus Introduces Faster Cloud Options

Spring has arrived at DNAnexus, ushering in important updates! Starting May 1, 2014, we are excited to announce your analyses on DNAnexus will be faster, thanks to new instance types .

What does that really mean? Here’s an example before we dive into all the details…  A specific exome pipeline (e.g., BWA-MEM, GATK-Lite) now runs in less than 4 hours! Previously, the run would have taken nearly 6 hours.

New instance types

We believe, and hope you do too, that DNAnexus is the best choice for expanding your genomic analysis infrastructure. Because, unlike local equipment, which from day one starts collecting dust in your server room while technological advances pile up, the cloud is always on the forefront of computing technology as newer, faster hardware is made available.

These new hardware options are in the form of new instance types (virtual computer configurations) on which your cloud analyses can run. And thanks to the flexibility and reproducibility aspects of the DNAnexus platform, you can start using these new instance types right away—simply launch your existing analyses on one of those new instance types (e.g., using the “–instance-type <…>” option of our “dx run” command-line tool) and enjoy a completely effortless hardware upgrade!

The new instance types are built on high-frequency Intel® processors of the Sandy Bridge and Ivy Bridge microarchitectures, support the Intel® Advanced Vector Extensions (Intel® AVX), and have solid-state drive (SSD) local storage technology for fast I/O performance.

The following table summarizes these new instance types. For a given column (which represents a certain number of cores and local storage capacity), there are up to three different instance types to choose from (with different amounts of memory). Overall these new instance types span a large spectrum, starting at 2 cores, 32 GB SSD, and 3.8 GB RAM, all the way to 32 cores, 640 GB SSD, and 244 GB RAM:

summary new instance types
In an effort to be more informative and transparent, we have also come up with a new, easy to remember, and consistent naming scheme:

  • The prefix (mem1, mem2, or mem3) denotes the memory capacity per core;
  • the infix (ssd1) denotes that these instances have solid-state drive technology;
  • the suffix (x2 through x32) denotes the number of cores.

New names for existing instance types

We liked the convenient new naming scheme so much that we have applied it to existing instance types as well, as shown in the following table.

Compared to the new instance types mentioned earlier, the existing instance types are distinguished by a different storage infix (hdd2), given their regular hard disk drive technology. More information is available on our wiki page, which explains the new naming conventions and includes a detailed list of all instance types.

new instance names
To ease the transition, existing instances can currently be called by either their original name or the new name; the DNAnexus system understands both. However, we encourage you to adopt the new names in a timely manner to avoid any future interruption.

We are very excited to announce these important updates, and we cannot wait to hear your success stories out of them. Drop us a note at support@dnanexus.com if you’d like to get in touch with us.

Security Advisory: Response to Heartbleed Vulnerability

On April 7, 2014, a serious vulnerability known as Heartbleed (CVE-2014-0160) was disclosed in the OpenSSL cryptography library, affecting many popular software packages and Internet services. The vulnerability could potentially be exploited to steal sensitive data such as encryption keys and user passwords. We have no evidence that any DNAnexus customer data or credentials were compromised using this vulnerability. However, out of an abundance of caution, we have taken the following steps below and will continue to implement security actions in response to this event.

At DNAnexus, the security of our clients is our top priority. As soon as the vulnerability was disclosed, we started identifying services on our platform that were affected. All such services were patched to eliminate the vulnerability within 8 hours after it was initially disclosed. After this initial response, we started a thorough analysis of how our systems and the security of our clients could have been affected.

At this time, we have no reason to believe any customer data or credentials were compromised using this vulnerability. Moreover, none of our services that handle genomic data were directly vulnerable. However, services that handle credential information were affected. The nature of this attack makes it hard to detect, and therefore we have decided to take the following precautions:

  • We have updated our affected SSL certificates, to eliminate the possibility that our private SSL keys were compromised.
  • Existing browser-based login sessions initiated before the patch date have been terminated, so you will need to log in again the next time you use the platform.
  • We have triggered early expiration of DNAnexus passwords set before the patch date, so the next time you log in to the platform, you will be prompted to reset your password.
  • The next time you log in, you will also see a security alert advising you to update any API keys that you may have issued on the platform.

To minimize the risk of compromise of your account from possible attacks including this one, we also recommend turning on Two-Factor Authentication (2FA) on the DNAnexus platform, or cycling it if it was already on. Follow these steps:

  • Log in to https://platform.dnanexus.com/
  • Select your name on the upper right and pull down the “Profile” menu item
  • Select the Account tab and click Security
  • If 2FA was previously on, turn it off using your current password and a 2FA Code
  • Turn on Two-Factor Authentication and link your account and authenticator application
  • Verify access using your current password and a Two-Factor Authentication Code, being sure to save your backup codes before pressing “Continue”

We welcome customer feedback – if you have any questions or comments about our security practices, please reach us at support@dnanexus.com.

 

Bring on the New Reference Genome!

GRCh38Like many of our fellow genomics scientists, we are eager to see the much-anticipated new human reference genome. From the Genome Reference Consortium — which consists of the Wellcome Trust Sanger Institute, the Genome Institute at Washington University, the National Center for Biotechnology Information, and the European Bioinformatics Institute — the new GRCh38 reference is expected to be a significant upgrade.

The release has been delayed a bit due to some processing issues, but you can keep an eye out for the new reference via NCBI. Why all the fuss about the latest version? For one thing, it now adds modeled centromeres and novel sequences. Beyond that, it updates for individual bases and fixes for tiling path or assembly errors. (A great overview of GRCh38 is available in this presentation given by NCBI’s Deanna Church in a Cold Spring Harbor workshop this month.) The reference also takes advantage of data from the 1,000 Genomes Project to correct SNPs and indels and to capture decoy sequence.

Scientists across the community are anticipating a computational frenzy once the new reference is released. With all these updates, it’s only natural that researchers with human data sets will want to dust off their sequence data and realign them to the new reference to see what they missed. At the annual meeting of the American Society of Human Genetics in October, Jeff Reid from the Human Genome Sequencing Center at Baylor College of Medicine said he was “terrified” by the idea of how much simultaneous demand he expects for computational resources just from this reference release.

That would indeed be scary for researchers with access only to limited on-premises compute infrastructure. But this is the perfect type of project for elastic cloud computing! No need to stress local resources with a massive burst of intensive demand when you can easily run your reanalysis in the cloud using a platform such as DNAnexus. Our scientific and engineering teams are on standby; just think of us as an extension of your lab offering additional computational resources in a secure and clinically compliant environment.

So bring on GRCh38 — we are ready for it!