First Two iPad Winners Announced, and Another Chance to Win!

Many thanks to everyone who has signed up so far at our DNAnexusX landing
page to find out about the new platform we’ll be launching later this year.
Our developers are working furiously on the final touches, and we can’t
wait to give you all a peek at the new product.

In addition to the updates we’ll be sending about the new platform as we get
closer to launch, people who sign up on the landing page are also entered
into a monthly drawing for a free iPad.  We’re delighted to announce that
our winner for April was Mike Warfe, solutions architect at Case Western
Reserve University, and our winner for May is Bingbing Yuan in
bioinformatics at the Whitehead Institute.
Congratulations to both of them!

We’ve more iPad giveaways planned for June and July, so it’s not too
late to sign up at the landing page to be automatically entered to win.
Simply go to dnanexusx.com and enter your e-mail address.

Relationships for Innovation

This week we announced new agreements with two premier healthcare institutions: Geisinger Health Systems (GHS) and the University of California, San Francisco (UCSF). We also announced, with Complete Genomics, our participation in its Genomics Discovery Partners program.

Each of these relationships opens exciting new opportunities. NGS technology generates terabytes of data requiring enormous storage capacities and supercomputing processing power to extract meaningful information. Academic research centers, university hospitals, and commercial organizations risk being overwhelmed by this rapidly growing amount of data. As researchers and clinicians seek to integrate these datasets into their work, industry leaders are increasingly investing to meet this data management analysis challenge.

We are excited to enable these industry leaders to innovate solutions with us on our cloud-based platform. GHS is integrating its genomic data assets with clinical applications, including parent-child trio studies for disease characterization and prevention. UCSF is uploading, managing, and analyzing sequencing data for large-scale genome sequencing research applications. Complete Genomics is offering our data management and visualization services to customers of their human genome sequencing service.

These relationships exemplify ways we help organizations to capitalize on opportunities created by the growing ubiquity of low-cost genomics data. Together we are applying these experiences to create new services and capabilities that support their customers, researchers, and clinicians.

Check back often for updates on these and other collaborations in the works.

Preserving and Enhancing an Important Community Resource

Today, DNAnexus is pleased to announce the launch of our hosted SRA site!

The DNAnexus SRA site is a hosted version of NCBI’s Sequence Read Archive (SRA). As the most comprehensive archive of publicly available next-generation sequencing data, the SRA is an important resource to researchers around the world. The SRA remains the single best resource of useful sequence data from research initiatives such as the 1,000 Genomes Project and institutions like the Broad Institute, Washington University, and the Wellcome Trust Sanger Institute.

DNAnexus has created a mirrored site of this resource by teaming up with Google, to provide access to all publicly accessible datasets for specific studies, experiments, samples, and runs that are currently available via the NCBI SRA website. (Note: Currently these data do not include the analysis data and the Trace Archive repository.)

The New Interface

In addition to maintaining free access to the SRA database, we have taken this opportunity to improve the experience of using and accessing these data. The new web-based user interface was built using the latest cloud-based technologies and genomic data standards. Central to this effort were the many conversations we had with researchers about how they search and interact with data of this type. Their feedback was the basis of our development plan, which drew on our own experience in developing web-based sequence data analysis solutions as well as Google’s big data expertise.

Searching and Browsing

Our main goal in developing the new interface was to vastly enhance the way you find data of interest, understand sample-to-project associations, and download files for subsequent analysis in your tool of choice.

The most significant difference you will notice is the new web-based searching and browsing interface. The new search tool allows you to simultaneously look across multiple data annotations and keywords for objects of interest that are embedded in the SRA database. Each search returns a ranked list of results with relevant metadata for easy follow-on browsing.

We have developed a number of features to simplify how you can scan results and quickly narrow in on relevant data. We are particularly excited about the links to published data. PubMed references now permit users to link directly to journals for descriptions of samples, experiments, studies, or runs as they appeared in the referenced publication.

Once you have identified samples of interest, you can easily download them. In addition to the SRA standard format, we have also made it possible to download these data in the more popular FASTQ format.

For more details on the sra.dnanexus.com functionality and how the website works, please visit the SRA FAQ.

Transforming Data into Real Insights Using DNAnexus

Since the SRA primarily contains raw sequence data, the ability to import them into a platform such as DNAnexus is essential for further analyses. For example, by uploading your results into DNAnexus you can access tools that will map your data to a reference genome so you can better understand data quality, a critical step in determining whether to move forward with the data. DNAnexus also allows you to analyze and visualize these data as a standalone dataset or in conjunction with other data already in the system, using our interactive web-based Genome Browser.

Analyze and Visualize SRA Data for Free

For the next 30 days, you can import SRA data directly into DNAnexus at no cost. If you already have a DNAnexus account, simply log in and import your SRA data. If you are not yet a user of DNAnexus, you can sign up for a free trial account and import your data. Once logged in, you can perform mapping, RNA-seq, ChIP-seq, variant analysis, and data visualization on your SRA data for a total of two years.

Special note for our users from academic institutions… We have just reduced the standard academic pricing by half!