Looking Back at SFAF in Santa Fe

Finishing in the FutureWe recently attended the Sequencing, Finishing, and Analysis in the Future (SFAF) meeting, hosted by the Los Alamos National Laboratory from May 29-31 in Santa Fe. DNAnexus was a sponsor of this year’s event, which included a star-studded roster of scientific speakers.

Among the great keynote presenters were Baylor’s Richard Gibbs; Mark Adams from the Venter Institute; and the NCBI’s Deanna Church.

As the conference name suggests, data analysis was a pillar of the event. There were several presentations on various hardware and software options, including data management and cloud computing. Other areas of interest included genome annotation pipelines and analytical tools for comparative genomics, structural variation, and more.

There were also a number of talks and posters centered on de novo bacterial and human genome sequence assembly methods, as well as metagenomic studies.

Andrey Kislyuk, one of our Senior Software Engineers, presented on deploying genomic applications in the cloud on DNAnexus. Anton Korobeynikov from the Algorithmic Biology Laboratory at the St. Petersburg Academic University, also presented on the improved SPAdes [1] , a new assembly tool (published in 2012) that has been ported as an app into the DNAnexus platform and is now available to all DNAnexus users.

SPAdes, which was recently recognized as a top performing assembler in the GAGE-B Evaluation, was designed specifically for single-cell genomics. Genome sequences from single cells have their own computational challenges, including lack of uniformity in read coverage and elevated numbers of chimeric reads and sequencing errors. Assemblers for next-gen sequencing are often confused by this data, which may have 100 times more coverage of erroneous segments than correct segments. SPAdes generates single-cell assemblies, providing information about genomes of bacteria that can’t be cultured that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is intended for both standard isolates and single-cell bacteria assemblies.

You can try SPAdes and a number of other apps today by signing up for a free DNAnexus beta account.

Interested in developing your own app? DNAnexus is currently accepting new members for our developer program. If interested, please contact us at developers@dnanexus.com to enroll.

Our new developer portal provides lots of information including FAQs, quick start guides, sample code, and other technical resources.

[1]  Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. Journal of Computational Biology. May 2012, 19(5): 455-477. doi:10.1089/cmb.2012.0021.

Just Launched: The DNAnexus Developer Program

Join a dynamic app incubator community!

Software Development KitCalling all bioinformaticians, computational scientists and hackers! DNAnexus, a company leveraging cloud computing to facilitate the analysis of extremely large biological data sets, has kicked off an app developer program and is looking to add novel genomics tools for users of our new platform.

Genomic data is the next frontier in truly challenging, Big Data problems. Our platform is designed to help scientists collaborate and analyze DNA data within a secure, web-based environment. Users will be able to upload or build workflows and project pipelines, choosing from their own tools, DNAnexus-provided apps, and now apps contributed by external developers like you.

Why should you care?

Uploading your app to the DNAnexus platform offers lots of advantages:

  • The DNAnexus platform is the most flexible and configurable API-based infrastructure for enabling genomic data analysis and data sharing.
  • The DNAnexus platform accepts DNA data from any sequencing instrument, so you can write for multiple sequencers and gain users among a much broader audience than a vendor-specific environment.
  • Join early and incur no out-of-pocket expenses for developing and testing your app. Receive a $1,000 credit toward cloud storage and compute resources.
  • Get recognition! We’ll be profiling our best-contributed apps and the genius developers behind them as we roll out the platform.
  • Easily showcase your app and its functionality on behemoth data sets.
  • Working with DNAnexus is easy and we are more than happy to provide free technical support while you are developing your app.
  • DNAnexus is building in monetization opportunities, so as the platform comes out of beta your app can create a flow of income.

Join Today!genomics hackers

Interested in learning more? Email developers@dnanexus.com with questions. Send the following information to join the program:

1. Your name and institution
2. Briefly explain the problem you aim to solve
3. Describe the genomics tool you plan to build

Join Us at Bio-IT World for a Personalized Demo and Chance to Win an iPad Mini!

Next week kicks off the annual Bio-IT World Conference & Expo, one of the best conferences dedicated to bioinformaticians and computational biologists. We look forward to it every year for the opportunity to rub elbows with die-hard developers, IT powerhouses, and the truly remarkable scientists who are just as comfortable working with lines of code as others are with lines of cells. Last year the meeting had more than 2,500 attendees from all over the world; it’s a can’t-miss venue for people who work hard to make sure the computational side of biology functions properly.

In that spirit, we hope to meet many of you at our booth (#311) for a personalized demo of the new DNAnexus, our cloud-based genomics platform. For the bioinformatics professional, the new DNAnexus eliminates up-front commitment to expensive hardware and maintenance. And since DNAnexus leverages Amazon Web Services for scalable and cost-effective data storage and computing, a research lab can access these resources, as there is need. The new DNAnexus is now in beta and you can request access for a free account today.IPad Mini Giveaway

To sweeten your personalized test drive of the new DNAnexus platform at Bio-IT World, we are giving away an iPad Mini! Here’s how to enter:

1. Sign up for a beta account
2. Upload your data so you can test-drive our system
3. Visit DNAnexus in booth #311 for a chance to win

DNAnexus scientists will be on hand to offer a custom data analysis and answer any questions you may have. This is a perfect opportunity to see how our new platform will perform in your lab! Even if you don’t have time to upload your data ahead of time, please stop by to learn more about the new platform and shoot the bioinformatics breeze.

Plus, join us in our booth for daily 10-minute mini-sessions during meeting breaks. We’ll be spotlighting a few new DNAnexus features, including compliance, collaboration and app building.

Wednesday – April 10th

10:00 am Instant Collaboration:
Compliance Meets Collaboration: Together at Last
Vince Ramey, Ph.D., Scientist, DNAnexus
3:30 pm App Building:
Build an App & Share With Your Team in 10 Minutes
Andrey Kislyuk, Ph.D., Sr. Engineer, DNAnexus

Thursday – April 11th

10:30 am App Building:
Build an App & Share With Your Team in 10 Minutes
Andrey Kislyuk, Ph.D., Sr. Engineer, DNAnexus
1:30 pm Instant Collaboration:
Compliance Meets Collaboration: Together at Last
Vince Ramey, Ph.D., Scientist, DNAnexus