Recovering from AGBT: Exhausted but Encouraged !

It’s hard to believe the whirlwind of the annual Advances in Genome Biology & Technology meeting is already over! The DNAnexus team had a terrific time at the conference, and we want to thank everyone who stopped by our suite and attended our Friday afternoon talk.

#agbt13This year’s meeting had more attendees (not to mention the thickest abstract book) than ever before. In many of the talks and posters, the challenge of data interpretation was front and center. Several scientists mentioned that the data sets they’re comparing and the analyses they’re performing pull together far more data than they’ve ever had to deal with. Indeed, the very first speaker of the meeting, Eric Boerwinkle from the University of Texas, told attendees that the community needs to keep pushing for better informatics and data interpretation tools. It was gratifying to see that so many scientists are making use of large, publicly available databases — ENCODE in particular was cited in several presentations.

The talks we found most interesting were about applications of next-gen sequencing technologies, ranging from clinical sequencing to epigenetics to microbiome studies. Christine Eng from Baylor College of Medicine spoke about whole exome sequencing in the clinic, noting that her team’s pilot project saw a 25% success rate (conservatively estimated) in using this information to diagnose a disease. She also said that clinical genomics will have trouble ramping up without more genetic counselors and geneticists; at the moment, there are just 3.5 such experts per million people in the US. In another talk, Leonid Moroz from the University of Florida captured attendees’ imaginations with a discussion on the biological mechanisms underlying memory persistence. He focused on epigenetic changes in the brain, finding that demethylation of just one strand of DNA seems to precede the formation of long-term memories in model organisms. Finally, the most-discussed talk of the conference came from Kjersti Aagaard at Baylor College of Medicine, who spoke about metagenomics in medicine. She presented data indicating that the placenta is not a sterile environment as previously thought, and that the placental microbiome is most closely related to the oral microbiome. For this technology audience, it was a real treat to see just how much compelling science is happening because of the sequencing tools that have been presented in previous years at AGBT.

It’s clear to us that the focus is rapidly moving from sequencing technologies and toward data interpretation as the real immediate technological challenge in the genomics community. This year, there were a number of companies presenting analysis tools, including Maverix Biomics, Ingenuity Systems, Personalis, and more. In fact, there seemed to be many more of these types of tools on display instead of the usual plethora of next-generation sequencing technologies that people tend to expect from the Marco Island conference. It was a fairly quiet year for instruments — no major sequencing technology headlines came out of the meeting — so it was great to have lots of attention on data interpretation and the tools enabling it.

We hope that we were able to offer conference attendees an optimistic view of the data analysis situation. People who came to our suite had the opportunity to get a guided tour of the new DNAnexus, and we were pleased at how much interest there was in a customizable cloud-based solution for managing and analyzing sequence data. We hosted several demos and have been thrilled to see how many people from the meeting have signed up for beta accounts with the new platform to help tame their own data sets.

agbt dnanexusOn Friday afternoon, our CEO and co-founder Andreas Sundquist gave a plenary presentation to introduce attendees to the new DNAnexus. Andreas’s talk provided a detailed look at the core attributes of the new DNAnexus — its configurabilityextensible toolbox with more than 40 Apps, instant collaboration environment, and security and compliance support. He also noted that users could choose an intuitive drag-and-drop interface or opt for the more hard-core command line to suit their own needs. When asked about data upload speeds and cloud capacity, Andreas said that current ethernet speeds are usually sufficient to upload sequence data in real time as it’s generated, and pointed out that Amazon’s cloud capacity — on which the DNAnexus service runs — currently has the infrastructure to run 1 million whole genome sequences per year.

agbt posterWe were also delighted to meet Franck Rapaport, the lucky winner of a 4-Day AGBT conference registration. Franck, who hails from Memorial Sloan-Kettering Cancer Center in New York City, was part of a team with a really interesting poster comparing differential expression tools for RNA-seq type data analysis.

Though scientists are certainly facing new challenges in data analysis, we think this is a great time for informatics innovation. Services such as the new DNAnexus, combined with great new algorithms and Apps, are helping to pave a path forward for a new era of genomics analysis in which infrastructure, workflow, and interpretation options are as seamless and simple as they should be.

What to Pack for AGBT 2013: Sunblock, Flip-flops, and Data !

agbt 2013Sequencing experts around the world are honing their slide decks, performing their last data analyses, and checking weather forecasts for a small island in Florida. It can only mean one thing: AGBT 2013 is almost upon us!

As a sponsor of this year’s Advances in Genome Biology & Technology conference, we are especially looking forward to our annual pilgrimage to Marco Island for the leading next-gen sequencing meeting. We hope to meet many of you in our suite (lanai #180) for a personalized one-on-one demo of the new DNAnexus, our latest cloud-based solution designed for bioinformaticians working with genomic data.

The new DNAnexus is currently open for beta testing. Sign up for a free account now, upload some sample data before the meeting, and we’ll sit down with you at the conference to show you the new product using your own data. It’s a great opportunity to see how our tool with its features will perform in your lab! If you’re among the first 100 people to use the code AGBT13 when you sign up, we’ll double your storage and analysis capacity during the beta testing period.

We also will have some brief talks and events in our suite, so even if you don’t have a chance to upload data ahead of time, please stop by to learn more about the new platform. We’ll have drinks and snacks as well, so feel free to come by for a friendly visit even if you don’t need a new sequence analysis tool!

Here’s the lineup:

Thursday – Feb 21
10:35am – 11:00am
Command-line Interface: The Greatest Typing Experience Since the Gutenberg Printing Press
Andrew Carroll, Ph.D., Scientist, DNAnexus

5:20pm – 5:45pm
App Building & Workflows: Your Programs + the Cloud = Accelerated Results
Vince Ramey, Ph.D., Scientist, DNAnexus

5:45pm – 6:45pm
Happy Hour – drinks, appetizers & music

Friday – Feb 22
10:35am – 11:00 am
App Building & Workflows: Your Programs + the Cloud = Accelerated Results
Vince Ramey, Ph.D., Scientist, DNAnexus

3:40pm – 4:00pm (At the Islands Ballroom)
DNAnexus Talk
Meet the new DNAnexus: An Extensible Genomics Cloud Platform Built for the Bioinformatician
Andreas Sundquist, Ph.D., CEO & Co-founder, DNAnexus

4:05pm – 4:30pm
Command-line Interface: The Greatest Typing Experience Since the Gutenberg Printing Press
Andrew Carroll, Ph.D., Scientist, DNAnexus

We also want to take this opportunity to announce the winner of our “Free four-day AGBT conference badge” giveaway: Franck Rapaport from Memorial Sloan-Kettering Cancer Center in New York City. Franck works with Ross Levine and Nicholas Socci performing sequence data analysis for acute myeloid leukemia in both clinical and research settings. He is also an author on one of the posters presented at the conference (poster #309: “Comparison of RNA-seq normalization and differential expression analysis methods using SEQC data”), so be sure to check it out and say hi. Congratulations, Franck! We look forward to meeting Franck and all the other AGBT attendees next week and hope to introduce many of you to the new DNAnexus.