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

Publication Watch: In Early 2013, Nice Flow of New Papers from DNAnexus Users

It’s been awhile since we checked in on publications using DNAnexus, so we headed over to PubMed to provide an update. With so many great new papers coming out — more than 10 just in the past few months — we wanted to take the opportunity to look at a few of them and see how they’re making use of DNAnexus.

 

In the Journal of Medical Genetics, scientists from Hebrew University Medical Center and colleagues at other organizations published a paper entitled “Agenesis of corpus callosum and optic nerve hypoplasia due to mutations in SLC25A1 encoding the mitochondrial citrate transporter” (published online February 2013). Lead author Simon Edvardson et al. report on the first known patient with agenesis of corpus callosum caused by a mitochondrial citrate carrier deficiency. The team performed exome sequencing and used DNAnexus for read alignment and variant calling. Two pathogenic variants were found in a gene responsible for the mitochondrial citrate transporter, and functional studies in yeast validated the findings by displaying the same biomolecular effects of the mutated proteins.

 

In the January issue of Antimicrobial Agents and Chemotherapy, a journal from the American Society for Microbiology, a research team from Georgetown University Medical Center and the Institute of Microbiology in Beijing released a paper called “Azole Susceptibility and Transcriptome Profiling in Candida albicans Mitochondrial Electron Transport Chain Complex I Mutants.” In the study, the authors looked at how mitochondrial changes in yeast alter susceptibility to certain azole compounds commonly used as antifungal agents. As part of the effort, the team used RNA-seq to generate a transcriptome profile of two mutants known to increase susceptibility to azoles. Data analysis was conducted through DNAnexus. The scientists found that both mutants showed downregulation of transporter genes that encode efflux proteins, a mechanism thought to be linked to the cell energy required for azole susceptibility.

 

In the journal Human Mutation, a paper entitled “A Deletion Mutation in TMEM38B Associated with Autosomal Recessive Osteogenesis Imperfecta” (published online in January) comes from a research group at Ben Gurion University and the Soroka Medical Center, both in Israel. The scientists studied patients with autosomal recessive osteogenesis imperfecta, or brittle bone disease, which could not be explained by any previously known mutation. The team used genome-wide linkage analysis and whole exome sequencing to identify a single mutation common to all three patients: a homozygous deletion mutation of an exon in TMEM38B. Sequence read alignment, variant calling, and annotation were done with DNAnexus tools.

 

Finally, a paper published early online in February in the journal Case Reports in Genetics called “Targeted Next-generation Re-sequencing of F5 gene Identifies Novel Multiple Variants Pattern in Severe Hereditary Factor V Deficiency“ comes from a group that used DNAnexus for data quality, exome coverage, and exome-wide SNP/indel analysis. The authors — scientists from Pennsylvania State University and MS Hershey Medical Center — present a study of four people with severe factor V deficiency in which they used next-gen sequencing to study the factor V gene locus. They found five coding mutations and 75 noncoding variants, including three missense mutations previously associated with other factor V phenotypes.

On DNA Day, We’re Thinking About (What Else?) Data

Today is DNA Day! This year it’s an especially big deal as we’re honoring the 60th anniversary of Watson and Crick’s famous discovery of the double-helix structure of DNA as well as the 10th anniversary of the completion of the Human Genome Project.

DNAnexusBack when Watson and Crick were poring over Rosalind Franklin’s DNA radiograph, they never could have imagined the data that would ultimately be generated by scientists reading the sequence of those DNA molecules. Indeed, even 40 years later at the start of the HGP, the data requirements for processing genome sequence would have been staggering to consider.

Check out this handy guide from the National Human Genome Research Institute presenting statistics from the earliest HGP days to today. In 1990, GenBank contained about 49 megabases of sequence; today, that has soared to some 150 terabases. The computational power needed to tackle this amount of genomic data didn’t even exist when the HGP got underway. Consider what kind of computer you were using in 1990: for us, that brings back fond memories of the Apple IIe, mainframes, and the earliest days of Internet (brought to us by Prodigy).

A couple of decades later, we have a far better appreciation for the elastic compute needs for genomic studies. Not only do scientists’ data needs spike and dip depending on where they are in a given experiment, but we all know that the amount of genome data being produced globally will continue to skyrocket. That’s why cloud computing has become such a popular option for sequence data analysis, storage, and management — it’s a simple way for researchers who don’t have massive in-house compute resources to go about their science without having to spend time thinking about IT.

So on DNA Day, we honor those pioneers who launched their unprecedented studies with a leap of faith: that the compute power they needed would somehow materialize in the nick of time. Fortunately, for all of us, that was a gamble that paid off!