Skip to main content
Premium Trial:

Request an Annual Quote

Illumina Launches Native Apps Program to Broaden BaseSpace's Reach

Premium

Making good on a promise it made about a year ago (BI 11/2/2012), this week Illumina launched a native application development program for BaseSpace that will offer tools that members of the general bioinformatics community can use to develop and run apps on its cloud infrastructure.

Initially, when Illumina launched BaseSpace on Amazon Web Services in April 2012, it focused on populating the platform with a mix of internally developed apps and apps developed by commercial partners such as Diagnomics, GenoLogics Life Sciences, Genomatix, Golden Helix, Ingenuity Systems, Knome, Omicia, Spiral Genetics, Omixon, Real Time Genomics, Station X, Integromics, Biomax Informatics, Biomatters, and Strand Life Sciences (BI 8/24/2012).

With the so-called Illumina native app engine program — which was launched during a developer meeting at the American Society of Human Genetics conference in Boston this week — Illumina is hoping to encourage participation from members of the broader life science community, including bioinformatics professionals, academics, and graduate students, Alex Dickinson, the company's senior vice president for cloud genomics, told BioInform.

The native apps program offers an "inviting environment" for these folks, he said, that includes software development kits written in the Java, Python, and Ruby programming languages. Interested researchers also have tools to create a user interface through which data can be uploaded and extracted from the cloud, and are provided with an infrastructure for hosting and running the apps.

To users, these apps will look exactly the same as those developed by Illumina's commercial partners, Dickinson said. They'll also be priced using the financial arrangement that Illumina operates with those vendors. Under the model, the developers themselves determine the apps' price points and receive 70 percent of revenues while Illumina takes 30 percent. Alternatively, developers can choose to run the apps at cost, meaning that customers will only have to pay to run their analyses on Amazon and the developers do not make any profits — an option that Illumina expects will likely appeal to academic developers.

Illumina launched BaseSpace about two years ago initially to provide free data-management, archiving, analysis, sharing, and storage tools for MiSeq users with plans to eventually integrate the cloud with its HiSeq sequencers as well (BI 10/14/2011).

Anticipating a bump in demand for analysis and storage space when the HiSeq was integrated with BaseSpace, last year Illumina decided to put a pricing structure in place that would limit the amount of free space for storing and processing genomic data in the cloud. Under the scheme, users would get one terabyte of free cloud space for storing and processing data and would then be able to purchase additional storage in increments of one terabyte or 10 terabytes — one terabyte would cost $250 per month or $2,000 upfront for a full year, while 10 terabytes would be $1,500 per month or an annual upfront fee of $12,000 (BI 7/27/2012).

Overall, the company is "pretty thrilled about how BaseSpace has been adopted" since its launch, Dickinson said. Currently, it has over 10,000 registered users analyzing and sharing data, with about 200 new participants joining the community each week. There are 20 apps available for use in BaseSpace, about half of which Illumina developed internally and the other half come from third-party development partners. Dickinson expects the number of apps to grow by about 50 percent by the end of the year.

"Illumina's interested in making sequencing a more valuable thing," and BaseSpace is its attempt to help researchers move from generating data to extracting knowledge from data, he said. "We want to create this environment and incent people … to put new and interesting applications up there that are going to help users actually extract knowledge out of the data."

Allowing developers to set their own pricing appears to have been a sound decision for the company but time will tell. "So far it's been smooth sailing, but we are in the very early stages of commercialization," Dickinson said.

Most of the companies that have developed apps for BaseSpace have chosen to make them free for users but, he said, it's possible that in the future some firms might decide to offer both free and priced versions of their apps, with the latter providing more features than the former. "I think that’s still shaking out, but it's too early to tell," he said.

Filed under

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.