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Illumina Opens Up BaseSpace Developer Portal, API to Encourage App Development


Illumina has opened up its BaseSpace developer portal to members of the bioinformatics community, providing them with tools to develop apps that can run on the company’s cloud infrastructure.

This is the same portal that the company provided for commercial bioinformatics developers earlier this year. Illumina has now expanded access to non-commercial developers as well.

The portal, which is currently available in beta, provides a free application programming interface as well as Python- and Java-based software development kits. Registered users can develop bioinformatics apps that run on web, mobile, or desktop devices, and use the API to move data between BaseSpace and apps hosted on developer sites.

Later, developers will also have the option of hosting their apps in BaseSpace directly as “Native Apps.” To take advantage of this capability, developers would be required to provide their apps as Amazon Machine Images.

The “Native Apps” capability isn’t available at the moment but Illumina expects to launch it early next year, Jordan Stockton, Illumina's associate director of product marketing, told BioInform this week.

He also said that since the company opened its portal to the community less than a month ago, around 100 developers have signed on to build apps using the API and SDK.

On the commercial side, 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 all plan to develop apps for BaseSpace (BI 4/27/2011 and BI 8/24/2012).

Some of the commercial developers will demonstrate their applications at the American Society of Human Genetics conference in San Francisco next week, although Stockton declined to state which companies would do so.

Illumina will also officially open the BaseSpace app store at the ASHG conference next week, the company said.

With the release of its developer portal and API, Illumina makes good on promises it made earlier this year when it announced a pricing structure for genomic data storage and processing in BaseSpace (BI 7/27/2012).

The company first launched BaseSpace over a year ago to improve data management for customers of its genomic analysis platforms beginning with its MiSeq personal sequencer system.

At the time, Alex Dickinson, Illumina's senior vice president, told BioInform that the company viewed BaseSpace as an "extension" of its product portfolio and that being able to "roll [BaseSpace] into our overall product offering just makes sense for us (BI 10/14/2011).”

Specifically, the addition of the portal addresses data access issues currently faced by informatics developers who often have trouble “prototyping [their programs] because data was either inconsistent or hard to get at,” Stockton told BioInform this week.

With the portal, not only can developers build apps using the API and SDK, but they also have access to data in BaseSpace that they can use to test-drive their apps as well as share those tools with other users, he said.

“It’s an interesting tool to build a great community of app developers,” he said. “It’s something we are really excited about because it transcends the sphere of people who normally we’ve thought of as commercial bioinformatics developers to anyone who wants to get involved and solve [a bioinformatics] problem.”

Furthermore, most users require a “smorgasbord” of tools to meet varying analysis needs, he pointed out.

“We think a combination of open source tools and commercial tools reflect the use needs and user behaviors today” and “this apps model is really well suited to that,” he said.

He noted that Illumina will provide the same level of support to both commercial and open source app developers.

“We are trying to be as inclusive as possible,” he said. “We’ve provided the same advantage to the academic developer as the commercial developer.”

There is no charge associated with accessing the developer portal or using the BaseSpace API, however as is the case with commercial vendors, developers can choose to charge a fee for the use of their apps, Stockton said.