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Illumina Expands BaseSpace to Include New Category of Internally Developed Research Apps


NEWYORK (GenomeWeb) – Illumina has launched a new category of applications for its BaseSpace cloud infrastructure called BaseSpace Labs, through which it intends to make applications developed internally by Illumina employees available to the community early on in the development process.

Essentially, BaseSpace Labs is a program that gives researchers "access to apps that are sort of newer and earlier in their maturity," Jordan Stockton, Illumina's marketing director for enterprise informatics, told BioInform. It's an opportunity for developers inside Illumina to get their apps out and get feedback from the community early on in the development, and also affords an opportunity for researchers to get involved in and contribute to early phase development projects, he said.

Developers within the company follow the same process used by third-party companies when it comes to building apps for BaseSpace. When they submit apps for publication, those apps are reviewed by a committee, and if approved are made available on the cloud. App usage will be monitored as well as any feedback provided. In time, Raymond Tecotzky, market manager for Illumina's informatics ecosystem told BioInform, apps that do well could be made part of BaseSpace's Core Apps, a group of applications for analyzing whole-genome or exome sequence, tumor-normal data, transcript assembly, expression profiling, and variant analysis — the list includes tools like TopHat, Cufflinks, and BWA.

Tecotzky said that Illumina released the first of what will be a series of applications planned for BaseSpace Labs last weekend. That new app, which is called FastQC, lets users check the quality of their raw sequence data prior to analyzing it. The company plans to release a second app for this category in the next few days called the Velvet de novo assembler app, Tecotzky said. There are other apps planned for release in this series, but the company is not disclosing details about what those will be at this time.

Meanwhile, Illumina said that the list of third parties developing applications for BaseSpace is growing. Some of the more recent additions to the commercial third-party developer ecosystem include Advaita Bioinformatics, which announced this summer that it had added iPathwayGuide — the company's gene-expression pathway analysis solution — to BaseSpace. Also, last month Advanced Biological Laboratories said that it had added DeepChek-HIV — a solution for analyzing deep sequencing data from HIV — to the BaseSpace Apps store.

The company is also seeing some interest in its native apps development program, Tecotzky said. Illumina launched the program last year hoping to encourage participation from members of the broader life science community including bioinformatics professionals, academics, and graduate students. Through the program it offers tools that these individuals can use to develop and run apps on its infrastructure and allows the developers to set their own pricing, operating under the same financial model that the company uses with its commercial app developers.

So far, Illumina has launched one app on BaseSpace under this program, Tecotzky said. In May, it released the Spades genome assembler, which was developed by researchers from St. Petersburg Academic University in Russia and the University of California, San Diego. It hopes to drum up more interest and participation in the program through a series of developer conferences planned for this year in Bangalore and San Francisco, Tecotzky said. At these meetings, it will provide training for participants to introduce them to the development process and guide them through the creation of a sample application, he said.

There's also growing interest from customers, with the number of users hooking up their sequencers to BaseSpace for analysis increasing "very rapidly," according to Stockton. He declined to disclose specific numbers, but he said that the company has noticed some interesting trends in terms of the research areas where the apps are used. For example, "we are seeing a lot of people in both the RNA sequencing space and the bacterial assembly and characterization space are using it pretty enthusiastically," he said.

Meanwhile, BaseSpace Onsite is also carving out a niche for itself in the market, according to Tecotzky. BaseSpace Onsite is the locally installable version of BaseSpace cloud that provides a subset of the capabilities available on the larger infrastructure. Illumina launched the system last year to provide an on-premises analysis option for customers of the company's sequencers, who for security and policy restrictions or limited bandwidth are unable to use the cloud to analyze their data. Users who deploy the system have access to the BaseSpace core apps as well as archival storage and sharing capabilities.

BaseSpace Onsite costs $60,000 for the first year — for the entire system including apps and storage — and an additional $15,000 per year after that to cover software licensing fees, Tecotzky said. That yearly fee enables the customer to get "all the latest and greatest software updates and upgrades to keep their [system] current." Currently, it's optimized to work with Illumina's NextSeq 500 sequencer only, but the company plans to link it to other sequencing platforms at some point in the future — though Stockton declined to disclose a timeline for when this will happen. The company also plans to make third-party commercial applications available to users of BaseSpace Onsite starting possibly next year.

Currently, there are about 40 apps available on BaseSpace. Illumina plans to have a total of 50 apps up and running on the infrastructure by the end of the year, Tecotzky said. Other long-term plans include providing support for higher throughput and automation, Stockton added, as well as new interfaces and features "that make sequencing data and analyzing data and processing data more of a hands-free, automated, simpler, hopefully less error-prone event."