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ABI Expands Software Community Program to Address Challenges of Next-Gen Sequencing

About a year after its launch, Applied Biosystems has expanded its Software Community Program to encourage the development of third-party software tools for its Sequencing by Oligonucleotide Ligation and Detection, or SOLiD, next-generation sequencing platform.
ABI promoted the expanded initiative at a two-day “jamboree” at its Foster City, Calif. office in July, in which 40 researchers from 30 academic and commercial entities gathered to discuss data sets, data file formats, and data conversion tools for next-gen sequencing.
ABI’s Michael Hadjisavas, director of commercial development, told BioInform that the program is an important part of the company’s strategy for entering the next-gen sequencing market, where bioinformatics is quickly becoming a bottleneck for some users.
“We want to reach out to the community and invite a dialogue in the area of software because we as a company cannot address all of the software requirements for the data interpretation of the myriad readouts that could be deployed,” he said. “We are looking to adopt a conciliatory posture to work with the community to develop the software tools needed for all those types of readouts.”
ABI launched an early-access program for the SOLiD sequencer earlier this year and plans to launch the system commercially in October. Hadjisavas said that placing useful software in the hands of potential users will be a key driver for the rollout of the product.
“The amount of data that a researcher would have … could be very substantial and overwhelming, and unless there are companion software elements in place, the ability of customers to really enjoy the value of these instruments can offer can be somewhat challenged, and that’s a problem,” he said.
The initiative is an extension of ABI’s Software Community Program, launched last year, which offers customers and third-party software partners free software, formats, file converters and other tools for managing data from its sequencers and other instruments [BioInform 09-08-06].
The program was an obvious departure from the company’s traditional strategy of keeping its file formats under wraps, and the new initiative is a continuation of that new philosophy of openness, Hadjisavas said.
With the initial Software Community Program, “we made the file formats available, and a couple of small tools available for download so people could access those files, but in the past AB has not been as quick to make the file formats open and available as we are here,” he said.
“We see this as a very different type of equipment — [that] next gen [sequencing] will develop so much data that analysis will be one of the bottlenecks.”
Next-Gen Jamboree
Lauren Lum, a spokesperson for ABI, told BioInform via e-mail that participants at the July jamboree included representatives from Baylor College of Medicine, Broad Institute, Cold Spring Harbor Laboratory, Columbia University, Geospiza, the Interdisciplinary Center for Biotechnology, the J. Craig Venter Institute, the Department of Energy’s Joint Genome Institute, the Kiel University Hospital at Christian-Albrechts University, Plant Research International, the University of California San Diego, the University of Delaware, the University of Queensland, and the Wellcome Trust Sanger Institute, as well as a handful of others.
Todd Smith, CEO and founder of Geospiza, attended the first day of the conference, and told BioInform that feedback from participants was quite positive.
”I thought Applied Biosystems did a very nice job of really talking about the details of the system, how it works and how they’re approaching problems,” he said.
Smith said talks centered around the introduction of the SOLiD platform and “the technical details of how it works ... It’s a different approach to base-calling that has redundancy and confirmation built into it. One of the things people find attractive about SOLiD is that it will give them higher data accuracy … There is a self-confirming quality, [with] certain rules to how a base can be called.”
Smith said that every base is sequenced twice in the system “so you can get a natural confirmation. It breaks into these different rules into what creates certain color patterns, and from those rules one can have error detection. And that’s pretty significant.”
In a follow-up e-mail, he told BioInform that “this project and other next-gen applications are going to produce more data than the community has experience with. The amount of data and kinds of information being produced make current ‘standard’ data handling techniques impossible. You cannot simply put 40 million 25-base reads in a folder on a desktop computer and expect to do anything with the data.”
He added that further, “current bioinformatics algorithms are not going to be able to work on the data in reasonable ways because they are not architected to handle such large data sets. So new strategies and applications will be needed to support these systems. These will range from high-performance file systems to software technologies designed specifically for extremely large volumes of scientific data.”
He said that Geospiza sees significant opportunity this area. “We have a great deal of experience working with high-throughput data analysis systems,” he said, adding that the company sees business opportunities resulting for Geospiza products and services.
“As we understand it, companies like Applied Biosystems, Illumina, and Roche have to balance the challenges of delivering software for the primary data delivery aspects of the systems, such as data collection, image analysis and base-calling, with delivering software tools that combine the primary data with other information to do the science that researchers want to do. The companies delivering the data collection platforms can gain great community benefit by opening and simplifying access to the data being produced.”
Hence, Geospiza sees a pathway to invest in new products for its customers. he said.

“We see this as a very different type of equipment — [that] next gen [sequencing] will develop so much data that analysis will be one of the bottlenecks.”

Boston College’s Garbor Marth, who was not at the event but has developed next-gen sequencing tools told BioInform’s sister publication In Sequence that ABI is pretty keen on getting the community involved, especially because of their color-space analysis.” The readouts [of the SOLiD technology] are unusual. And the tools, although we think that they can be modified fairly easily to color-space reads, have to be done,” he said.
He added, “But I think their main motivation [for promoting this initiative] is that they [ABI] know there are a lot of good bioinformaticians out there, and they know that they will be competitive with their informaticians.”
Marth said ABI’s informatics expertise tends to be tied to the instrument, while third parties are more likely to develop downstream analytical tools.
“They focus on those aspects of the machine that have to do with proprietary technology, they focus on image processing, typically, and do a good job at that. Things that are close to the machine they typically do themselves,” he said.
“Once it comes to the domain of the quantity, such as the bases, the base quality values, and so on, when you actually compose a sequence trace from the images, at that point, there is a lot of expertise out there that is not specific, necessarily, to their [ABI’s SOLiD] machine,” Marth said.
Whether that “expertise” was present at the jamboree or not, this type of next-gen sequencing dialogue for software developers is precedent-setting, according to Michael Rhodes, applications manager at ABI.
When colleague Hadjisavas was asked about further meetings, he said, “We think we are keeping our options open, but internally we are discussing having a similar type of event at least on an annual basis.”
The company said that it expects the program to advance application development in research areas such as whole-genome sequencing, chromatin immunoprecipitation, microbial sequencing, gene expression, microRNA discovery and detection of rare genetic variants.
Further information on the initiative is available here
— Julia Karow, editor of In Sequence, contributed to this article

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