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Ag-bio Firm Ceres Launches Beta to Test Cloud Version of Internally Built Genome Browser

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NEW YORK (GenomeWeb) – Agriculture biotechnology firm Ceres is looking for testers for a cloud-based version of Persephone, an internally developed genome browser for exploring various kinds of genomic data, as part of a beta that the company launched this week.

Participants in the beta project will have access to the full capabilities of a pre-release version of Persephone CloudService — which runs on Amazon Web Services — for 30 days and will provide feedback that will help shape the ongoing development of the software-as-a-service, Ceres said. The company plans to launch the full version of the solution in January 2015.

"The bioinformatics market is experiencing rapid growth, but lacks common data formats and integrated solutions to control data overload," Tim Swaller, Ceres' vice president of Genomics Technologies, said in a statement. "We believe the Persephone viewer can provide a common, standardized way to visualize data across the numerous analysis pipelines and software solutions currently available."

Ceres already sells licenses to a client-server install version of Persephone that's being used in multiple life science companies, and the company uses it internally for various purposes such as intellectual property management, biotechnology research and development, and marker-assisted breeding.

Persephone lets users integrate and explore data generated internally and from public resources, and it includes Ceres' own custom genome annotations. The software is designed to display data such as genetic maps, scaffolds, physical maps, gene models, synteny, QTLs, SNPs, RNA-Seq, and SNP chip, among others. Users can explore information in the browser by trait or by genotype, for example. Persephone can also be used for studies in plants, humans, animals, microbes, and more.

The features in the software are the result of collaborations between Ceres software engineers, scientists, and bioinformaticians, Swaller told BioInform. Ceres' internal research and development efforts rely heavily on genomics, he said, and the company has pipelines for gene annotation, gene expression, DNA sequencing, and more.

But all that data needed to be consolidated and presented to the company's researchers and scientists in an easy-to-use format. And so Persephone was born about 14 years ago. Over the years, the solution has been honed and improved based on feedback from users about how these datasets should be manipulated and integrated, Swaller said. The result is a convenient-to-use, high-performance solution that lets users integrate and move "seamlessly" between datasets. It believes these features set the software apart from existing browsers.

So far, Ceres has licensed its local version of Persephone primarily to large life sciences and biosciences companies, Swaller said. But with the cloud version it hopes to cater more to individual users in academia and other settings who want to use Persephone but may not have the resources or the infrastructure in place to install and run it locally. The two versions of the system are essentially the same, Swaller said. The only difference is in the types of data.

People who license the local version typically use it to view their own data, he said. However users of the cloud version will have access to publically available data from resources such as GenBank, Gramene, the 1000 Genomes Project, and so on, annotated with Ceres' internal annotation pipelines. These datasets will be stored in Amazon Web Services. Cloud users will also be able incorporate and integrate their own data into the system but the data will be stored locally on their infrastructure so there is no security risk, he said.

Pricing for the server-client installation of the software is negotiable. Ceres currently offers floating and named user licensing options; maintenance, development, and support plans; and a custom development option. When the cloud version of the solution comes online, Ceres plans to have two options: Persephone CloudService, where, for a monthly fee, users will be able to explore public sources; and Persephone Cloud-Plus, where users will have the option to incorporate their own data into the system. The company is still mulling pricing for the cloud version of Persephone and intends to seek feedback from beta testers on this point.

It is also contemplating offering additional informatics services — additional storage for example — around its SaaS offering further down the road, Swaller said. For now, however, Ceres' emphasis is on developing and marketing Persephone in the cloud, he said.

Founded in 2006, Ceres primarily sells seeds for crops that are used to produce renewable transportation fuels, electricity, and bio-based products. The company also licenses its genetics technology, software, and biotech traits to other organizations.

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