Ceres, Inc., an agricultural biotechnology and seed company, announced that the company has licensed its Persephone genome visualization application to Bayer CropScience. The multi-year software license and collaboration agreement provides a non-exclusive license to Bayer as well as professional services including support, customizations and maintenance. Bayer is the second multi-national life sciences company to license Persephone as its primary genome browser.
Originally developed for in-house use by Ceres, Persephone allows researchers to rapidly zoom in and out of massive amounts of genetic data, from a chromosome level to a single building block of DNA. On top of this data, users can layer and cross reference related information in much the same way geographic mapping services allow users to add weather information or business locations to a geographic map.
"We are proud to have Bayer select Persephone as its primary genome browser for its in-house R&D, and we look forward to working with Bayer for many years to come," said Richard Hamilton, president and CEO of Ceres. "The explosion of low cost full genome DNA sequencing, from plant science to biomedical research, is creating incredibly large data sets that are rich sources of information if mined effectively. Persephone provides us with a significant near-term opportunity to leverage our expertise in bioinformatics and genetic analysis, while accelerating our own internal research and development work," Hamilton said.
Jakob de Vlieg, Ph.D., head of the computational life sciences group at Bayer CropScience said, "Our company will benefit from implementing this integrated solution, as this platform is allowing interactive querying and integrated visualization of various omics data. The Persephone genome browser impressed both our geneticists and bioinformaticians with its performance and user friendly interface. Persephone will allow them to make decisions on experimental approaches."
Tim Swaller, Ceres' vice president of genomics technologies, noted that speed is taken for granted across most software markets, but the genetics market has struggled with massive datasets generated by DNA sequencing and genetic testing. For instance, a typical genome contains multiple terabytes of data. Plant genomes, which can be larger than the human genome, have been some of the most challenging.
To help solve the speed problem, and expand the way researchers can explore and mine genetic data, Persephone software engineers have developed a number of proprietary data-compression methods and other optimizations. "The speed itself changes the way researchers can use their data. It encourages more exploratory research and better utilization of genetic data," said Swaller. Ceres has used Persephone in its marker-assisted breeding and biotech trait pipelines to speed the development of elite parental breeding lines and improved sorghum hybrids for Brazil.
Swaller said that Persephone can be deployed across a number of life science technology platforms that utilize genetic data. Ceres currently offers Persephone as a client-server installation and is developing a Software as a Service (SaaS) model that is intended to provide individual researchers with an online tool to visualize and compare genetic information stored in public databases. The company has targeted the deployment of a cloud-based beta version of Persephone by the end of this year.
"We believe there is a large number of individual researchers currently that could benefit from the Persephone interface," Swaller said. He noted that Ceres is also exploring opportunities for the software outside of the plant sciences.