Applied Biosystems's software development community has established two formal agreements intended to help scientists address next-generation sequencing bioinformatics challenges
Geospiza and GenomeQuest will develop bioinformatics tools that are expected to advance data analysis and management for life scientists utilising data generated by the Solid system, described as the life science industry's highest throughput system for next-generation sequencing.
Geospiza, a provider of fully integrated data management infrastructure solutions for genetic analysis, has signed an agreement expanding its relationship with Applied Biosystems to include next-generation sequencing instrumentation.
Applied Biosystems also formed an agreement with GenomeQuest, which provides an integrated sequence information platform allowing researchers to search and analyse genomic sequence data as a hosted service or as a hardware appliance.
The Solid system is capable of generating sequence data that exceeds 4gigabases (GB), which is more than the approximately three billion bases of the human genome.
The solutions offered by Geospiza and GenomeQuest are expected to help address managing this vast amount of genomic data by providing complementary services, including the IT infrastructure to manage the data, as well as the ability to process the data and align it to a reference sequence.
Applied Biosystems expects that its relationships with Geospiza and GenomeQuest will help drive innovation and speed the development of new tools that will enable researchers to find answers faster and more cost-effectively, thereby helping scientists to realise the full potential of next-generation genomic analysis.
Applied Biosystems has shared file formats, sample data sets and analysis pipeline information with Geospiza and GenomeQuest so that they may configure their products, services and capabilities to address customer challenges associated with generating, analysing and managing research data in key applications for the Solid system.
As part of its participation in Applied Biosystems's software development community, Geospiza developed a software system designed to automate sequencing workflows for capillary electrophoresis (CE) instrumentation.
Applied Biosystems's agreement with Geospiza is expected to extend Geospiza's Finch Suite software and its knowledge of 3130 series genetic analysers and 3730 series DNA analysers to Solid system-specific IT infrastructure support, software and tools with its new FinchLab Next Gen Edition product.
As life scientists expand their research capabilities by using the solid system, Geospiza expects to support these customers by processing both CE and Solid data through a single data processing pipeline, which will enable them to integrate and visualise the two data sets from both technologies.
This integrated solution is expected to enable researchers to utilise both the Solid system for discovery applications and CE systems for validation, connecting the research continuum.
This development is expected to benefit many organisations, including the University of Washington which is a user of the FinchLab software and an early adopter of the Solid system.
Scientists in the university's high throughput sequencing laboratory recognise the challenges associated with the vast amount of data being generated from next-generation sequencing systems.
"As a Geospiza FinchLab customer and a laboratory that has acquired a Solid system sequencer, any collaborative effort between Geospiza and Applied Biosystems to help laboratory directors meet the coming next-generation sequencer data management and analytics challenges would be a welcome relationship for the research community," said Michael Dorschner, director of the laboratory.
Geospiza plans to deepen the integration between its FinchLab Next Gen Edition software product and the Solid system to provide a comprehensive solution that includes data management systems to define experiments, and the ability to track data through production, and process genetic analysis platforms in a scaleable high capacity storage system.
"By expanding our long-standing relationship with Applied Biosystems, we are answering the call for bioinformatics solutions to help accelerate research on next-generation genomics analysis platforms," said Rob Arnold, president, Geospiza.
"Laboratory directors and end users should benefit equally from the more natural workflow as they switch between the software and the instrument for data generation, management and analysis.
"Our platform is specifically designed to scale with the lab as their needs grow".
GenomeQuest to provide data alignment and analysis solutions.
GenomeQuest has an integrated solution based on its database of reference sequences that is expected to transform raw sequence data from the Solid system into information that will reveal insights resulting from the sequencing run.
GenomeQuest's solution is also expected to enable Solid system customers to seek assistance with data alignment and analysis, including single nucleotide polymorphism (SNP) detection.
In addition to increasing productivity, GenomeQuest's solution enables scalability as customers accelerate their use of next-generation genomic analysis platforms.
"Our relationship with Applied Biosystems should ensure that Solid system customers will have a robust informatics platform that supports their needs, now and in the future," said Ron Ranauro, CEO of GenomeQuest.
"The research community has clearly indicated that they need more than algorithms to adequately handle the immense volume of data generated by next-generation platforms".
Applied Biosystems's software development community helps drive innovation in next-generation sequencing.
Through this, Applied Biosystems says it is the first manufacturer of next-generation instrument systems to make software development tools widely available to the bioinformatics community.
This community supports life scientists and independent software vendors in the development and potential commercialisation of bioinformatics applications for next-generation genomic analysis platforms.
Applied Biosystems established the software development community in 2006 to encourage innovation in life science research software applications and to create a collaborative environment that provides a widely accessible pool of resources that will enable customers and independent service providers to develop and bring to market innovative new applications that allow the research community to find more answers, faster and more cost-effectively.
The software development community represents Applied Biosystems's commitment to fostering innovation in life science technologies for industry leading genetic analysers, and real-time PCR sequence detection systems.
The company expanded the community in 2007 to directly address the industry wide challenges associated with analysing and managing the vast amounts of research data generated by ultra high throughput technology.
Since its inception, hundreds of researchers, independent software vendors, Solid system customers and bioinformatics service providers have visited the software development community site to investigate file formats, and download sample data sets and data analysis tools that have the potential to help them develop informatics tools for expanding the utility of the large volumes of genomic information generated by the Solid system.
"Through our software development community, Applied Biosystems is providing life scientists and independent software developers the tools and resources necessary to develop software applications that help researchers manage the vast amount of data generated by the Solid system," said Roger Canales, senior manager of Solid software development community.
"Geospiza and GenomeQuest are leading the industry by providing researchers the ability to consistently and cost-effectively produce, analyse and deliver meaningful scientific results from their next-generation genomic analysis projects."
