Posted by
Nathan Lillegard on May 14, 2010 |
Corvallis and Eugene, Oregon
CenterSpace Software, a leading provider of enterprise class numerical component libraries for the .NET platform, and Floragenex, an innovative genomic research services company, today announced that they have teamed up to build a genomics data analysis pipeline in the cloud.
Rapid growth of the research services business at Floragenex requires expansion of computing resources beyond the company’s current infrastructure. CenterSpace has deep knowledge of high-powered analytical software and experience developing applications utilizing the cloud computing power of Amazon Web Services. Together, the two companies are working to build a cloud-computing infrastructure to improve ease of use, lower costs, and accelerate data throughput for Floragenex.
“The new system retrieves genetic sequence data from the sequencing facility of choice, places it into storage in the cloud and runs analyses based on the particular needs of the project. The Floragenex end user can login to a web page to select their data, choose their parameters and run their analysis. The work can be done on Amazon EC2 computers and results are archived on Amazon S3 for easy retrieval. The costs are small and the benefits large,” says Trevor Misfeldt, CEO of CenterSpace Software.
“The massive volume of data that genome sequencers produce has required us to look for creative ways to scale our business. Working with CenterSpace allows us to lay the foundation for continued growth without making capital investments in IT hardware,” says Nathan Lillegard, CEO of Floragenex. “The bioinformatics work we do for our customers is particularly well suited to cloud computing, with large sets of data requiring intensive but discreet data processing. Building a cloud infrastructure now will allow us to grow our business and expand our service offerings more responsively.”
About CenterSpace Software
CenterSpace Software is a leading provider of enterprise class numerical component libraries for the .NET platform. Developers worldwide use CenterSpace products to develop .NET financial, engineering, and scientific applications. CenterSpace Software has offices in Corvallis, OR, and can be found on the Internet at http://www.centerspace.net.
About Floragenex
Floragenex is a research services company focused on genomic technology applications in plant sciences. Floragenex enables scientists to do more, expanding their capability using a suite of advanced genomic services matched to the specific resources and goals of each project. Floragenex is based in Eugene, OR, and can be found on the internet at http://www.floragenex.com.
Posted by
Nathan Lillegard on Feb 28, 2010 |
Local colleagues of Floragenex co-founder Dr. Eric Johnson recently published a paper in PLoS Genetics demonstrating the application of RAD technology to population genetics and evolutionary biology questions.
While not a plant sciences publication, the type of project completed by this group has been done by Floragenex for researchers working in a variety of plant species. The RAD system has proven here and in other species that whole genome genotyping via sequencing is a very feasible approach to take with the right genetics and proper planning.
More information can be found on this particular publication at the animal and biomedical focused blog at Biota Sciences, or at Genome Web.
Posted by
Nathan Lillegard on Feb 12, 2010 |
It’s not every week that there are two interesting genomics stories in the local press. I recognize that the world of plant genomics is global. We’re engaged with people from around the globe. It’s exciting to see how the fundamental principles of biology and the shared excitement for the possibilities unlocked by advancing sequencing technology create a global community of researchers so passionate about making a difference. But, it’s worth noting that thinking globally, acting locally is a good strategy.
Beer. A fine topic for a Friday… Oregon is home to a thriving craft and home brewing community. Here we like to make our own, drink the local brew, and wax poetic about the finish and aroma of a pint the way a Napa Valley sommelier describes a cabernet. One of the critical ingredients in beer is hops. Oregon happens to be one of the best places in the world to grow hops – sounds like an opportunity!
It is, and a company called Indie Hops is making a push towards developing new varieties of hops at Oregon State. What does this have to do with genomics? With today’s technologies, the $1 Million they’re investing in research can go a really long ways to advancing the breeding process with genetic markers, diagnostic tests, or even sequencing the Humulus genome. That in turn creates new varieties of hops faster, which gives us better beer; everyone is happy!
The other big news of the week is the publication of the Brachypodium genome. This project, led in part by Tood Mockler and others at the Oregon State Center for Genome Resources and Biocomputing, is a major achievement in the world of grass and cereals research. It’s exciting to see such important work being done right up the road. Congratulations to Todd and the hundreds of collaborators around the world on finishing such an important project. Now, go enjoy a Oregon microbrew to celebrate.
Posted by
Nathan Lillegard on Jan 23, 2010 |
As a wrap-up piece for a series on genetic technology in agriculture, the NY Times wrote focused on Tomorrow’s Table: Organic Farming, Genetics, and the Future of Food, an excellent book written by two UC Davis professors; a geneticist wife and an organic farmer husband. I’ve read the book and highly recommend it to anyone interested in the topic of genetic technology in agriculture.
This post at the sustainability website Grist is unsurprisingly skeptical of the concept of sustainability and GMO seeds going hand in hand, I think that the coverage of the book is a positive step for education of the general public about what is a complex scientific topic. This book provides a thorough explanation of the differences between conventional breeding using molecular markers and the techniques of transgenic breeding. If we’re going to have a good public debate about this topic, having some facts as the basis for the debate is critical.
Bringing that debate to the forefront of my local community, Oregon is now in the thick of the discussion. The Oregonian notes that the debate on GMO seeds is now right in our backyard. Oregon has a diverse agricultural industry, from high value specialty crops to rolling fields of wheat. It turns out that this is also a great place to grow seeds – seeds for GM sugar beets. The debate about the technology that enables our agricultural prosperity, is not confined to the corn fields of Iowa and the soybean fields of the South, but is something that everyone needs to consider as we become more attune to the global and local supply chain for our food.
Posted by
Nathan Lillegard on Jan 22, 2010 |
At the annual ‘world cup of genomics’ at the Plant and Animal Genome XVIII conference in San Diego, Floragenex debuted results from its RAD LongRead sequencing method. The results of a pilot study were displayed in a poster authored by Floragenex, VP of Research, Dr. Rick Nipper. A PDF copy of the poster is available here.
The RAD LongRead technology is an extension of the patented Restriction site Associated DNA (RAD) sample preparation method, developed by Floragenex. The technique enables researchers who want SNP information in species lacking an assembled reference genome a path towards developing SNP based high-throughput assays. The 300-600 contigs that can be generated from the Illumina Genome Analyzer system using this sample preparation method and Floragenex bioinformatics tools, offer researchers wishing to use any of the leading commercial genotyping platforms, enough flanking sequence to design effective assays.
Floragenex and its animal sciences/biomedical division, Biota Sciences, offers RAD LongRead sample preparation, sequencing, and analysis services to customers working in any organism.
