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.

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.

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.

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.

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.

Launched by Floragenex to leverage its proprietary next-gen sequencing technology for researchers in vertebrate, invertebrate and other species, Biota Sciences provides services focused on meeting its clients’ research goals.

“Through Floragenex and Biota Sciences, we can create solutions for plant and animal researchers with our suite of sequencing technologies,” says Nathan Lillegard, Floragenex CEO. “We provide more sequence information per dollar, more detailed bioinformatics analysis custom tailored to our clients’ research design. Our services enable our customers to focus on their biology and analysis, rather than navigating the challenges of matching their goals with technology.”

Biota Sciences’ Services:

• SNP discovery and assay development: With or without a reference genome, services engagements are focused on delivering research ready date to be converted for your SNP genotyping system of choice.
• Linkage Mapping/Positional Cloning: Identifying polymorphic sequences associated with your trait or gene of interest as a critical tool for marker assisted selection and gene discovery efforts.
• Custom Genomic Research: Genome-wide association studies, targeted resequencing, physical map development, and whole genome sequencing projects are planned, executed, and delivered to meet your objectives and match your budget.

Supported by the resources and experience of the Floragenex lab and bioinformatics team, Biota Sciences services are lead by Dr. Jason Boone. Dr. Boone brings a genuine passion for enabling advances in genomics for all species. Biota Sciences engagements include meiotic mapping in model fish species, phylogenetic analysis of emerging research organisms, and evolutionary questions in endangered species.

In this well written and researched article, the other side of agricultural biotechnology gets some very good press. The technology described is marker assisted breeding – using genetic information to accelerate the tried and true process of crossing and selection to develop new varieties of plants. In an interesting twist of perspectives, Forbes announced that Monsanto is the 2009 company of the year. The title ‘The Planet Versus Monsanto’ is appropriate.

The ‘other side’ of ag-biotech is part of what Floragenex supports. Finding the specific segments of DNA (genetic markers) that can be linked to a specific trait, is now much quicker and easier than ever before. This technology is hitting its stride and heading up the adoption curve, as the cost of getting and applying that information keeps dropping. Projects that took years just a few years ago are being completed in months.

The scale of what Monsanto has and will accomplish in terms of the world’s food supply is astounding.  When you think about the facts of our situation; population going up, arable land holding constant or decreasing, and climate changing, it’s hard to bet against a company that sees those macro economic factors as an opportunity.

While there are many that vilify the corporate giant from St. Louis, I’d also ask those same people to think about what they ate today. Given that Monsanto’s vegetable group is one of the largest vegetable seed producers in the world, the chances are pretty good that something they purchased in the last month, whether it’s fresh broccoli or ethanol in their Prius, can be traced back to Monsanto.

The seed industry is an evolving business that deserves more attention in this country. It’s an important piece of the economy that will get more coverage as we pay more attention to where our food comes from and who profits from our choices as consumers.

Customer Goals

• Expand the current genetic map for OWB.
• Evaluate RAD based sequencing in comparison to other SNP development and genotyping systems.
• Obtain sequence information that can be used as a reference for future genomic studies.

SNP Discovery

Floragenex sequenced two parental lines to identify polymorphisms in the bi-parental mapping population. These sequenced based markers would serve as potential markers on a genetic map.

SNP Genotyping

To evaluate the effectiveness of RAD based markers, 93 doubled haploid progeny of OWB were genotyped using RAD based sequencing. From that sequence information Floragenex assayed over 400 new SNP markers that were then placed on an existing genetic map. This information will be used in future studies focused on identifying important regions of the barley genome.

SNP Discovery and Genotyping: Linkage Map (download PDF)