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Jun 23, 2011

New genomics tools on display in CORE webcast

A new recorded webcast that highlights the work of a consortium of researchers focused on improving existing oat varieties is now available on our website. The recorded webcast includes a presentation by Dr. Eric Jackson, Research Molecular Biologist for the US Department of Agriculture (USDA), on the work of the global Collaborative Oat Research Enterprise (CORE) as well as a demonstration of a few of the features coming in JMP Genomics 5.1 this fall.

In the on-demand webcast, Eric discusses marker-assisted breeding techniques and shares the work that led to the discovery of novel genes controlling oat grain fiber. The CORE team used high-throughput genomics approaches to improve knowledge about markers in the complex oat genome and develop predictive assays for use in future breeding programs. Eric used JMP Genomics to perform some of the analyses that contributed to the CORE’s findings.

The webcast also features a presentation by JMP Life Sciences Specialist Jordan Hiller about the new Recombination and Linkage Groups, Linkage Map Order, and Linkage Map Viewer processes that will appear in our upcoming release.

These new features were added at the request of several large JMP Genomics license sites, including USDA. We greatly appreciate the cooperation of users like Eric who were willing to work with us to make these new features happen. It is an ideal situation to work with customers who are willing to share information on their current workflows, real data sets, and make suggestions for improvements in prototypes. Like so many JMP Genomics processes, these new tools pair the interactive capabilities of JMP with the processing power of SAS behind the scenes.

We believe our new features cover many needs of users in the linkage map space. The Recombination and Linkage Groups process can estimate recombination fractions for several common types of experimental crosses and determines an initial set of linkage groups to use when building new maps from scratch. If you're just interested in visualizing existing maps, you will love the 3D graphics of the Linkage Map Viewer.

If you already have consensus linkage groups identified, you can simply use those in Linkage Map Order to perform ordering within the pre-defined groups. Linkage Map Order features a standard marker ordering algorithm that calls multidimensional scaling methods in PROC MDS. However, with the click of a radio button, JMP Genomics users who also license SAS/OR can take advantage of advanced marker order optimization methods in SAS PROC OPTMODEL. Finally, you can compare orders between existing maps and new maps built within JMP Genomics using interactive tools like Graph Builder in JMP.

After watching Eric's webcast and Jordan's demo, let us know your feedback on the new functionality. We're gathering requirements in this and other areas for the next version, JMP Genomics 6, which will be released next year on the upcoming JMP 10 platform. We'll be hosting a new features webcast for JMP Genomics 5.1 later in the summer. If you've got comments on the recorded webcast, or are an existing user and can't wait to see a preview of what's coming, please contact us at

Community Member

Great things happen when users are partners in software development process - JMP Blog wrote:

[...] check out an earlier blog post I wrote about Ericâ s webcast and the new [...]

Community Member

JMP Genomics at Plant and Animal Genomes Meeting wrote:

[...] thanks to a collaboration with JMP champion Eric Jackson of USDA-ARS, and to the efforts of our JMP Genomics development team, we have made rapid progress [...]