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Jun 23, 2011

Great things happen when users are partners in software development process

Now it’s time to follow up my earlier blog post about JMP Genomics user Dr. Eric Jackson winning the Herbert L. Rothbart Outstanding Early Career Research Scientist, a national award for USDA-ARS. I wanted to share some of our team’s experiences that speak to Eric’s creativity and energy as a partner. I’m sure our experiences are different from those of the scientists in academia and industry who collaborate with Eric on the scientific front, but Eric’s ability to work with partners in many different areas speaks volumes about why he has been so successful. Of course, I also have an ulterior motive, and that is to encourage other users to share their thoughts and ideas about how to further improve our software.

Just to give some context, Eric has been a JMP Genomics user for a couple of years now and published several recent papers that used JMP Genomics for selected analyses. These included examples of using JMP Genomics for association mapping in wheat (Gurang et al.) and genetic diversity analysis in oat (Oliver et al.).

Early in 2011, Eric began encouraging our development team to think about a different, complementary approach to association analyses. He was interested in seeing JMP Genomics use genotype data for offspring from experimental crosses used in designed breeding strategies to create genetic linkage maps. Eric frequently constructs maps using other software and thought that the interactivity of JMP Genomics would be a great benefit to process of map creation. It was good timing for us, as we had other customers in the agricultural genomics space making the same requests.

Why would anyone want to create a linkage map in these days of whole genome sequencing, you might ask? Well, although EST sequencing has been an important tool for generating a catalog of genetic markers in oat (thanks to Eric’s collaborators in the Oat CORE project), getting a complete and correct sequence assembly of the whole oat genome is next to impossible because of its large size and hexaploid nature. Assembling the genome would be extremely difficult due to the high similarity between the three different but related ancestral genomes that together make up the oat genome. Genetic linkage maps provide a lower resolution road map than a complete genome sequence, but these ordered sets of genetic markers can still be used to help identify areas of the genome that harbor genes controlling desirable agronomic traits.

Eric’s willingness to share his thoughts about the ideal linkage mapping workflow was tremendously helpful to developers Kelci Miclaus and Russ Wolfinger as they worked on several new linkage map-related processes which will appear in next month’s JMP Genomics 5.1 release. With the first iteration of this functionality, we will offer processes for identifying linkage marker groups, which in most cases correspond roughly to chromosomes, as well as processes for ordering markers within linkage groups and visualizing maps created in JMP Genomics or other software. We’re excited to be able to take advantage of SAS Analytics to offer methods for advanced marker ordering, and are already planning a number of enhancements to appear in our next release, JMP Genomics 6.0. Many of these enhancements have come from suggestions offered by existing users who have seen demos of the new linkage map functionality.

I would like to impress on all the JMP Genomics users out there that we want you to share your thoughts and ideas about our software. We need to hear from you about how we can make JMP Genomics more useful to you. We want to hear the good, the bad and the ugly from you so that we can continue to improve our product. We know that no product can cover the diverse genomics analysis space completely, and there will certainly be some problems that don’t make sense for us to try to tackle within our software. But we certainly hope you’ll give us the chance to listen to your analysis problems and tell us how you think JMP Genomics could help. Please email any ideas you may have to

To learn more about Eric’s research collaborations and see a demo of the new linkage mapping functionality by JMP Life Sciences Specialist Jordan Hiller, you can watch the recorded webcast CORE Exploration: Markers to Maps to Genes, All in One Setting.

Or check out an earlier blog post I wrote about Eric’s webcast and the new functionality.

Now that JMP Genomics 5.1 has been released to new and existing users, our website has plenty of new details about all the new features we’ve added. Be sure to check them out.

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