Subscribe Bookmark


Jun 23, 2011

JMP Genomics 3.0 is into production!

As JMP Genomics product manager, I’m pleased to announce that JMP Genomics 3.0 has been finalized and is scheduled to be released at the end of May. An amazing effort from our stellar development, testing, documentation and support teams has produced some excellent new features and guidance on how to use them. I’m amazed at the amount of new work that has been accomplished since the release of our 2.0.4 Web update late last year. With the 3.0 release date around the corner, we’re already thinking about our next update. But first, let me say a little about the 3.0 release about to be launched.

JMP Genomics has come a long way in both functionality and appearance since its initial release in March 2006. By riding on the new JMP 7 platform, JMP Genomics 3.0 offers beautiful new 3-D graphics, including the 3-D PCA plots that users demanded (thank you, C.H.). You can see a 3-D graphic prominently displayed on the front cover of the new special edition of sascom magazine, which features JMP. Many of our existing processes have been enhanced to use the new 3-D graphics. We also have some great-looking new icons in our genomics menu (thank you, G.M.!).

JMP Genomics 3.0 addresses a number of user requests with new and enhanced features. Streamlined genetics tools support very large whole-genome association studies, and we’ve added new SNP-SNP and SNP-trait interaction discovery capabilities. Our new Workflow Builder process lets users link sets of commonly used JMP Genomics analyses settings into reusable workflows. A new estimate builder allows point-and-click creation of estimate statements for use with our ANOVA and Mixed Model processes. A new UCSC Genome browser link process creates link tables and lets users specify variables to create custom tracks for upload to the browser to display statistical results obtained using JMP Genomics in genomic context. We’re quite excited about the enhanced predictive modeling capabilities of JMP Genomics 3.0, and the new Cross-Validation Model Comparison (CVMC) platform for comparing the performance of different cross-validated predictive models on the same data sets. Our development and testing team has already given CVMC a workout in preparation for their planned presentations at the 7th meeting of the MicroArray Quality Control consortium, a group of 150 scientists from across the nation who will meet here at SAS May 24-25.

Speaking of meetings, the JMP User Conference is scheduled for June 12-13 in Cary, with some pre-conference JMP Genomics training on Monday, June 11; a genomics track on Tuesday afternoon; and an advanced JMP Genomics workshop planned for Wednesday afternoon. With all the buzz about JMP 7, the user conference will be quite exciting, and we’re looking forward to welcoming a representative from our partner Ingenuity Systems, developers of Ingenuity Pathways Analysis (IPA). Our IPA Upload process, first featured in JMP Genomics 2.0.4, allows users to upload gene lists directly from JMP Genomics into the IPA Web application for pathways analysis and functional annotation. Additional partner companies for JMP Genomics now include both Affymetrix and Illumina, which provide our users with tools to generate expression and SNP data to analyze.

I want to say thank you again to our users for their suggestions and support, and to the JMP and JMP Genomics teams for working so many long hours on JMP Genomics 3.0. If you’re a user with ideas or suggestions for our next update, we hope you’ll e-mail them to Thanks!