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Jun 23, 2011

Getting Familiar with JMP Genomics 5

There is so much that is new to share about JMP Genomics 5! Beyond its rich library of prebuilt analysis interfaces and graphics for genomics data, JMP Genomics offers our users full access to all the new features offered by the JMP 9 platform. I highly recommend that JMP Genomics users read up on the new features in JMP 9 on the JMP website and here in the JMP Blog. This new JMP 9 release is really amazing! You will find many tools that will help you explore, filter and interact with your genomics data sets.


When you start JMP Genomics 5, the first thing you will notice is the simple elegance of the new user interface, which takes full advantage of JMP 9’s new windows management environment. Just a word of caution: You may find it takes a couple of minutes to get used to the absence of the main window found in previous JMP versions! I have been a JMP user since version 5, and I have to admit I found it a little disorienting at first. However, I’m sure that, like me, you will quickly come to appreciate how easy it is now to move windows around, especially if you’re working across multiple monitors.


JMP Genomics Starter window


In one of the open windows, you will notice newly updated Genomics Tips of the Day. I encourage you to take a look through these. I suspect even power users will learn some new tricks about JMP Genomics (and JMP) here. We’ve tried to include a mix of tips that cover frequently asked questions from JMP Genomics users and useful JMP shortcuts. By the way, if you have ideas for Tips to add in future versions, don’t hesitate to e-mail us to let us know.


JMP Genomics Tip of the Day


We also automatically open our new JMP Genomics Starter, a customizable home window that mirrors the organization of our Genomics menu. You can leave the Starter permanently open on your desktop and use it to navigate through all our available Genomics tools. If you wish to customize your Starter view, simply click the Customize button to hide individual processes or whole sections of the menu. Once you have created a Starter profile that you like, you may even export it to share it with other users. This makes it easier for administrators to simplify the set of choices available to new JMP Genomics users, or to create one or more customized Starter views for users working in different functional areas.


When you do open the Genomics menu (or examine the Starter window), you will see a new menu section called Getting Started. In this section, you will find the new JMP Genomics Wizard, a tool that makes easier than ever to get started with new data sets. This interactive interface guides you through setting up the import of sample information and downloading library or annotation files (if required). It even automatically sets up the appropriate import process for you to bring in data from popular genomics data platforms or text formats.


If you run a JMP Genomics import tool or view results from an analysis process, you will see that graphics and follow-up analysis options are now organized into tabbed reports. The underlying tables for graphics presented in our tabbed reports are now hidden to simplify the presentation of complex analysis results. You can still easily recall the hidden tables to view details, or use the pull-down menu for a tab to open any graphic in a new window (e.g., to compare graphics from different tabs side by side). You can also close all tables and graphics from a single button at the bottom of the tabbed report, too.


Example of a tabbed report in JMP Genomics


This user interface change was enabled by new scripting functions in JMP 9 and was implemented in response to user feedback. We had heard that the many multiple tables and graphics launched at the completion of a JMP Genomics process run could be overwhelming at times, especially for new users. Given this feedback, tabbed reports were a high priority on the to-do list when we moved JMP Genomics development over onto JMP 9. We expect tabbed reports to be a standard output convention for most processes in our life sciences products going forward. In fact, the development team is already working on a similar conversion of output results for JMP Clinical in preparation for a February release on the JMP 9 platform.