JMP Genomics Programming Guide

As a programmer of JMP Genomics Analytical Processes, you have the capability to control one of the most powerful systems available for processing scientific data from sources such as genetic markers, microarrays, DNA sequencers, and spectrometers. This guide is designed to provide you with all the information that you need to understand and construct processes in order to surface them to scientific and Bioinformatics users. It contains several prototypical examples that you can modify and use to create your own processes.

To take maximal advantage of JMP Genomics software, you need SAS expertise in the following areas:

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DATA step programming

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statistical procedure invocation

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macro language

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JMP Scripting Language (JSL).

If you are not familiar with one or more of these areas, you should consider obtaining training before tackling JMP Genomics analytical process writing. A variety of educational resources are currently available; please refer to the SAS Learning Center (http://support.sas.com/training/) for more details. The last chapter of this volume, Additional Resources, lists some recommended reference materials. You can also learn many of the required concepts by studying the examples in this guide.

It is assumed you have general SAS coding experience and that you are consulting this guide to learn the conventions required to write JMP Genomics processes. The focus of this guide is on these conventions rather than the actual code, although this guide makes extensive use of examples to illustrate the concepts. Keep in mind that all of the SAS and XML code accompanying the routines that ship with JMP Genomics products are open for your perusal and modification. This is a rich library of examples from which you can borrow needed code snippets. In addition, there is an extensive collection of generic macro functions defined in files like UtilityMacros.sas that you should use whenever possible.

Please note the examples for this guide use code from JMP Genomics Version 5.0. Your installation might contain some differences due to subsequent upgrades.

Note: Both JMP Genomics and JMP Clinical share a common structure and organization. In most cases where this Programming Guide specifies Genomics, you can substitute Clinical.

JMP Genomics processes enable you to establish standard operating procedures within your institution and relieve you of the burden of performing one-off analyses for every experiment. While writing processes offers some challenges, once constructed, they are a tremendously valuable and reusable asset for both you and your colleagues. They enable you to be much more efficient with your time and to propagate high-grade analyses that leverage your expertise. In this respect, and in several others, writing JMP Genomics processes can be a very rewarding endeavor. Let's get started.

Next: Getting Started