Workflow Builder

The Workflow Builder takes advantage of JMP Clinical’s ability to save settings to enable you to string together groups of processes into a comprehensive analysis series. A typical, well-designed workflow can take you all the way from the initial data import, through preliminary analysis, quality control, statistical analysis, modeling and annotation of results. The workflow series can be saved for use again and again for different data sets, so long as the basic experimental design remains constant. Existing workflows can also be edited as desired to accommodate changes in experimental design.

What do I need?

To run the Workflow Builder, you first need to decide which specific processes you want to run as a group and in what order. Each should have its own input data set, which might or might not have been created by a previous process in the workflow. If the workflow requires an import of raw data, the appropriate data import engine as well as each of the processes to be used in the workflow must be configured and the settings saved in one settings folder. Finally, an output folder must be created, into which all of the resulting data sets, analyses, graphics, and other output are placed.

The Workflow Builder is not intended for first time users. Instead, it was designed for power users who have already explored the many options offered through JMP Clinical . It is assumed that you are familiar with the processes, and have settled upon one or more standard protocols for your analyses. You also likely have saved specific settings for each of the processes.

Tip : When saving settings for individual processes, you can now opt to save those settings to a newly saved workflow by checking the Save to Workflow box. If the Workflow Builder is open, the new setting is added to the current workflow. If the Workflow Builder is not open, saving a new setting with this box checked launches the Workflow Builder with the newly saved setting in place.

The set of saved settings that comprise a workflow can be edited either in the dialog for that process or in the Workflow Builder itself. If you are not familiar with the individual processes that you want to use, consult the specific chapters for those processes for more information.

Output/Results

As the workflow runs, the individual processes open sequentially, run, and record their output to a specified journal . From the journal, you can open and examine the specific windows resulting from each of the processes of the workflow. As you evaluate the output of this workflow, you can opt to go back, modify the settings in the individual processes, and rerun the workflow until you are satisfied with the analysis.

As an alternative to hand-editing data set paths, you can perform the following steps:

1	Individually run each process in the desired workflow in the usual way from the Genomics (or Clinical ) menu, specifying the output folder to be the same for each.

2	Launch Workflow Builder , choose a Workflow folder and make sure the Change Output Folder to Workflow Folder in Settings Moved to Right Panel check box is checked.

3	Choose the output folder from Step 1 as the Folder of Available Settings parameter.

4	Move the desired settings to the right panel in the order in which you want to run them. The settings are copied to the Workflow folder, and the Output folder as well as paths to the input data sets are changed.

5	Run the workflow.

As you become more experienced with workflows, you can apply them directly to new experiments. In this case it is suggested that you use generic names for all input and output data sets, and use folder names to identify the experiments. That way, the results will not contain data set names from previous experiments.

Click on the buttons to open the results for the selected processes.