# System Operations

This document is intended to describe how JMP Clinical interacts with the clinical and nonclinical study data that is added to a JMP Clinical Study. JMP Clinical can add data from files appropriately formatted only in the following data model standards: CDISC SEND, SDTM and/or ADaM data models. A study includes a collection of input data folders, settings, and an output folder. Specifically, a study consists of a Study Name associated with one or more data set folders along with a unique Output Folder.

Study Data

The study data must be located either on the local machine where JMP Clinical is installed or on a network drive available to the local machine. The study data must be formatted as one or more SAS data sets (.sas7bdat) or SAS transport files (.xpt). In the case where SAS transport files are used, JMP Clinical converts these files to the SAS data set format in the same directory (assuming that the user has Write access) for use with the software. Other than for this conversion, JMP Clinical reads data only from the input study folder. JMP Clinical never modifies the original data. Therefore, study data already formatted as SAS data sets can be made read-only. Access to this data can be controlled using s user permissions.

Adding a Study

When data are added to a study, the data are read to obtain 1. the domain names, 2. the variable names, labels and types, and 3. an initial content assessment. This assessment includes whether values of a column are missing or not. In addition, when the Track Snapshot Changes feature is selected, the keys for each domain must be sorted properly so that changes to any source data can be detected. All of this information (metadata) is stored so that upon successful addition of the study, the software can determine which pre-conditional requirements are met, and which specific reports can be run.

Running Reports

When JMP Clinical runs a report, all necessary data are copied to a temporary SAS work folder in preparation for analysis. The analysis is then run and the resulting data are saved to the Output Folder for storage. The SAS code, log file, and resulting output data and report files are all stored in this folder. Once this copy step is complete, the contents of the SAS work folder are deleted by the system. Reports can either be rerun or archived for sharing or storage purposes. This standard protocol ensures traceability from the input study data to the output of the system.