MSparkles automatically creates and manages a configuration file for each dataset. These configuration files are saved in your PCs documents folder. Here MSparkles creates a subfolder, named MSparkles projects. You can find all configuration files in the project manager on the left side of MSparkles' main window. By creating logical dataset groups (folders) you can easily manage vast numbers of datasets. Creating logical groups and organizing your data in MSparkles does not affect how your data is sored on your comnputer or your sever in any way. You can even add datasets located on different folders or harddrives to one MSparkles group.
MSparkles does not copy your data. Instead, it sores the path of your data and loads it from its original location. This way, you can have your data e.g. on a network drive or an external disk without filling up your computer's local storage.

All data generated by MSparkles are, by default, stored in the location of the original dataset. Analysis resutls and reports are sotred in a sub-folder with the name of the dataset, prefixed with Results. MSparkles never changes the original dataset, so you do not need to work on copies of your data. However, after pre-processing and F₀ computation, a new Dataset is saved, with the pre-processed data and F₀, respectvely. This is done to save computation time, in case a dataset needs to be partially re-processed.

The structure of datasets and folders within MSparkles is completely independent of the physical organization of your files on your storage system. MSparkles creates a new folder, MSparkles projects, in your Documents folder (on windows systems this is typically 'C:\Users\UserName\Documents'). This folder contains MSparkles' project files to organize your datasets and also rebuilds your folder structure within MSparkles by creating sub-folders.

 

You can always jump directly to the original location of a dataset, by selecting the dataset of interest, and then clicking on Open folder in the menu-bar. BY clicking Open results folder from the drop-down menu of the Open folder button, MSparkles will open the folder containing all generated results for the selected dataset.