tranSMART Arborist

An arborist [...] is a professional in the practice of arboriculture, which is the cultivation, management, and study of individual trees, shrubs, vines, and other perennial woody plants (Wikipedia)

Graphical tool to help you prepare your data for loading into the tranSMART data warehouse.

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Functionality

• Browse your file system for tranSMART study folders or create a new one
• Create and edit your clinical and expression parameter files
• Create and edit your study tree, as represented in the column mapping file
• Adding data files to your study tree
• Manually adding, deleting and drag-and-drop reordering of nodes in the tree
• Editing the values in the columns file for each node

Installation

Keep in mind the application has only been tested on Mac OS X 10.10 or newer, and Windows 7 or newer. Although for now the application runs on both Python2 and Python3 we recommend the latter.

• Clone this repository and run the setup with python3 setup.py install.
• Use git clone --recursive OR run git module init and git module update to also download a transmart test dataset.
• Download the latest stable release from this repository

Starting the application

• Run python3 runserver.py in your terminal, this should open The Arborist in your default webbrowser.
• Additional running options can be viewed by running python3 runserver.py --help

Loading data

Once your data is prepared we suggest using transmart-batch for loading it into tranSMART.

For additional documentation

See these docs.