Quickstart Tutorial for Mac - DeepPhe/DeepPhe-Release Wiki

Before beginning this tutorial, please install DeepPhe using the DeepPhe Installer.

Overview

This tutorial will take you through the following steps:

  1. Starting the DeepPhe Database
  2. Starting the DeepPhe GUI
  3. Configuring the DeepPhe GUI to process the provided example fictitious patient reports
  4. Processing the fictitious patient reports and saving the results to the DeepPhe Database, and to various output files
  5. Viewing the results in the DeepPhe Visualizer

Starting the DeepPhe Database

The first thing we will need to do is start the DeepPhe database so the DeepPhe GUI has a place to store results, and those results can be viewed in the DeepPhe Visualizer.

DeepPhe uses a Neo4j Database to store results. To start the DeepPhe database, go to your DeepPhe installation directory ("DeepPhe" in your Applications folder by default), and click the start-neo4j.command.

*Note: Wherever you put your DeepPhe folder, "java" will ask to access those files. Press "OK" to allow this to continue with the tutorial.

Once the DeepPhe Database is running you will see a terminal that looks as follows.

Those familiar with databases can monitor this window for debug messages written by DeepPhe. Most users can happily ignore this window, but it must remain open while using DeepPhe or the DeepPhe-Visualizer.

Starting the DeepPhe GUI

Now that the database is running, we are ready to start the DeepPhe GUI. We start the DeepPhe GUI by clicking on the DeepPhe GUI icon in the DeepPhe directory inside the DeepPhe installation folder.

Open your Applications folder and click on the DeepPhe Folder, and click on the DeepPhe subdirectory:

Then click the DeepPheGUI executable:

Configuring the DeepPhe GUI

Welcome to the DeepPhe GUI

Before we run, we first need to configure the GUI to process the example patient reports. Set the parameters as follows:

On my system, the parameters are set as follows:

Process Patient Reports

We are all set and ready to run. To run DeepPhe, click the green button at the top of the screen that looks like a person on a run.

DeepPhe will run and display a "COMPLETE" message when it's finished.

deepphe-run-complete

Depending on the version of DeepPhe you are running, DeepPhe will either close automatically or ask you to press a button to close DeepPhe. If the DeepPhe software didn't close automatically, you can close it now.

View Results in the DeepPhe Visualizer

With the patient reports processed by DeepPhe, we can now view the results written to the database in the DeepPhe Visualizer.

Open your Applications folder and click on the DeepPhe Folder, and click on the DeepPhe-Viz subdirectory:

Then click the start-viz.command script:

This script will start Node.js, install some required packages...

The DeepPhe Visualizer will automatically open in a browser window.

viz

View Text File Output

Coming soon.