IDRT - Integrated Data Repository Toolkit
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This section describes how to get started with i2b2 Wizard. Please make sure you have followed the previous sections closely.

Installing OpenSSH

Note: This is only applicable for Ubuntu Linux. It's similar for other distributions.


Then reboot the virtual machine by typing:


Copying the i2b2 Wizard files to the VM

First, rename the i2b2 Wizard directory so that it does not contain spaces, e.g. to "i2b2wizard".


From now on, it is highly recommended to not continue working in the VirtualBox window (because it's slow). Better connect remotely to the VM via SSH, e.g. with putty on Windows systems. Don't forget to copy the i2b2 source file to ./packages as explained in 220. Preparing the installation.

Preparing the i2b2 Wizard

The first time you want to start the i2b2 Wizard, you might need to perform some preparations. Execute the following commands inside the i2b2 Wizard directory:


Now it is highly recommended to create a "snapshot" of your VirtualBox virtual machine before running the i2b2 Wizard. If something goes wrong, you can easily revert to a "clean" machine.

Launching i2b2 Wizard

Launch the i2b2 Wizard by executing


If everything is OK, you will be greeted by i2b2 Wizard after a few seconds (it will probably install the required tool "dialog" first) and asked to select your configuration (see below).

Setting the configuration (i2b2 Version, database type)

You may encounter the following message:


Again, just hit ENTER - and welcome to the main menu!

Preparing the i2b2 hive (= server)

To download and to install the required server software, select System Setup => Install Required Packages. This will take a considerable amount of time depending on your internet connection speed. Please note that if you have selected to use a Oracle database and i2b2 Wizard has not been reconfigured to connect to Oracle database outside "localhost", i2b2 Wizard will attempt to install Oracle XE. In this case, the Oracle software license is accepted automatically by i2b2 Wizard.


After all software components have been installed, go to the Menu (Main Menu =>) System Setup => Hive Tasks and select Load I2B2PM and I2B2HIVE.

Creating an i2b2 project and user

To create an i2b2 project, go to Projects & Users and select Create i2b2 Project. Enter your desired parameters as shown in the following screenshot:


For all the roles and permissions please refer to the official i2b2 documentation (, click on "i2b2 Source" and download the file

Starting the i2b2 server   

Launch JBoss by selecting JBoss Control => Start JBoss from the main menu. This automatically deploys the i2b2 source code and configuration.

If you want to start JBoss automatically upon system startup, you could have a look at Please note that providing detailed instructions is out of the scope of this document and the procedure is different for various operating systems.

Logging into i2b2

You can now log into your new project. To access it via the i2b2 Web Client, open http://localhost/Web Client in your browser (replace "localhost" with the IP if you want to access it from a different machine).


Note that this project contains no data (including no i2b2 ontology) and therefore throws errors if you want to use it. To upload data, you can use the IDRT tools.

Loading the Boston Demodata

If you want to load the Boston Demodata as well, select Boston Demodata => Load Boston Demodata from the main menu. This creates the project as well as the two i2b2 users "i2b2" and "demo". Their passwords are "demouser".
Please note that loading the Demodata will take very long - about 30 minutes. It is OK if error messages appear after the import (because there are/were errors in the Demodata SQL files).