XNAT Workshop 2016 Home

Workshop Agenda

Time	Day 1: Administration	Day 2: DevOps	Day 3: Computing	Day 4: Programming	Day 5: Impromptu Topics
8:00	Check-in and Breakfast	Breakfast	Breakfast	Breakfast	Breakfast
9:00	Daily Welcome Dan Marcus	Daily Welcome Dan Marcus	Daily Welcome Dan Marcus	Daily Welcome Dan Marcus	Daily Welcome Dan Marcus
9:30	Installation and Basic Use Rick Herrick	IT Planning Chip Schweiss	Pipelines Mohana Ramaratnam	XNAT Under The Hood Tim Olsen/Rick Herrick	TBD
11:00	XNAT Administration Jenny Gurney	XNAT at Scale Chip Schweiss/Jenny Gurney	XNAT Computing John Flavin	XNAT Customization Rick Herrick/Tim Olsen	TBD
12:00	Lunch XNAT staff available to assist in setting up laptops	Lunch	Lunch	Lunch	Lunch
1:00	Practical Session 1: Administration	Practical Session 2: Backend Administration	Practical Session 3: Computing	Practical Session 4: Programming	No practical
1:00	Breakouts	Breakouts	Breakouts	Breakouts	Breakouts
4:00	Guest Talks Using XNAT to manage large scale trials in dementia Using XNAT at the University of Amsterdam DPUK: A distributed network of XNAT installations XNAT for Clinical Trials	Guest Talks Automated Test Suites for XNAT Large Scale Image Processing with DAX XNAT for the Human Connectome Project XNAT Desktop	Guest Talks XNAT in Cancer Diagnosis, Therapy and Research OpenMOLE Building XNAT Types from the NDA Data Dictionary Service XNAT for Large Scale Clinical data	Guest Talks Python interface for XNAT Static & Dynamic DICOM Anonymization XNAT to XNAT Data Synchronization Workshop 2016 Guest Talk - Visits and Protocols Plugin	Adjourn
Evenings
6:00	Suggestion: Shakespeare in the Park	Workshop Banquet Urban Chestnut Grove Brewery & Bierhall	Workshop Dinner Hosted by Radiologics CIC @4240

Breakouts: There will be breakout rooms available each day for individual project development and discussion. View and add hackathon/breakout projects.
Guest Talks: The end of each day includes time for brief 10- to 15- minute talks by any attendee. View guest talk schedule.

Highlighted Content

Each day of the XNAT Workshop agenda will be split into two types of sessions: Lectures in the morning, and Practicals in the afternoon. To participate in the practical sessions, attendees are expected to bring a sufficiently powered laptop to run XNAT virtual machines. There will be wi-fi connections available in the conference center, but users are also strongly encouraged to download necessary components prior to the start of the Workshop to minimize delays and setup time. Please contact us if you have questions about the required hardware.

Laptop Requirements & Recommendations

Operating Systems:

Mac OS 10.8 and up (preferred)
Linux: Debian-based (Debian, Ubuntu, Linux Mint) or Red Hat/Fedora-based (RHEL, Fedora, CentOS, Scientific Linux)
Windows 7 and up

Hard Drive: At least 40 GB of free hard drive space available, SSD preferred for performance

Processor: 2 gHz and up recommended

RAM: 8 GB and up recommended

Required Software

A fully supported browser. Most modern browsers–Chrome, Firefox, Safari, Internet Explorer, Opera–work with XNAT. If you are using Internet Explorer, you should have at least IE 10. Note that Microsoft Edge is not supported at this time!
The Java 8 JRE for upload and download applets.
VirtualBox. You can use other virtualization platforms that support Vagrant, including Parallels and VMWare Workstation or Fusion, but the xnatstack base box and all of the xnat-vagrant configurations are based on using VirtualBox as the provider. That means you'd need to use another Vagrant base box, install any missing dependencies, and manage the configuration and installation of XNAT manually. Since VirtualBox is available free of charge and can exist alongside the other virtualization providers, we've opted to just support it for now.
Vagrant required to create an XNAT virtual machine (Vagrant can be installed on OS X using homebrew or on most Linux variations using the standard package manager for the platform)
Vagrant Manager provides a convenient interface for managing vagrant machines.
Git for cloning data from XNAT development repositories.
Windows users only: Cygwin or Git Bash (which comes with Git). Optionally, if you are comfortable with MobaXterm, that is usable with some minor workarounds.
An environment for code editing in practicals and hackathon projects. We recommend the following applications, all of which are either open-source or offer fully functional trials.

- Recommended IDE: IntelliJ
- Recommended simple code editor: Sublime Text
- Recommended source control software: SourceTree
- Recommended XML editor: OxygenXML

Predownload the XNAT Vagrant Base Box

Many of the practical sessions and hackathon sessions presume the use of Vagrant to create virtual machines that run the XNAT application. The XNAT team has created a Vagrant base box that has many of the services required to run XNAT already installed, greatly reducing the time required to build new instances. This is the xnatstack Vagrant base box. You should download and install this base box before leaving for XNAT Workshop 2016: this is a fairly large download and will be even slower if all attendees are trying to download it at the same time on the same wireless connection!.

To download the box, run the following command:

CODE

vagrant box add nrgxnat/xnatstack-ubuntu1404-docker --provider virtualbox

This will download the base box and cache it in your Vagrant data folder.

You can check for available updates to the xnatstack Vagrant base box by running the following command:

BASH

vagrant box update --box nrgxnat/xnatstack-ubuntu1404-docker

Taking care of this ahead of time will leave you more time to focus on the important parts of the sessions and practical exercises. If for some reason you don't get it downloaded ahead of the workshop, don't worry – we'll have it available on USB thumbdrives when you arrive.

You can also download the XNAT Vagrant base box by creating a new Vagrant project that references the box, then creating a VM instance from that project. Run these commands to do this:

BASH

$ vagrant init nrgxnat/xnatstack-ubuntu1404-docker
$ vagrant up

The first command creates a very basic Vagrantfile. After deleting all the comments in that file, you're left with this:

RUBY

Vagrant.configure(2) do |config|
  config.vm.box = "nrgxnat/xnatstack-ubuntu1404-docker"
end

When you run the vagrant up command, this will reference the Vagrantfile and create a new virtual machine based on the XNAT base box.

If you want to further configure your virtual machine, you can have a look at the Part 1 Installing XNAT practical session documentation or use the XNAT Vagrant project to automate a great deal of the setup and configuration.

Notes for Windows Users