Location: Farrell Learning and Teaching Center, Connor Auditorium

660 S Euclid Ave, St. Louis, MO 63110

Washington University School of Medicine

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

 

Guest Talks Guest Talks Guest Talks Adjourn
Evenings          
6:00 Suggestion: Shakespeare in the Park

Workshop Banquet

Urban Chestnut Grove Brewery & Bierhall

Workshop Dinner
Hosted by Radiologics

CIC @4240

Suggestion: Shakespeare in the Park


Free Classical Concert

(take Metrolink to Civic

Center and 9 min walk from there)

 


Highlighted Content

Instructions on getting from the airport to the Workshop and Hotels


Step 1: From the airport, get onto a Metrolink Train heading eastbound. 


  • If flying into the East Terminal (Southwest Airlines), exit the terminal by baggage claim into the parking garage. The Metrolink Platform is located at the far end of the garage. There is an elevator up to the platform. 
  • If flying into the Main Terminal (All other airlines), go upstairs from baggage claim to the ticketing area. Walk east past the American Airlines Credit Union, following signs to the Metrolink Platform. 
  • The Metrolink does not use tokens or turnstiles; rather, they have ticket inspectors who walk the trains. Simply buy a one-way ticket at the airport platform. This should be pre-validated. If not, there are red validation machines. 
  • Ride the Metrolink to the Central West End station. This will be eight or nine stops, depending on which terminal you boarded on. 


Step 2: Getting around the Central West End. 

Exit the Metrolink platform and go up the stairs on the western end of the platform. This will put you in the center of Washington University School of Medicine / Barnes-Jewish Hospital campus. Here is a Google Map that highlights Workshop locations, hotels and recommended restaurants in the area. 

 

Step 3: Feeling adventurous? 

St Louis has Uber, which makes it easy to get around and explore the city in relative safety. Here are some neighborhoods and attractions that you may be interested in: 

 

Step 4: Going Home

Simply reverse your steps in Step 1, with one important detail: Get on a Westbound Red Line train. Way-finding on Metrolink platforms is not very good, compared to most other mass-transit systems. Be sure to be watchful for a train with red signage displaying "Lambert Airport" as its final destination. 

 

 

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.

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:

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:

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:

$ 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:

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

We have documented several common (and a few uncommon) problems that Windows users have run into with installing and using Vagrant. Running Vagrant from Cygwin or MobaXterm will likely help. Here are some more helpful hints: Troubleshooting XNAT Vagrant Installation for Windows Use. We highly recommend running through the Vagrant's "Getting Started" sequence before the Workshop to make sure you're able to run Vagrant on your local machine.




Workshop Updates