An abbreviated (but still information-packed) version of the 2012 XNAT Workshop is going to be delivered in Munich on September 13-14, immediately following this year's INCF Neuroinformatics conference. There will be no cost for attendees, and registration is now available!
You can see the working agenda here, to see how much XNAT 1.6 goodness can be packed into a two-day span. The answer? A lot.
We've had a few emails come in asking about videos of our Workshop talks. The good news is, we're working on it. The bad news is that our first three sessions didn't get recorded, so we're having to re-stage them.
Because most of the workshop was intended to be hands-on, we are editing the talks down to shorter snippets that we can also use in our XNAT 1.6 Documentation. Hopefully, you all will find this useful as well, so that instead of clicking a link to start a two-hour video, you can select from a series of 10-15 minute clips. Here are three examples from our developer workshop:
As we complete our video production, this site will receive a face-lift to call attention to the video archive.
The virtual machine image for the upcoming XNAT workshop is now available for download! You can grab your own copy right here:
We've done a fair amount of our own testing, but if you find any major problems, first please test the integrity of your downloaded archive by running an md5 or sha1 checksum and, if that's OK, send an email or comment on this post.
You can find more information installing and configuring the virtual machine on the relevant session page.
Those attending the workshop will also get another copy of the VM on arrival at the workshop on Monday. It'll be on a super-swell XNAT-branded USB stick as shown below. That oughta get you fired up.
While the computing world is all about wireless this and tablet that, old man ethernet is steadily getting pushed out of the spotlight. "Well, that's fine," says Mr. Cat5. "Let the new kids have their fun, but people know when heavy lifting is required, they'll have to drag me out and plug me in."
That's certainly the case at the XNAT Workshop. If you plan on relying on strong internet access, a handy ethernet cable will attach you to Wash U's fast, strong internet backbone. (See: Speedtest.net results.) Moreover, Connor Auditorium thoughtfully places plenty of power/network ports directly into your tabletop surface.
Meanwhile, there are public wireless accounts available, but they are spotty at best, and will time you out after two hours of activity.
Most activities in the workshop will be run off the XNAT 1.6 VM, which we recommend that you run locally. However, it's nice to know that old man ethernet is still as strong as ever, should you need him.
The main reason to come to the XNAT Workshop is of course learning and talking about XNAT. But you can only do so much of that on a daily basis and everyone has to eat. So we have a few evening events scheduled for after the daily sessions!
There will be an XNAT Workshop dinner on the evening of Monday, June 25, at Wildflower Restaurant. Wildflower is conveniently located right off campus and a short block and a half from the Parkway Hotel where many conference attendees are staying.
Create Your Own Mexican Fajita Buffet (Buffet style, serving from 5:30-9:30pm)
- Beef or Chicken
- Prepared with onions, red & green peppers
- Guacamole, sour cream, shredded lettuce, grated cheese, salsa, warm flour tortillas
- Dessert: Cinnamon Churros
There will be an open bar serving sodas, tea, and coffee. Nearby we will have the following appetizers:
- Crab Cakes with a Chipotle Aioli
- Sesame & Wasabi Tuna bites with a ginger & soy dipping sauce
- Spinach Artichoke & Feta stuffed Phyllo
There will be a cash bar in which you have to pay for any alcoholic beverages you order (because of issues with the terms of grant funding for many of our events, we can't cover the costs of alcoholic beverages).
There will also be an XNAT Happy Hour on the evening of Tuesday, June 26, at Brennan’s. Brennan's is also nearby, a few blocks further into the Central West End.
Food Stations (Food will continue to be served for the duration of our event, from 5:30-9:30pm)
- Chicken flatbreads
- Veggie flatbreads
- Margarita flatbreads
- Hummus, tabouleh platter
- Roasted vegetables platter
- Fresh fruit
- Meat and cheese platters
As with dinner on Monday, because of grant funding, we can't cover the costs of alcoholic beverages.
Lastly, on Thursday evening, there will be a much more informal happy hour get-together for those attending the XNAT Developers Workshop. This will be non-sponsored and free-form. Location, time, and duration to be determined by the ambitiousness or lack thereof of anyone who might want to attend! This could be walking distance again or maybe we'll load up into cars and get away from the immediate area to some of the other destination locations in St. Louis...
As I think I've mentioned before, workshop participants are going to be getting a USB flash drive. The drive will hold a virtual machine configured with the latest and greatest beta of XNAT 1.6 configured with sample projects and data. These projects and data reflect the scenario we're using to provide a context for the various workshop sessions (more information on the planned sessions coming soon!).
Since so much of the workshop will revolve around working with this virtual machine, we wanted to provide you with information to help get your system configured before arriving. The more of this set-up you complete before you arrive, the more you get to take advantage of at the workshop itself!
The first thing you'll need to be concerned with is your laptop. We strongly encourage all attendees to bring their own laptop. When it comes to running virtual machines, the more powerful the laptop the better! If you can't bring your own laptop, then you may be able to share with another attendee. Alternatively, we'll be offering laptop rentals from the Washington University School of Medicine IT department. The rental fee is $50 per day. We'll have specifications for these laptops available shortly; I'll add them in an update when they're made available to us. If you want to rent a laptop, please contact us soon to reserve one.
After much back-and-forth'ing (does that really qualify as a verb?), we've decided to provide the XNAT Workshop virtual machine without snapshots. This is due to limitations in VMWare Player and the snapshots making the virtual machine incompatible with VirtualBox. The next section of this post has been updated to reflect the availability of VirtualBox as an alternative for the virtualization platform.
The next issue is the virtualization platform for the virtual machine. The following products are commonly available:
- For Windows, VMWare offers the free VMWare Player
- If you have a license or want to use a trial version, the more full-featured Windows product from VMWare is VMWare Workstation
- For OS X, VMWare has a trial (non-free) version of VMWare Fusion; note that this has some fairly specific system requirements, including Intel-based 64-bit OS X 10.6.7 or later (including Lion)
- For Windows, Linux, and OS X, you can use the free VirtualBox product
All of the VMWare products, including the free and trial versions, require you to create an account with VMWare to download the installers. If you want to use one of the VMWare products, you should register and install before coming to the workshop!
We are providing the virtual machine in the VMX format for VMWare products. That means that, if you choose to use a VMWare product, you'll automatically get the default hardware settings and be able to open the VM directly. If you use VirtualBox, you'll need to create a new machine instance and use the virtual disk (vmdk file) from the XNAT Workshop virtual machine.
We plan on making the virtual machine itself available on the NRG FTP site ahead of time. Stay tuned for the URL for this if you'd like to get the VM installed before arriving as well (find out how to subscribe to this wiki space).
It's worth noting that we're planning on using the Monday lunch period to complete VM installation and configuration and resolve any issues that might arise, so we won't be mean to you if you don't have all of this done beforehand. We're just trying to help everyone get as prepared as possible to free up our time for the more meaningful XNAT-specific work we hope to do!
As you may have noticed, we have been migrating our XNAT Documentation over to Confluence over the past month, which is giving us a lot of flexibility. For example, we can use Confluence "spaces" like XNAT Admins use Projects, to manage permissions and invite collaboration from multiple sets of users.
However, there is also a learning curve and a lot of new quirks to get used to. One of them - the means of changing your password isn't readily apparent. (You'd think there would be a handy link right in the "Profile" section, wouldn't you?) So for anyone who has been wanting to do this, here is the link you should use:
Clicking this link takes you to a form that allows you to set a new password for yourself. You'll face one more bit of user confusion first, though:
The "Reset" button doesn't reset the form, as in most HTML form conventions ... it's the command you have to click to Submit your password-reset function. (It's also in the wrong place... Submit buttons should be placed on the right, not the left.)
We'll continue to post to the XNAT discussion group when major updates are posted to the workshop wiki. But if you prefer more timely updates or just want to be able to monitor the wiki through your favorite news feed reader or the like, well... that's pretty easy to do.
All of the different ways of subscribing are described in excruciating detail in the Atlassian Confluence documentation. For convenience, though, here's the basic procedure:
- Create a user account on the workshop wiki.
- Once you're logged in, go to the Browse->Advanced menu command.
- Look down at the lower-right corner to see the Subscribe panel:
- To subscribe to all updates to the 2012 XNAT Workshop space, click the Start Watching This Space link.
- To subscribe just to blog posts in the space, click the Start Watching Space Blogs link.
- To get updates in a news feed or RSS viewer, click the RSS Feeds link. The available RSS feed links will be displayed, which you can just enter into, e.g. Google Reader, Flipboard, or whatever RSS viewer you prefer.
We're still working on the last bits of logistics around the 2012 XNAT Workshop, but the basics are fairly well set. The workshop sessions will be held at the Farrell Learning and Training Center on the Washington University School of Medicine campus. Most of the sessions will be held in the Connor Auditorium, with some break-out and technical sessions taking place in common areas outside the auditorium. In addition, there will be off-site after-hours events at restaurants in the near-by Central West End neighborhood of St. Louis (details for these are pending and will be provided before the start of the workshop; most likely there will be a dinner on Monday and happy-hour on Tuesday after the end of the workshop sessions).
There are three separate tracks available at the workshop:
- The PI track, held on Monday, is intended to give a big-picture overview of XNAT and its capabilities. This will include discussions of projects that use XNAT, XNAT's capabilities including a new feature review of XNAT 1.6, and discussion of XNAT's roadmap for future development efforts.
- The administrative track, which will run Monday through Wednesday, is intended to provide a practical, somewhat technical perspective on the practical implementation and use of an XNAT installation. This will include managing the data structures in your installation–i.e. creating and managing projects, subjects, and users, access management, anonymization and de-identification–as well as extending and customizing XNAT, with the addition of standard and custom data-type extensions, REST API extensions, scripting, interface modifications, and so on.
- The developer track closes out the week on Thursday and Friday. This will be very free-form and consist of groups of developers cooperating on various projects, including requirements for specific XNAT installations, custom data-type or interface development, and packaging of share-able data types for inclusion on the XNAT Marketplace. The XNAT development team will participate in all of these groups and be available for discussions of coding issues as well as the technical details of existing features and new features in XNAT 1.6.
Based on the incoming registrations, it looks like we'll have a pretty large overlap between the administrative and developer tracks, so that's pretty nice. We'll have some real experts out in the field once the dust has cleared!
There will also be some optional lunch-time sessions each day of the administrative track:
- Monday, we're planning on having workshop participants do "blitz sessions": short presentations on the work you're doing, how you're using or planning to use XNAT, and the various challenges and requirements you either anticipate or have overcome in the process.
- Tuesday, we'll have a presentation from NRG's in-house IT team on best practices for standing up and maintaining large-scale XNAT installations, from stem to stern.
- Wednesday, we'll be discussing the XNAT development roadmap, from 1.6 to 1.7 to 2.0 and beyond.
Watch out for posts later today or early tomorrow about:
- The virtual machine we'll be providing for workshop participants and how to take greatest advantage of it.
- Participating in our lunch-time blitz sessions: how to let us know you'd like to present, the format and restrictions for your presentation, and so on.
If you attended the previous XNAT workshop in 2010, or maybe watched some of the videos on the XNAT documentation wiki, you might expect the same sort of traditional lecture presentation: someone talking, with a few examples, everyone else taking notes. But we decided to go instead with what we hope to be a more engaging and practically oriented format this time around. We've also timed the workshop to map closely to our 1.6 release schedule. This means that the workshop will be a great time to engage with the XNAT development team if you're just learning about XNAT, but should also be valuable for our existing users to learn about many of the new features in XNAT 1.6.
The format of the workshop will be oriented around solving a problem with XNAT 1.6. In this case, you'll take the role of a system administrator responsible for rolling out a new XNAT installation to host the BOGUS (Big Open Group Unified Study) project. This will include:
- Defining project requirements
- Creating and installing data type extensions (including the use of community-created data types through modules on the XNAT Marketplace)
- Configuring projects and protocols for the study requirements
- Enabling and customizing site-wide and project-specific anonymization scripts
- Entering and uploading data into the system
- Processing data and creating resource reconstructions with pipelines
- Searching and advanced searching
- Reporting and analysis
All of this will be presented in a step-by-step scenario where you'll get to work hands-on to implement each stage of the project. XNAT developers will be available to work through any issues that arise and the virtual machines provided as part of the workshop collateral will have snapshots that will capture a "clean" implementation of each step as well.
We're excited about this practical approach to presenting XNAT and also eager to get the cool new features in the latest release of XNAT 1.6 into people's hands. The 2012 XNAT Workshop should be a great way to come up to speed on all of these and may help even experienced XNAT hands learn something new!