Dear Consortium Members and Affiliates,
What it is, my peoples!? This is your SBGrid newsletter.
Hopefully many of you tuned into the Schrodinger and SHARP/autoSHARP webinars that were held during the last few weeks. Those were the last webinars for the summer season. We will soon begin planning for the fall webinar lineup, so please let us know if there is a software application or developer you would like to learn more about.
Registration for the July 27th Phenix Workshop is closed, and applicants should be hearing from us shortly. Stay tuned and keep an eye on our website for more information.
Pawel Penczek is the lucky subject of the latest structural biology tale on the SBGrid website. His application for cryo-EM image analysis, SPARX, is available as a part of the EMAN2 installation.
The July renewals for SBGrid Consortium memberships are fast approaching and most of the renewal invoices have been sent out by now. Please keep in mind that generous discounts apply for multiple labs at the same institution, so please contact us at accounts@sbgrid.org if there are any other labs at your institute interested in SBGrid membership. We can revise your invoice if new labs have plans to join by July 1.
OS X 10.8 was announced at Apple's World Wide Developer Conference this month, and its tentative release is scheduled for this fall. With that information in mind, we will be dropping OS X 10.5 support in the next few months, so please update your older Intel Macs to a newer release. On a related note, if you have decomissioned the last of your PowerPC Macs, please email us at bugs@sbgrid.org to request removal of the powermac software branch. It will save you some disk space and speed up the updates for everyone. Thanks!
On another related note, we have seen the ratio of 32 to 64-bit Linux workstations move from 60-40 in favor of 32-bit to 80-20 for 64-bit over the last 18 months, and we can see moving the 32-bit Linux branch into maintenance mode (i.e. no updates, only bug fixes) within the next 12 months. Please keep this in mind as you update your Linux workstations and servers.
Last night's update was mammoth in size, and it's still ongoing for some sites. It includes new versions of the Schrodinger Suite, PHENIX, XPLOR-NIH, NMR relax, Rosetta, NAMD, EMAN2 and XMIPP as well as the new applications SIMPLE and XDSAPP.
See ya later, alligators.
New Members
We have had more than 25 new labs join in the last few months! That's quite exciting.
Bernd Reif and Dierk Niessing are new members affiliated with the Technical University of Munich.
Nine labs at the University of Texas Southwestern Medical Center joined us this month: Yuh-Min Chook, Johann Deisenhofer, Meewhi Kim, Xin Liu, Zbyszek Otwinowski, Michael Rosen, Daniel Rosenbaum, Hongtao Yu and Luke Rice.
Wes Sundquist at the University of Utah.
Four new members at LaTrobe University in Australia: Begonas Heras, Megan Maher, Matthew Perugini and Brian Smith.
Gaya Amarasinghe at Washington University School of Medicine.
Meng-Chiao Ho at Academia Sinica in Taiwan.
June Medford at Colorado State.
Craig Bingman at the University of Wisconsin.
And six new members at the University of Iowa: Mishtu Dey, Ernie Fuentes, Lokesh Gakhar, Rob Pipe, Miles Pufall and Madeline Shea.
Welcome to all of our new members!
Software Updates
The following software updates will be available later tonight or tomorrow:
Linux and Mac OS X Intel
The Schrodinger Suite has been updated to version 2012-1. There is a new Consortium license for this application, and it includes 125 general purpose license tokens and 40 dedicated GLIDE tokens. We are working to set up GLIDE docking runs on a cluster hosted here at HMS and should have that running shortly. We have also set up a Schrodinger users mailing list for coordination of license access, news and other updates. At least one person at each site using Schrodinger should sign up for this list.
This new Schrodinger release includes support for OS X for the first time, but note that the OS X version does not include Desmond.
PHENIX has been updated to the latest release version 1.8-1069. The change log has details on the numerous new features and bug fixes. The excellent PHENIX documentation is online as well.
XPLOR-NIH has been updated to version 2.31. Charles Schwieters, the developer, maintains a nice change log listing bug fixes and new features as well as other documentation.
relax has been updated to version 1.3.16. This is probably the final release in the 1.x branch and future development efforts will concentrate on the 2.0 release. The relax website has the usual bits.
Rosetta has been updated to version 3.4. There is a list of new features and a manual on the Rosetta website.
NAMD has been updated to version 2.9. The enormous NAMD website has details, docs and more.
EMAN2 has been updated to version 2.05. Have fun digging through the voluminous EMAN2 website.
SIMPLE is a new application for single-particle image processing that does ab initio 3D reconstruction, heterogeneity analysis and high-resolution refinement. A workflow reference and manual can be found on the SIMPLE website.
XDSAPP is another new application purporting to be an easy to use graphical interface to the power of XDS. Version 0.21 is installed. There is a short help file on the XDSAPP website.
Linux
XMIPP has added version 3.0 for 32 and 64-bit linux. The OS X version should follow in the coming months. This new version is still somewhat unstable and we have not yet made it the default, but if you're interested in the new features and tools in XMIPP 3.0, you can test it out with a ~/.sbgrid.conf override file.