Dear Consortium Members and Affiliates,
We are hosting the annual meeting of the Open Science Grid Consortium at Harvard Medical School next week (ahm.sbgrid.org). This event will include workshops on grid computing technologies, discussion panels on future of US and Global Cyberinfrastructure and biomedical computing symposium. Close to 150 research computing specialist from dozens of US institutions registered to attend. Please visit the ahm2011 website for more information.
We've made a major revision of the SBGrid setup script and configuration files. Overriding the version of a program can now be done through ~/.sbgrid.conf instead of ~/.sbgrid.sh or ~/.sbgrid.csh. The biggest advantage for users of the new system is that it checks for correctness, ensuring that the version you ask for actually exists and is available. For the moment, this is enabled for Bash users by default, and csh/tcsh users can enable it by creating the ~/.sbgrid.conf. In addition, site admins can create site-specific or machine-specific overrides. Full documentation is available on the SBGrid wiki.
The update this month includes new versions of Python, NumPy, SciPy, Raster3D, NMRPipe, NMR Relax, ADXV, and Theseus. It also adds the new packages TiltPicker, PyRosetta, CS-ROSETTA, and CatDCD, as well as the VMD plugin Cionize.
New Members
The Wucherpfennig Lab at Dana-Farber Cancer Institute is our newest member!
Software Updates
The following software updates will be available tonight or tomorrow:
Linux and Mac OS X (PPC and Intel)
NMRPipe has been updated to the latest version. The NMRPipe website has the usual information.
ADXV is now at version 1.9.7. ADXV's website has more information on the new release.
CatDCD is a new addition, at version 4.0. It is a simple utility that functions similarly to the Unix 'cat' command; it concatenates multiple DCD files into a single DCD. The standard information is available at CatDCD's website.
OS X Intel and Linux
Python has been updated to version 2.7. This major update includes most of the plugins that are available in our previous version of Python, and it should work with all of our software, but mistakes do happen. Don't hesitate to let us know if it breaks something!
NumPy has been updated to version 1.5.1 as a part of the new Python. The NumPy website has an updated manual for the new version. Requested by members at Alber Lab.
SciPy has been updated with NumPy, and is now at version 0.9.0rc1. The SciPy website has information on the new release. Also requested by members at Alber Lab.
PyRosetta is a new package for the software suite. PyRosetta is an interactive, Python-based interface to Rosetta. Documentation and other information is available at the PyRosetta website.
CS-ROSETTA is another new addition. According to the author, "To date, interpretation of isotropic chemical shifts in structural terms is largely based on empirical correlations gained from the mining of protein chemical shifts deposited in the BMRB, in conjunction with the known corresponding 3D structures. Chemical-Shift-ROSETTA (CS-ROSETTA) is a robust protocol to exploit this relation for de novo protein structure generation". More information is online at the CS-ROSETTA website
NMR Relax has been updated to version 1.3.10. This is a new feature release, and adds support for reading PDC files. More information is available at the Relax website
Theseus is now at version 1.6.1. The Theseus website has the usual info.
Raster3D has been updated to version 3. The new version now has dynamic allocation for large structures and internal handling of labels. More info at the Raster3D website.
Linux
TiltPicker is a new addition to the distribution. TiltPicker is a graphical interface for "picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR)". Additional information is available at TiltPicker's website.
Bug Reports
SPIDER on Linux was mistakenly missing the "web" utility. We've updated the scripts involved and added a symlink to fix the issue. Thanks goes to Fred at IBS Grenoble, Desiree and Sabuj at Vanderbilt, and Andreas at Walz for pointing this out.
Thanks for your bug reports!
Dear Consortium Members and Affiliates,
Howzya! The barest hints of Spring are poking through here in Boston, and now they are predicting snow storm for April 1st. Yay! We have a quick software update for you this month that includes a few changes to the shell initialization files, some changes to our supported operating systems policy and a licensing change for SHELX users. Read on for details.
We have moved to the new ~/.sbgrid.conf file for all software version overrides and SBGrid-specific shell settings for both sh and csh-based shells. You can find the details and some hints on how to use this functionality on the version overrides wiki page. We have also added an option to hush the license message during shell start up in order to reduce screen clutter.
Also new for this month we have added Red Hat 6 to our supported operating systems list. We have also slightly amended our official support policy for Linux distributions. We still use and recommend CentOS, Red Hat and Fedora-based systems; we build and test the scientific software on these distributions, and the majority of our Linux users are using one of these distributions. But we also have labs using the software with Ubuntu, Debian and OpenSuSE. While we don't explicitly test the software on these distributions, it is known to work, and we will work to resolve problems reported by users of these Linux distributions. So please open tickets if you encounter software problems one of these other Linux distributions.
With the addition of Red Hat 6 and the soon to be released CentOS 6, we are announcing the end of life for Red Hat 4 and CentOS 4 support. Within the next 60 days, we will stop building and testing on these distributions. Existing software will continue to work, but we will not generally be adding new packages or updating existing software for these platforms. Please plan accordingly.
George Sheldrick has asked that we not include SHELX with the default SBGrid installation. If you want us to support SHELX with your SBGrid installation, please ensure that you are in compliance with the SHELX licensing requirements. Once you have faxed or mailed the completed license form, let us know, and we will add SHELX to your installation. We apologize for the inconvenience.
The update this month includes a number of updates to existing packages, including ATSAS, Coot, EMAN2, NMRPipe, PHENIX, PyMOL, SPIDER, and xia2, as well as a new addition called Phoelix. This update also includes the Coot plugin RCrane developed by Kevin Keating of Yale's Pyle Lab.
Software Updates
Linux and Mac OSX (PPC and Intel)
NMRPipe has been updated to version 20110228, hot on the heels of the previous release. NMRPipe's website has more information.
XIA2 is now at version 0.3.3.0. This release has quite a few bug fixes and now checks your input for mistakes. Check XIA2's website for the usual information.
Coot is updated to revision 3440 for Linux and revision 3427 for OS X. Documentation is available at Coot's website. Requested by the Mayer Lab at NIH. We have created an option for you to use the new PDB version 3 monomers with Coot. Add the line "COOT_USE_NEW_DICT=true" to your ~/.sbgrid.conf file and Coot will honor that option during start up. For more information on version overrides and shell settings for the SBGrid environment, please see the wiki page.
OS X Intel and Linux
The PHENIX nightly build is now at dev-697. To use this version you will need to explicitly enable nightly builds in your ~/.sbgrid.conf file. The PHENIX site has the usual documentation. Also requested by Mayer Lab.
SPIDER was updated to 19.04. This adds a new operation for "denoising using mean shift." Go to the project's site for additional information.
EMAN2 is now at version 2.01. That's right, it has finally hit 2.0. Their website has documentation and more.
PyMOL now has version 1.4 available. This version is native 64-bit, giving users access to more than 4 GB of memory. Due to compatibility issues, version 1.3 remains the default on all platforms. Try it yourself by enabling it in your ~/.sbgrid.conf file. PyMOL's site has more on this release.
Linux
Phoelix is a new addition to the SBGrid software tree. According to the authors it is intended for "image processing of helical macromolecular complexes." You can find more information through Phoelix's website.
RCrane is a Coot plugin by Kevin Keating. RCrane "allows for accurate and semi-automated building of RNA structure into electron density maps." Neat! This is a pre-release build, and is currently only functioning with the newest versions of Coot. SBGrid is proud to work with Kevin to distribute his work.
OS X Intel
ATSAS is now at version 2.4.0. Visit the ATSAS website for release information and other docs.
Bug Reports
Raster3D's "render" program on OS X was not properly linked against its dependencies. This is now fixed, and should operate normally. Thanks to Patricia Amara of IBS Grenoble for pointing this out to us.
EMAN doesn't work with Python 2.7, and it is now forced to use Python 2.5. Kudos to Brad Battey of Skiniotis Lab for the help.
WXPython was broken in Python 2.7 on Linux due to some missing libraries. Those libraries are now in place. Special credit goes to Sabuj Pattanayek of VCSB for helping us resolve the issue.
Thanks to everyone who submits bug reports and helps us make SBGrid better.