You can now register for Python Programming for Scientists webinar here.
SBGrid Taster Webinar: *Computational Science with Python and Matlab*
Lecturer: Ian Stokes-Rees, Harvard Medical School
December 16th, 2010, 1PM-2:20PM, EST
This web-based course is a taster for scientists with little or no previous programming experience. In 80 minutes you will get a quick overview of the power of Python and Matlab to help you write scripts, process data, organize the execution of external programs, and visualize results. This will include a 20 minute exercise in the middle of the tutorial. Please install the Enthought Python Distribution in advance of the course.
Dear Consortium Members and Affiliates,
The Basics of Docking webinar went very well. We initially limited attendance to 25 members, but had so many applicants that we scrambled and found a way to add more seats for a total attendance of 40 people. Our next webinar will offer a broad overview of using Python and Matlab for scientific programming. This webinar is a taster for scientists with little or no previous programming experience. In 80 minutes you will get a quick overview of the power of Python and Matlab to help you write scripts, process data, organize the execution of external programs, and visualize results. Please install the Enthought Python Distribution in advance of the course. Space is limited so please register soon.
The linux PATH length in the shell has finally fully eclipsed the 4092 character limit of older versions of the tcsh shell. If you're getting a "word too long" error on shell initialization, this is the culprit. The fix is to update your version of tcsh to version 6.16 or newer. To facilitate that, we have built tcsh 6.17 RPMs for CentOS/Red Hat 4/5 32/64-bit and placed them in the software tree at /programs/i386-linux/system/RPMS. These RPMs are built from a combination of the Red Hat and Fedora patches and contain all the latest fixes for tcsh.
We are pleased to welcome a new member to the SBGrid team. Ben McClure joins us to work on the maintenance and improvement of the scientific software suite. Ben hails from Pennsylvania where he studied computer engineering at Penn State. With the additional manpower, we hope to cut down on the wait time for updates and new software requests. Ben's effects can already be felt as the update this month contains 23 software titles!
With the Christmas and New Years holidays fast approaching, we decided to go with a combined November and December update. The update this month includes new versions of 3DNA, HKL2000, MES (Minimal Ensemble Search), EMBOSS, Primer3, Priism (part of IVE), AMIGOSII, CCP4mg, IMP, EMAN2, Coot, CNS, YUP, surfv/surfcv, DynDom3D, NMRPipe, Suprim, Burnham-Brandeis Helical Package, GNU Plotutils, a PHENIX nightly release, Untangle, NMRView, Chimera and Surface Racer. Whew!
Merry Christmas and Happy Holidays!
New Members
Our newest member is Chung-I Chang working at the Academia Sinica Institute of Biological Chemistry in Taiwan. His lab is currently researching the interactions of pattern-recognition receptors (PRRs) with microbial ligands.
Software Updates
The following software updates will be available tonight or tomorrow:
Linux and Mac OS X (PPC and Intel)
3DNA has been updated to version 2.0. Manual, forums and more are on the 3DNA website. Requested by the Eichman Lab at Vanderbilt.
MES, the Minimal Ensemble Search tool, is a new package for us. This software is used for small angle x-ray scattering experiments as it searches for the minimal ensemble of the conformations from the pool of all input conformations using genetic algorithm. More info on the FOXS website and at the MES home page hosted at the LBL Beamline. Requested by the Kuriyan Lab at Berkeley.
EMBOSS has been updated to version 6.3.1. The gigantic EMBOSS home page has it all. Requested by the Harrison Lab at HMS.
Primer3, a tool for designing PCR primers that works in conjunction with EMBOSS, has been added to the tree. Requested by the Harrison Lab at HMS.
Priism is a "collection of tools for processing, analyzing, and visualizing multidimensional imagery with a focus on 3D wide-field optical microscopy and EM tomography" and is another new package in the tree. The Priism home page has documentation. Requested by the Ohi Lab at Vanderbilt.
AMIGOSII has been updated to version 1.0.1. Thanks go out to Kevin Keating in the Pyle Lab for letting us know about the update.
IMP, the Integrative Modeling Platform, is a tool for building hybrid methods of structure determination. This is a new package for the software tree, and the IMP home page has documentation, a wiki and some examples of how it can be used.
NMRPipe has been updated to release 20101030. The Big NMRPipe Reference Page has documentation, tutorials and more.
A PHENIX nightly version, dev-606, has been added to the software tree. This is not the default version, but you can select it in your shell using an overrides file. You can also the new version "nightly" in order to track the latest nightly version of PHENIX in the software tree. Requested by the Springer Lab at the Immune Disease Institute.
CNS version 1.3 has been updated to the latest patch set. The usual shout out to Axel Brunger for keeping us informed.
YUP, an implementation of the Yammp molecular modeling tool in python, has been added to the tree. The YUP home page has documentation and tutorials on how to use it. Requested by the Darst Lab at Rockefeller.
DynDom3D is a new version of the venerable DynDom package. There is a DynDom home page with some examples, but it doesn't have a ton of info.
GNU Plotutils is a new package for the tree. This plotting utility is used for viewing the output of many programs in the software tree.
NMRView has been updated to version 8.0rc43. Bruce Johnson is inexorably marching on towards an 8.0 final release, but we're not quite there yet. He has put up a nice NMRView manual along the way.
Surface Racer has been updated to version 5.0 for linux and both OS X branches. The readme in the program directory has some details on use, and the reference is on the Surface Racer home page.
OS X Intel and Linux
CCP4mg has been updated to version 2.4.3. Stuart McNicholas, the lead developer, has a nice gallery of images created with CCP4mg. Requested by the Sliz Lab at HMS.
EMAN2 has been updated to version 2.0rc3. The EMAN2 wiki is filling up with documentation and tutorials as well as lots of example images. Requested by the Kornberg Lab at Stanford.
Coot has been updated to a recent nightly build for both linux and OS X Intel. The new Coot home page is hosted at Paul Emsley's roost at Oxford University. Requested by everyone.
surfv/surfcv, tools for calculating solvent accessible surface areas, have been built (or rebuilt) to run under the latest OS X Intel and linux releases. The surfv/surfcv READMEs are online. Requested by Jeruzalmi Lab at Harvard University.
Suprim is a new package for the software tree. This package is used in the processing of transmission electron micrographs. While it's hosted at Scripps, it appears that the code is mostly orphaned and there is precious little documentation on it.
BBHP, the Burnham-Brandeis Helical Package, is a part of the Correlative Analysis (CoAn) suite developed at Burnham for "correlation-based docking of atomic models into lower-resolution densities generated by electron microscopy and image reconstruction". The CoAn web site has tutorials, documentation and more. Requested by the Leschziner Lab at Harvard University.
HKL2000 has been updated to version 700l1. This version runs on OS X Intel 10.5, and it is set as the default on both linux and OS X. The previous HKL2000 update turned out to be very buggy, so please let us know if you experience problems with this one. Requested by Vanderbilt, Tufts, Rosalind-Franklin.
Chimera has been updated to version 1.5. The gigantic website contains information on all things Chimera.
Linux
Untangle is a new package for the software tree. This software is used to "separate overlapping diffraction patterns from a set of crystals with slightly different orientations". Additional details are on the Untangle web site.
OS X Intel
The pure X11-based version of PyMOL for OS X Intel has been updated. This version contains the SuperSym plugin. Requested by the Mayer Lab at NIH.
Bug Reports
ARP/wARP's arp_solvent.sh script had a bug in it. Fixed with a patch from the ARP/wARP development group. Reported by Shiven Shandilya in the Schiffer Lab at Umass Medical.
SPIDER was crashing due to an environmental setting put in place by the CNS environment. Solved by adding wrappers for the SPIDER binaries. Reported by Berith Isaac, Po-Lin Chiu, Hui-Ting Chou and Natacha Opalka.
NMRPipe was crashing due to library conflicts found in the DYLD_LIBRARY_PATH. Resolved by tweaking the library path order so NMRPipe finds its preferred libraries. Reported by Remy Sounier, Chou Lab, HMS.
The CCP4 utility pdb_extract was missing its help file. The files were copied into place and all is well. Reported by Bryan Lepore, Van den Berg Lab, Umass Medical.
The CCP4 monomer library was missing a few files in the OS X versions that are available in the linux version. The missing files were copied to the OS X branches, so now the monomer library matches on all systems. Reported by Dave Gohara, DiCera Lab, St. Louis School of Medicine.
Our shell configuration scripts had an error that only evinced itself on OS X 10.4 hosts that had to do with how backslash escaping works in older versions of the bash shell. Fixed by tweaking the escape method to one that works on all hosts. Fun! Reported by Matt Whorton, Mackinnon Lab, Rockefeller University.
Thanks for your bug reports. Namaste!