Dear Consortium Members and Affiliates,
The November software update is happening this evening and includes updates for Jalview, IMOD, 3DNA, DSSP and iMosflm as well as two new applications, ARIA and EMAN2. For labs with IMAGIC licenses, please watch for an additional email with details on our new IMAGIC configuration process.We would like to highlight the 3DNA build, because it was our first collaboration with an external software developer where we offered access to our hardware for development purposes. We have a network of machines configured for building and testing software across multiple Linux and OS X versions, and we are in the planning stages of making this network available to external developers of scientific software. Please contact us if this is a service that might be of use in your software development efforts.
We are also pleased to announce that the latest hardware revision of the SBGrid Scientific Workstation is now available. See below for more details.
We expect the next update to happen on December 17th.
Our latest workstation features the 64-bit Intel Core 2 processor starting at 2.66GHz and is available with either dual or quad core options up to speeds exceeding 3GHz. Included is an Intel motherboard with the X48 chipset for excellent stability and compatibility. Onboard Gigabit ethernet, USB 2.0, and Firewire are standard. The workstation features DDR3-1333 RAM capable of delivering over 20 GB/s of bandwidth. Configurations include either 4GB or 8GB of memory. For 3D stereo support, NVIDIA Quadro FX cards are available utilizing the high speed PCI-E 2.0 interface. A DVD writer and 250GB Hard drive are standard, as are serial ports for compatibility with SGI dials. All of this is available in a quiet mid-tower case with a high quality Antec power supply.
We have tested the system with the CentOS 5.2 Linux distribution. CentOS 5.2 installs without difficulty and correctly detects and supports all the hardware in the system. With an NVIDIA Quadro card and their proprietary drivers, stereo is fully supported for applications like Coot and O.
To view the complete system specifications and for ordering info, please see our informational PDF.
The following software updates will be available later tonight:
Linux and Mac OS X (PPC and Intel)
Jalview has been updated to version 2.4. This new version offers a host of new features and many bug fixes. Full details can be found in the release notes as well as documentation and the FAQ.
EMAN2 is a new installation. This is a nightly release from late October and includes the SPARX toolkit for Cryo-EM image processing. Note that EMAN2/SPARX is under heavy development right now, and this release probably includes some bugs. The OS X versions only run under OS X 10.5 or higher. SPARX information can be found on the SPARX wiki and EMAN2 documentation can be found on the EMAN2 home page.
IMOD has been updated to version 3.11.5. This version should fix a bug related to eTomo that was causing it to crash in our environment. Release notes and documentation are available on the website.
Linux and Mac OS X Intel only
CNS has received a bug fix update for version 1.21. The CNS website is at its usual place.
Mac OS X Intel and PowerPC only
DSSP has been updated to version 20060404. This is mostly a bug fix release to bring the software up to date for all supported platforms. Details including a user guide are available on the DSSP website.
iMosflm, the new Mosflm graphical interface, has been updated to version 1.0. The 1.0 release has almost all the functionality of the old X11 based ipmosflm GUI. Documentation, including a tutorial and the full guide, are on the iMosflm website. This is currently a linux-only application due to some difficulties integrating the required Tcl/Tk modules into the SBGrid environment, but we are working toward having this application available on OS X in the near future.
ARIA version 2.2 is a new program for SBGrid. ARIA (Ambiguous Restraints for Iterative Assignment) is software for automated NOE assignment and NMR structure calculation. It automates the assignment process through the use of an iterative structure calculation scheme. Additionally, a refinement in explicit water improves the quality of the calculated structures, validation tests help spectroscopists to judge the quality of the final structures, and the support of the CCPN data model simplifies the exchange of information with other NMR software packages. The ARIA website has more details.
Mac OS X Intel only
3DNA version 1.5 is now available on the OS X Intel platform. This build brings the OS X Intel platform into parity with our other supported platforms. The 3DNA usage notes and FAQ are available on the website.