Computational Resources: |
To quote from a document describing IU's cyberinfrastructure, "Indiana University has a cyberinfra-structure that is among the best at any university in the world, including supercomputers, data storage systems, visualization environments, and access to high performance research networks." These resources are freely available to IU students, staff and faculty and our facility makes extensive use of them as an integral part of its operation.
The JEOL JEM 3200FS writes images and spectra to the WAN area of the IU Data Capacitor, a large capacity (~400 terabyte) Lustre filesystem providing high-speed and high-bandwith communication for all the IU campuses and for TeraGrid users. At the end of each day, newly recorded data are backed up to the Massive Data Storage Service (MDSS), a very large (~4 petabyte) redundant storage system available to IU faculty, staff and graduate students.
The Data Capacitor is also mounted on the IU supercomputing systems Quarry and BigRed. All users of the 3200FS will need to obtain an account on Quarry in order to access data collected using the 3200FS. We have worked with the High Performance Applications group of IU Research Technologies to install an assortment of image processing software on these systems. To make accessing these programs as easy as possible, we have also created a SoftEnv working environment for our users. Setting up the SoftEnv environment to access data and to use these programs is described elsewhere.
The following programs or packages are currently installed on Quarry:
- auto3dem - highly parallelized package for icoahedral virus images from Tim Baker's lab at UCSD
- Bsoft - Bernard Heymann's suite of programs for image processing
- CCP4 - Software for Macromolecular X-Ray Crystallography (along with programs like phaser, coot, clustalW and Fasta)
- electra - Giovanni Cardone's resolution estimating software (v 0.5.6) for tomography (fsceo and nloo)
- EMAN1 - package for single particle images from Steve Ludtke and others at NCMI
- imageJ - the image display and manipulation program developed at the NIH
- IMOD - David Mastronarde's tomography software from the Boulder Laboratory for 3-D Electron Microscopy of Cells
- MRC Image2010 - the MRC Cambridge Image Processsing System for the analysis of 2d crystals, electron diffraction patterns, helical structures, etc.
- SPIDER - program for single particle images from Joachim Frank's group at Albany & Columbia
- Xmipp - package for single particle images from the Biocomputing Unit at the Centro Nacional de Biotecnologia (CNB) in Madrid
We hope to have these programs running on BigRed in the future and also to add the following packages:
- 2dx - Henning Stahlberg's GUI for the MRC's 2d crystallography software
- frealign - Niko Grigorieff's program for high-resolution refinement of single particle EM structures
- UCSF chimera - extensible program for interactive visualization and analyis of molecular structures
In addition to the computational resources described here, we are also assembling a series of tutorials that use these programs. They are intended to be a way to gain hands-on experience with some of this image processing software.
In addition to these image processing programs, we are also attempting to make it as simple as possible for users to access these computational resources. Towards this end, we have created a series of GUI's that will launch certain types of image processing jobs to the queue manager on Quarry. This is all described elsewhere.
Please send suggestions for additional software and any questions about things described on this page to the director of the cryoEM facility.
Note: Users may also want to have these image processing programs running on computers in their labs (and visualization tools available on personal laptops). Please contact the director about the details involved in purchasing an appropriate computer if necessary, setting up programs so they are as compatible as possible with the software on the clusters. etc.
