To quote from a document describing IU's cyberinfrastructure
"The cyberinfrastructure at Indiana University is among the best at any university in the world. Its supercomputers, data storage systems, visualization environments, and access to high performance research networks are intended to help you, the researcher, achieve breakthroughs in your scholarship by making possible new calculations, analyses, and visualizations of massive amounts of data."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 Scholarly Data Archive (SDA), 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, Big Red, Mason and Big Red II. 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 Scientific Applications and Performance Tuning group of the IU Pervasive Technology Institute to install an assortment of image processing software on these systems. To make accessing these programs as easy as possible, we have created a Modules working environment on Quarry for our users. Setting up the Modules 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 & EMAN2 - packages 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.
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 David Morgan.
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 David 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.