Computation

Computational Resources

To quote from a document describing Indiana University'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.

At present, the vast majority of these resources are intended to be used with images acquired using the JEOL JEM 3200FS and FEI Teneo VolumeScope. However, we hope to include images from the JEOL JEM 1010 and the JEOL JEM 1400plus into our computational framework in the future.

The 3200FS and Teneo save images and other data to the WAN area of the IU Data Capacitor, a large capacity (~340 terabyte) Lustre filesystem providing high-speed and high-bandwidth communication for all the IU campuses and for XSEDE users. Every few days, all the newly recorded data are backed up to the Scholarly Data Archive (SDA), a very large (~15 petabyte) redundant storage system available to IU faculty, staff and graduate students.

The Data Capacitor is also mounted on the IU supercomputing systems Karst, Carbonate and Big Red 2. All users of the 3200FS and the Teneo will need to obtain an account on Karst in order to access data collected using the 3200FS.

Obtain a Karst account

Obtain additional computer accounts

We have worked closely with the Scientific Applications and Performance Tuning group of the IU Pervasive Technology Institute both to archive images acquired in the EMC and to install an assortment of image processing software on these systems.

Read more about EMC's Scalable Compute Archive (EMC-SCA)

To make accessing the programs on the IU cluster as easy as possible, we have created a Modules working environment on Karst for our users. For use of this software on other clusters such as BigRed 2 or Carbonate, contact David Morgan at dagmorga@indiana.edu.

Get Help Setting Up the Modules Environment to Access Data

The following programs or packages are currently installed on Karst (and some are available on either Carbonate or BigRed 2):

  • auto3dem - highly parallelized package for icosahedral virus images from Tim Baker's lab at UCSD
  • Bsoft - Bernard Heymann's suite of programs for cryoTEM image processing
  • cisTEM - Niko Grigorieff's image processing GUI for high resolution refinement of single particle EM structures
  • CCP4 - software for macromolecular X-ray crystallography (along with programs like phaser, coot, clustalW and Fasta)
  • UCSF chimera - highly extensible program for interactive visualization and analysis of molecular structures
  • electra - Giovanni Cardone's resolution estimating software (v 0.5.6) for tomography (includes fsceo and nloo)
  • em2em - stand alone file conversion program from Image Science's Imagic package
  • eman1 & eman2 - packages for single particle images from Steve Ludtke and others at NCMI (note that eman1 is no longer being updated)
  • frealign - Niko Grigorieff's program for high-resolution refinement of single particle EM structures (new frealign versions are currently tied to cisTEM)
  • 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 Medical Research Council Laboratory for Molecular Biology's (MRC-LMB in Cambridge, UK) image processing package for the analysis of 2d crystals, electron diffraction patterns, helical structures, etc.
  • phenix - software suite for the automated determination of molecular structures using X-ray crystallography and other methods
  • R modules - custom modules for the statistical computing and graphics package R that are used by various scripts written for Karst
  • relion - package for single particle images from Sjors Scheres at the MRC-LMB (Cambridge, UK)
  • scipion - GUI-based working environment from the Biocomputing Unit at the Centro Nacional de Biotecnologia (CNB) in Madrid (and other contributors) that integrates many of the image processing programs listed here into a unified, user-friendly environment
  • Sculptor - program for multi-resolution docking and visualization
  • Situs - program for modeling atomic resolution structures into low resolution density maps (i.e., the sort of data generated by cryoTEM, tomography and small angle X-ray scattering studies)
  • 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 (note that new xmipp releases are currently tied to scipion)

We attempt to keep the programs listed here up-to-date, though we are often a release or two behind with the packages that offer frequent releases. You should be able to determine the version number of any of this software if you have an account on Karst, and if you need a different version for some reason, please contact David Morgan at dagmorga@indiana.edu.

We hope to have all of these programs running on Carbonate and Big Red 2 in the future and also to add other packages including:

  • 2dx - Henning Stahlberg's GUI for the MRC's 2d crystallography software

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.

Explore our Tutorials for Image Processing with Karst

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 managers on Karst, Carbonate and BigRed2.

Learn about Submitting Jobs to the Queue Manager using Karst

Note about lab and personal PC's: Individual users and/or labs 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 Morgan at dagmorga@indiana.edu about the details involved in purchasing appropriate computers if necessary, setting up programs so they are as compatible as possible with the software on the clusters. etc.

Additional Computational Resources

Digital Imaging and Graphics

Additional resources for digital imaging and graphics, including information on dm3 files, compressing images, sending graphics, and using the Scalable Computer Archive.

Karst Computer Cluster

Additional resources for the Karst computer cluster, including information on first-time logins, image processing with Karst, submitting jobs to the queue manager, and the Rappture graphical user interfaces.

Linux Help

Additional resources for Linux, including information on environmental variables, commonly used commands, reserved characters, and scripting within Linux.