Last modified:March 19, 2025

Data analysis

command line interface

The command line is a text interface for interacting with a computer.

• command line
• shell script
• iteration
• useful commands

scientific applications

Most 3rd party software is located in /usr/local.

To find software, use the which command.

• MATLAB
  • Software availability
  • Compatibility
  • Graphics
  • SPM
  • Toolboxes
  • PC Installation
• FSL
  • Installation
  • X2Go display problems
  • Tutorial
  • Documentation
• FreeSurfer
  • Configuration
  • Tutorial
  • Documentation
• Python
  • modules
  • Jupyter Notebook
• R Project
  • rstudio
  • packages
• AFNI
  • version

Grid Engine

Grid Engine is batch processing software that queues and schedules jobs, so you can efficiently use computing resources, and analyze data in parallel.

• how to use SGE
  • run a job with a memory reservation
  • analyze data in parallel
• commands
  • qsub
  • qload
  • qdel
  • qstat
  • qacct
• memory reservation
  • determine memory requirement
  • reserve memory
  • modify reservation
  • restricted access
• troubleshooting
  • qstat
  • qquota
  • qstats
  • log files
  • qmem
• additional resources