» Welcome to sun.cs.lsus.edu «

This Linux server is for use by LSU-S students and faculty. This is a growing system, so please check back with this page often. To access this system we ask that you use Secure Shell (ssh). Secure shell clients typically come bundled with Linux/Unix operating systems and Mac OS X. To access this server using Windows, you can download a non-commercial version of the SSH Workstation client from http://www.ssh.com. If you are using a Linux or Unix-like operating system that does not come with ssh, it can be obtained from the OpenSSH Project along with documentation.

Along with standard GNU utilities, you will find the following software:

• Emacs - GNU Emacs 21.3.1 and XEmacs 21.5.18
  
  Emacs is a popular and versatile text editor with useful programming features. Two implementations of Emacs have been installed: GNU Emacs and XEmacs. Both GNU Emacs and XEmacs have X Window and terminal support. If Emacs finds that you have X Window running (and the $DISPLAY environment variable set), it will automatically launch the graphical version.
  
  To run GNU Emacs: emacs <file>
  To run XEmacs: xemacs <file>
  
  Emacs includes a built in tutorial and extensive help system. To run the tutorial, type <Ctrl>-h followed by t. Emacs denotes this key command as C-h t. If you are running Emacs under X Window you can select Emacs tutorial from the Help menu.
  
  
• Sun Java 1.4.2 and Sun Java 1.5.0
  
  

  Note about using Java 1.5:  Java/JDK 1.4.2 is the default version installed on this machine.  If you want to access Java/JDK 1.5, you will need to add it to your PATH environment variable before the entry to the default Java path: Bourne based shells (bash, zsh): PATH=/usr/lib/jvm/java-1.5.0-sun/bin:$PATH export PATH C shells (tcsh, csh): set path=( /usr/lib/jvm/java-1.5.0-sun/bin $path )

  
  
• Intel 32-bit C/C++ compiler and debugger 9.0 for non-commercial use
  
  This software is installed in /opt/intel/cc/9.0 and /opt/intel/idb/9.0, respectively.
  
  For more information, type man icc
  
  
• gnuplot 4.0 and gnuplot 4.1-development
  
  Currently gnuplot 4.0 (stable) and gnuplot 4.1 (development/beta) are installed.  By typing gnuplot on the command line, gnuplot 4.0 will launch.  gnuplot 4.1 is installed as /usr/local/bin/gnuplot.   If you wish to use gnuplot 4.1 you must type it's full path /usr/local/bin/gnuplot.
  
  For more information on gnuplot, visit http://www.gnuplot.info
  
  
• Imagemagick 6.1.8
  
  For more information visit imagemagick.org
  
  
• R version 2.2.1
  
  R is a software package for statistical computing and graphics.  For more information about R and to obtain manuals for using R, please visit http://www.r-project.org
  
  
• JGR 1.3 - Java GUI for R
  
  JGR (a.k.a "Jaguar") is a graphical user interface for the R package using Java. To run JGR, type run-jgr while running an X environment.
  
  
• ParaView
  
  ParaView is "an application designed with the need to visualize large data sets in mind". It is installed under /usr/local. For more information please visit http://www.paraview.org
  
  
• OpenDX
  
  OpenDX is an "open source software project based on IBM's Visualization Data Explorer". It can be found under /usr/local/dx. For more information please visit http://opendx.org/
  
  
• Weka 3.4.7
  
  From http://www.cs.waikato.ac.nz/ml/weka/: "Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code."
  
  For more information, visit http://www.cs.waikato.ac.nz/ml/weka/
  
  
• POV-Ray 3.6.1
  
  POV-Ray is installed as /usr/local/bin/povray .  You can get more information on using povray by typing man povray or by visiting http://www.povray.org.
  
  

Biomedical Informatics

• BioConductor release 1.6
  
  BioConductor is an open source software package for the analysis of genomic data.  For more information on BioConductor please visit http://www.bioconductor.org.
  
  
• RNAhybrid 2.1
  
  "RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA."
  - from http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/
  
  RNAhybrid is installed on sun as /usr/local/bin/RNAhybrid. Under /usr/local/bin you will also find RNAeffective and RNAeffective.
  
  
• Gnome Data Mine Tools (gdatamine)
  
  "The gnome-datamine-tools is a growing collection of tools packaged to provide a freely available single collection of data mining tools."
  - from http://www.togaware.com/datamining/gdatamine/
  
  These are installed under /usr/local/bin as gdmapriori ,gdmbayes, and gdmdtree.
  
  The Gnome Data Mine Tools can be obtained from http://www.togaware.com/datamining/gdatamine/
  
  
• AlignACE and CompareACE
  
  "AlignACE (Aligns Nucleic Acid Conserved Elements) is a program which finds sequence elements conserved in a set of DNA sequences"
  - from http://atlas.med.harvard.edu/download/index.html
  
  These are installed under /usr/local/bin as AlignACE and CompareACE. More information on AlignACE and CompareACE, including how to download them, can be found at http://atlas.med.harvard.edu/download/index.html.