What Runs Where on Athena - Full Table of Applications
Athena Help
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apropos
finds man pages containing key words
athinfo
supplies info about workstation
info
information browser for gnu software
locate
finds files by matching path components
man, xman
standard UNIX man page viewer
sendbug
bug reporting utility
stanley
supplies, updates information about a username
stella
supplies, updates information about a workstation
tellme
tells public workstation root passwd, Athena cluster combo
whichlocker
outland
tells which locker a program is in
yelp
Gnome help browser- misc applications, system man and info pages
Database
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LibreOffice Database
database component of LibreOffice office suite
mysql
mysql
mysql SQL client and server
psql (PostgreSQL)
PostgresQL database client
sqlplus (Oracle)
oracle10g
Oracle database SQL client
MIT Information
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Course Descriptions & Schedules
runs on Web
cview, xcluster
displays current Athena cluster usage
Humanities Enrollment Tools
Enrollment Tools on Web
Freshman Housing Lottery
lottery page on Web
Phys. Ed. Lottery
lottery page on Web
SIS
course information, grades, registration on Web
MIT Library Reference
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Ask Us!
library consultants on Web
Cn3D, entrez
molecular image viewer, biomolecular databases
Research Guides
library information for finding online bibliographic resources
Reference Materials
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Artha
simple thesaurus based on Wordnet
dict
command-line dictionary using various online databases
gnome-dictionary
simple network-based GUI dictionary
Oxford English Dictionary
runs on Web
rolodex
sipb
database of common local phone numbers
Shakespeare
on Web, here
webster, xwebster (dictionary)
sipb
Web version
whats
sipb
acronym expander (both MIT and general acronyms)
Wordnet
Encyclopedia and thesaurus-like utility
Internet Exploration
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chromium-browser
Google's Web browser
firefox
default Athena Web browser
konqueror
Web browser based on KDE desktop environment
liferea
RSS reader
lynx
text-only Web browser
opera
Web browser
scripts
scripts
Web hosting service allowing automatic configuration for many popular Web-based services (MediaWiki, WordPress, Joomla...)
weblint
checks html pages for correct syntax
w3m
terminal-based Web browser
Screen Accessories
Window Managers
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metacity
debathena default window manager (if previously deselected, select Athena Default Session from the Session: dropdown list on the login screen)
mwm
window manager adhering to the Motif look-and-feel (select Motif Window Manager from the Session: dropdown list on the login screen)
twm
simple, basic window manager (select TWM from the Session: dropdown list on the login screen)
Window maker
window manager designed to provide integration with the GNUstep Desktop Environment; Web page (select Window maker from the Session: dropdown list on the login screen)
XMonad
dynamically tiling window manager written in Haskell; Web page (select XMonad from the Session: dropdown list on the login screen)
Utilities
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Eterm
customizable color vt102 terminal emulator
gnome-calculator
calculator
gnome-control-center
allows setting various desktop preferences
gnome-terminal
enhanced terminal window
ical
tcl
calendar
less
bi-directional text pager
more
text pager
nautilus
file manager and desktop environment
pscal
postscript
hardcopy calendar
remmina
remote desktop client for GNOME environment supporting a variety of protocols
rxvt
"slimmed down" terminal emulator
screen
screen manager that multiplexes a terminal between processes
vinagre
remote desktop viewing application
xcal
calendar
xcalc
calculator
xclock
clock
xfontsel
displays samples and information about available fonts
xload
load gauge
xlock
screen saver, locks display
xtc
calendar
Athena calendar
xterm
creates new, empty terminal window
Communication
Text Software
Graphics Software
Graphics (drawing)
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bitmap
bitmap file editor
convert (ImageMagick)
utility to convert to/from various image formats
dia
drawing program for creating diagrams; author Website, with documentation
DjVu Libre utilities
toolset for manipulating DjVu image files; author Web pages
ds9
ds9
astronomical image analysis application supporting FITS image format
eagle
eaglecad
circuit board design application; provider site , MIT distributor
eog
image file viewer
FreeSurfer
freesurfer
software suite for processing and analyzing human brain MRI images
FreeWRL
VRML2/VRML97/X3D file viewer
FSL
fsl
library of analysis tools for FMRI, MRI and DTI brain imaging data
FWTools (openev)
fwtools
utilities for viewing and manipulating GIS image data; supports multiple formats including jpeg2000
geomview
3d image viewer; author Web pages
gerbv
Gerber circuit board design file viewer
gimp
image manipulation application; author Web page
GLE
language for generating 2d graphics
GLUT
toolkit for building OpenGL graphics applications
GNU plot utilities
utility for plotting graphs in various image formats
Graphviz, xdot
layout programs and viewer for graph visualization
inkscape
GUI editor for Scalable Vector Graphics (SVG) drawing files
ipe
extensible drawing editor that interfaces to LaTeX
ivview
VRML1/Inventor file viewer
LibreOffice Drawing
drawing component of LibreOffice office suite
LibreOffice Presentation Graphics
presentation graphics component of LibreOffice office suite
Magicpoint
utility for presenting slide shows
NetPBM Utilities
utility to convert to/from various graphic formats
OpenGL
3d graphics libraries
Open Inventor
3d image generation system; local Web page
orbisnap
orbisnap
VRML2/VRML97 file viewer
POV-Ray
povray
ray-tracing image renderer
pstoedit
utility to convert PostScript files to editable formats
rayshade
rayshade
ray-tracing image renderer
Scribus
page layout application
Seismic Unix
cwpsu
command-line utilities for analysis and visualization of seismic data
Slicer
slicer
package for biological and medical image visualization and analysis
SPM
spm
MATLAB-based utilities for analysis of brain imaging data sequences
tgif
structured drawing program
TrackVis
trackvis
software tool that can visualize and analyze fiber track data from diffusion MR imaging
trimage
lossless image file compressor and metadata remover
xcircuit
drawing program for circuit diagrams; Author Website
xfig
drawing program
xpaint
drawing program
xv
graphics
image file viewer; online manual
xwd, xwud
utility that saves window images to files
Graphics (CAD)
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ac3d
ac3d
3d image modeler
blender
3d modeling, animation, rendering, post-production and playback application
FreeCAD
parametric 3d CAD modeler
LibreCAD
2d CAD application
Graphics (video)
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mplayer
video media file player that can handle multiple formats
totem
GNOME video media player based on GStreamer
vlc
video media file player that can handle multiple formats
xine
video media file player that can handle multiple formats
Audio Software
Numerical/Math Software
Analysis/Plotting Software
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Axiom
axiom-math
symbolic math system
CoCoA
cocoa
specialized computer algebra system
dc
desk calculator
euler
interactive numerical analysis language with notebooks, graphics capabilities
Fermat
fermat
specialized computer algebra system
Fiji
imj-fiji
multifeatured image analysis tool for life sciences
fityk
fits curves to experimental data points
Gephi
gephi
interactive graph visualization and exploration application
gnuplot
data plotting utility; FAQ
Grace
2d numerical plotting; Web page , user's guide
maple, mint
maple
symbolic math system; local Web page
Mathematica
math
symbolic math system
matlab, simulink
matlab
digital signal processing & data analysis system; local Web page , online docs for latest release , FAQ
maxima
freely distributable symbolic algebra system; documentation
nickle
desk calculator, prototyper for numerical algorithms
octave
digital signal processing & data analysis system
ParaView
3d data analysis and visualization
PARI/GP
computer algebra system designed for fast computations in number theory
R
r
statistical analysis and graphics system
Reduce
reduce
symbolic math system with many add-on packages
ROOT
root
software framework for data analysis
SAGE
pure and applied mathematics system incorporating notebooks and interfaces to other mathematics applications
sas
sas
statistical analysis system; local Web page
scilab
scientific software for numeric computation, digital signal processing & data analysis
singular
computer algebra system for polynomial computations
splus
splus
statistical analysis system; local Web page
stata
stata
statistical analysis system
tecplot
tecplot
sophisticated data plotting system; local Web page
Spreadsheets
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gnumeric
GNU spreadsheet
LibreOffice Spreadsheet
spreadsheet component of LibreOffice office suite
sc
simple spreadsheet
xess
xess
sophisticated, programmable spreadsheet; local Web page
Languages/Debuggers
C
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cc
sunsoft_v12.6
Oracle C compiler
gcc
gcc-6plus
gnu C compiler; gcc Web page
lint
sunsoft_v12.6
Oracle C code checker
C++
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CC
sunsoft_v12.6
Oracle C++ compiler
g++
gcc-6plus
gnu C++ compiler; gcc Web page
FORTRAN
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f77
sunsoft_v12.6
Oracle FORTRAN 77 compiler
f90/f95
sunsoft_v12.6
Oracle FORTRAN 90/95 compiler
gfortran
gcc-6plus
gnu FORTRAN 77/90 compiler
g95
g95
FORTRAN 95 compiler, supports some FORTRAN 2003 and FORTRAN 2008 features
ftnchek
lint-like utility for checking FORTRAN code
Other Languages
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mlisp (Allegro Common Lisp)
acl
Common Lisp compiler/interpreter
AMPL
ampl
modeling language for mathematical programming ; limited availability (see detail description)
awk
pattern scanning language interpreter
Ceylon
ceylon
Open Source language from Red Hat targeted for JavaScript and Java virtual machines
clisp
Common Lisp compiler/interpreter
Clojure
LISP-like dynamic programming language based on Java
cobra
mono
Cobra language compiler, running within Mono environment
Dart
dart-lang
Open Source language from Google intended for structured Web application design
Egison
egison
functional programming language that emphasizes non-linear pattern matching
EiffelStudio
eiffel
IDE and command-line compiler for Eiffel programming language
Erlang
compiler and runtime for Erlang functional programming language
Fabric
fabric
federated, distributed language for securely and reliably storing, sharing and computing information
Fantom
fantom
programming language that runs on the JRE and JavaScript, supporting functional programming and concurrency
Frege
frege-lang
non-strict, pure functional programming language in the spirit of Haskell, compiled to Java and run in a JVM
fsharpc (F# compiler, mono)
mono
F# compiler, running within Mono environment
Gambas
IDE for Visual Basic-like language
gcj
gcc-6plus
gnu Java compiler
gdc (D language compiler)
D language native compiler, based on gcc
GDL (IDL clone)
interpreter, incremental compiler for GNU Data Language
ghc (Glasgow Haskell Compiler)
compiler, interpreter for Haskell functional programming language
GNAT
gcc-6plus
GNU Ada compiler
Go
ggo, gcc-6plus
compilers for Go system programming language
gprolog
interpreter, compiler for Prolog programming language
HACK
hacklang
language similar to php for web programming; supports static and dynamic typing
Haxe
haxe
language and compiler that can produce applications and source code for multiple platforms
Hugs 98 (Haskell)
interactive programming environment for Haskell 98 programming language
J
j
mathematical programming language related to APL with full graphics capabilities
Java Development Kit
java
Java programming language tool suite; local Web page
Julia
julia
high-level dynamic programming language for technical computation
jython
python interpreter that allows direct access to Java classes
Kotlin
kotlin
statically typed programming language that compiles to JVM bytecodes and JavaScript
logo
interactive, graphics based language interpreter
lua
extensible, general- purpose scripting language designed for speed and ease of use
mcs (C# compiler, mono)
mono
C# compiler, part of Mono computing environment
nasm
80x86 assembler, supports range of object formats and macros
newLISP
newlisp
extensible, embeddable lisp-like scripting language
Nim
nim-lang
systems programming language with extensive metaprogramming support, generics and exceptions tracking built in
OCaml
compiler, interpreter for Caml functional programming language
Perl
multi-purpose scripting language interpreter; online docs
Picat
picat
logic-based, multi-paradigm programming language for general-purpose applications
Processing
processing
Java-based language for programming images, animation and interactions
python
general purpose scripting language interpreter; also NumPy numeric package
racket
racket
Scheme interpreter, development environment
ruby
object-oriented scripting language interpreter
rust
rust-lang
block-structured expression language oriented towards creating and maintaining boundaries
scala
object-oriented, functional language that interoperates with Java and .NET
scheme
scheme
MIT Scheme language interpreter
SCM
Scheme interpreter and library
Sikuli
visual scripting language that allows automated generation and testing of graphical user interfaces
sml
compiler and development environment for ML functional programming language
SWI Prolog
Prolog language compiler, development environment
yorick
interpreted scientific language with graphics support
Debuggers/Development Environments
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ant
Java build tool, conceptually similar to "make"
antlr, antlrworks
antlr
language tool and IDE for developing recognizers, interpreters and compilers for languages specified in grammatical description files
CMake
cross-platform build system generator
[Cscope\|istdraft:What Runs Where on Athena - Languages/#Cscope|]
cscope
developer's tool for browsing source code
dbx
sunsoft_v12.6
Oracle debugger for a variety of languages
Eclipse
eclipse-sdk
open, extensible IDE with Java implementation
gdb
gnu debugger
IntelliJ IDEA
kotlin
Java development environment with support for Kotlin programming language
JBuilder Personal Edition
jbuilder
Borland Java development environment
NetBeans
netbeans
Oracle integrated development environment
Oracle Developer Studio
sunsoft_v12.6
Oracle Integrated development environment
TotalView
totalview
C, C++ and Fortran debugger for multiprocessor and multithreaded systems
valgrind
profiler, Linux/i386 dynamic memory allocation debugger
Programming Libraries
Graphics Libraries
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OpenDX
3d data visualization system
Visualization Toolkit
graphics library toolkit for 3d image visualization; author Web page
Math Libraries
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GNU Scientific Library
numerical analysis library; online docs
IT++
mathematical and digital signal processing library; online docs
LAPACK
numeric linear algebra libraries
Netlib
archive containing Lapack, other code; runs on Web
Numerical Recipes
recipes
numerical analysis library; online books
User Interfaces/Widgets
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boost C++ libraries
multipurpose additions to the C++ Standard Library
FLTK
cross-platform C++ GUI builder and widget toolkit
guile
version of the Scheme programming language that can be used as an embedded scripting language
Motif
dynamic and static libraries of 2d X Windows graphics "widgets"
Qt
C++ based GUI builder and "widget" set
Tcl, Tk
programming environment for creating GUI interfaces
Xaw, Xt, Xlib
dynamic and static libraries of 2d X Windows graphics "widget" components
Simulation & Modeling
Bioinformatics
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AFNI
seven
viewing & analysis of functional MRI brain images
Biopython
seven
gene sequence processing and analysis tools
BLAST
application for finding regions of local similarity between molecular sequences
CLC Sequence Viewer
clcbio
tool suite for bioinformatics analysis
clustalw
general purpose multiple sequence alignment program for DNA or proteins
COPASI
copasi
application for simulation and analysis of biochemical networks and their dynamics
Cytoscape
cytoscape
application for visualizing molecular interaction networks and biological pathways
emboss
collection of tools for molecular analysis of genomic data
Geneious
geneious
integrated bioinformatics tool suite for manipulating, finding and exploring biological data
GENSCAN
seven
tool for predicting locations and exon-intron structures of genes
hmmer
set of tools that profile hidden Markov models for protein sequence analysis
Integrative Genomics Viewer
igv
visualization tool for interactive exploration of large integrated genomic datasets
meme/mast
meme
meme: tool for discovering motifs in a group of related DNA or protein sequences. mast: tool for searching biological databases for known motifs
NEURON
neuron
simulator of neurons and networks of neurons; Web page
Osprey
osprey
tool for visualization of biological interaction networks
phylip
collection of tools for inferring phylogenies
primer3
program for designing Polymerase Chain Reaction primers
SnapGene
snapgene
program for planning, visualizing and documenting molecular biology procedures
UGENE
ugene
bioinformatics application that integrates multiple biological tools and algorithms. These can be arranged in a workflow scheme using UGENE Workflow Designer
Finite Element Analysis
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Abaqus
abaqus
software suite for finite element analysis and computer-aided engineering
CalculiX
calculix
3d structural analysis finite-element program, with pre- and post-processor
EasyMesh
easymesh
2d Delaunay mesh generator
Elmer
multiphysics finite-element application
FreeFem++
finite-element analysis, partial differential equation solver
Gerris Flow Solver
solver and viewing application for 2d and 3d solution of partial differential equations describing flow
Gmsh/GetDP
gmsh
Gmsh is a 3d mesh generator with pre- and post-processing capbility; GetDP is a finite-element solver integrated with Gmsh
OpenFOAM
libraries and tools for computational fluid dynamics and multiphysics applications
tetgen
3d tetrahedral mesh generator and Delaunay triangulator
triangle
2d mesh generator and Delaunay triangulator
Geographic Information Systems
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ArcExplorer
arcims
Geographic Information System file viewer; docs
Molecular Modeling & Dynamics
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AIMAll
aimall
package for performing quantitative and visual analyses of molecular systems
Avogadro
molecule editor and visualizer
babel
utility that converts molecular description files to/from other formats
Cambridge Structural Database
cambsd
database of chemical and crystallographic information for small organic and metal-organic compounds
CPMD
cpmd
parallelized plane wave/pseudopotential implementation of Density Functional Theory
Deep View (Swiss-Pdb viewer)
deepview
structural analysis and display of protein molecular chemistry models; online docs
DINO
dino
realtime 3D visualization program for structural biology data
Discovery Studio Visualizer
dsvisualizer
visualization and analysis of molecular images and sequences
Espresso
espresso
programs for quantum-mechanical simulations based on Density Functional Theory
GAMESS, MacMolPlt
gamess
computational molecular chemistry modeler
Gaussian, Gaussview
gaussian
computational molecular chemistry modeler
Jmol
3d molecule image viewer in Java
Mercury
cambsd
crystal structure visualization tool
molden
molden
application that computes and displays molecular density patterns
molekel
molekel
3d molecule image viewer
molscript
molscript
tool for generating 3d molecular images
molSimplify
molsimplify
molecular editor and analyzer with capabilities for handling transition metal complexes
Multiwfn
multiwfn
multifunctional wavefunction analyser
ORCA
orca-chem
computational molecular chemistry modeler; also includes NBO (calculates bond orbitals with maximum electron density)
platon
platon
crystallographic computational chemistry tool
Psi4
psi4
suite of ab-initio quantum chemistry programs
PyMOL
pymol
multi-featured molecular structure viewer
Q-Chem (Open MPI), iqmol
qchem
ab-initio quantum chemistry program (OpenMPI parallel implementation); iqmol is a molecular editor and visualization package integrated with Q-Chem
Q-Chem (MPICH), iqmol
qchemmpich
ab-initio quantum chemistry program (MPICH parallel implementation); ; iqmol is a molecular editor and visualization package integrated with Q-Chem
rasmol
3d molecule image viewer
Star Biochem
3d Java molecular viewing application, accessible on Web
VMD/NAMD
vmd
VMD: 3d molecule image viewer, supports animation, rendering; local docs ; NAMD: molecular chemistry computational dynamics; local docs
XCrySDen
xcrysden
crystalline and molecular structure visualization program
XDrawChem
2d chemical formula drawing program
Other Simulations
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Alloy
alloy
language and tool for describing and exploring structures
AVL, XFOIL
aeroutil
applications for the design and analysis of subsonic aircraft and airfoils
CHEMKIN PRO
chemkinpro
advanced gas phase chemical kinetics analysis simulation
Coq
formal proof management system based on an internal formal language
Dakota
dakota
software for design optimization and uncertainty quantification
Electric VLSI
VLSI circuit design and simulation application
FORTE
forte
computational fluid dynamics package that incorporates CHEMKIN PRO's solver technology
gEDA
suite of of electronic design tools, currently offering schematic capture and simulation tools
GNU Linear Programming Kit
solver/library routines for solving linear programming problems
ipopt
ipopt
large-scale nonlinear optimization package
JFLAP
jflap
package of graphical tools for learning concepts of Formal Languages and Automata Theory
LabVIEW
labview
system-design platform and development environment for "G", a visual, dataflow programming language
lpsolve
lpsolve
Mixed Integer Linear Programming solver
Magic
interactive editor for VLSI layouts
Meep, MPB, Harminv
meep_v1.3
utilities for analysis of time-domain signals
ngspice
mixed-level/mixed-signal circuit simulator
oof
oof
computation of macroscopic material properties from images of microstructure
OpenModelica
modeling language and simulator development environment for mathematical models of physical systems
Qucs
qucs
integrated circuit simulator
RMG
rmgchem
automatic chemical reaction mechanism generator
sketch
sketch
software synthesis tool for rapid development of tuned, bug-free algorithm implementations
SmartSim
smartsim
digital logic circuit design and simulation package
snopt
snopt
general-purpose solver for constrained optimization
spin
spin
LTL model checking system in asynchronous software systems design; local online docs
Stanford University Unstructured
su2
software tools for performing Partial Differential Equation analysis and solving PDE constrained optimization problems
TAO/PETSc
tao-petsc
PETSc is a suite of data structures and routines for solution of scientific applications; TAO, based on PETSc, is software for solving large-scale optimization problems
TensorFlow, Torch
mach-learn
numerical computation applications and libraries for machine learning and A.I. simulation
TLA Toolbox
tla
IDE for TLA+ tools. TLA+ is a formal specification language used to design, model, document, and verify concurrent systems
Miscellaneous Utilities
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aptitude
command-line package manager
blanche
Moira list maintenance utility; Web version (MIT only)
brasero
records data on CD-R, DVD-R and R/W drives
cdrecord
records data on CD-R, CD-R/W drives
clean
consult
removes control characters from text files (converts DOS to UNIX newlines)
CrashPlan
network backup system
cvs
version control system
dos2unix, unix2dos
converts text file newline between UNIX/DOS formats
dosemu
simulates a DOS computer
dsgrep
utility to search Discuss meetings for text strings
fs commands
AFS file system commands; online docs
g3data
extracts numeric data values from graphs published in image format
git
fast, scalable distributed version control system
GnuCash
personal finance manager
gpg
tool for encrypting and digitally signing files; Web page
helpquota
consult
utility that helps deal with "over quota" problems
hesinfo
Hesiod information utility (users, filesystems..)
hfs, xhfs
Macintosh disk access utility
lastupd
consult
utility that tells when servers of a given type were last updated
listmaint
Moira list maintenance utility; Web version (MIT only)
lookup
consult
utility to find server a locker is on
lsof
lists open files on computer
mailmaint
mailing list maintenance utility
hg (Mercurial)
distributed source code management system
moira
interface to Moira database; also on Web (MIT only)
Mtools
PC/ZIP disk access utility suite
OpenRefine
refine
tool for cleaning and transforming messy data
pgp
mail encryption utility; quickstart guide
ps
lists processes running on computer
rblanche
consult
utility for recursively listing members of mailing lists
recode
utility that converts files between character sets and "surfaces"
renew, grenew
renews user's Kerberos tickets and AFS tokens
setup
utility that attaches lockers, performs initialization commands
svn (Subversion)
version control system
synaptic
GUI package manager
Tabula
tabula
utility for extracting data tables from text-based (non-scanned) pdfs
units
converts physical quantities between different units
xmoira
utility for managing user's Email forwarding, finger information and default shell
zap-firefox-certs
infoagents
deletes damaged or expired browser certificates
Zip utilities
data compression utilities