On this page:
Numerical/Math Software
Languages/Debuggers
Programming Libraries
Simulation & Modeling
Miscellaneous Utilities
Help/Information
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Athena Help |
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finds man pages containing key words |
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supplies info about workstation |
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information browser for gnu software |
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finds files by matching path components |
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standard UNIX man page viewer |
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Athena-specific information; on Web |
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bug reporting utility |
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| stanley | supplies, updates information about a username | |
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supplies, updates information about a workstation |
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tells public workstation root passwd, Athena cluster combo |
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outland |
tells which locker a program is in |
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Gnome help browser- misc applications, system man and info pages |
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Database |
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database component of LibreOffice office suite |
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mysql |
mysql SQL client and server |
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| psql (PostgreSQL) | PostgresQL database client | |
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oracle10g |
Oracle database SQL client |
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MIT Information |
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displays current Athena cluster usage |
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course information, grades, registration on Web |
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MIT Library Reference |
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| Cn3D, entrez | molecular image viewer, biomolecular databases | |
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library information for finding online bibliographic resources |
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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 | |
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sipb |
database of common local phone numbers |
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on Web, here |
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sipb |
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sipb |
acronym expander (both MIT and general acronyms) |
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Encyclopedia and thesaurus-like utility |
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Internet Exploration |
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| chromium-browser | Google's Web browser | |
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default Athena Web browser |
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Web browser based on KDE desktop environment |
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| liferea | RSS reader | |
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text-only Web browser |
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Web browser |
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scripts |
Web hosting service allowing automatic configuration for many popular Web-based services (MediaWiki, WordPress, Joomla...) |
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checks html pages for correct syntax |
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terminal-based Web browser |
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Screen Accessories
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Window Managers |
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debathena default window manager (if previously deselected, select Athena Default Session from the Session: dropdown list on the login screen) |
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| 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) | |
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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) |
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dynamically tiling window manager written in Haskell; Web page (select XMonad from the Session: dropdown list on the login screen) |
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Utilities |
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| Eterm | customizable color vt102 terminal emulator | |
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calculator |
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allows setting various desktop preferences |
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enhanced terminal window |
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tcl |
calendar |
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bi-directional text pager |
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text pager |
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file manager and desktop environment |
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postscript |
hardcopy calendar |
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| remmina | remote desktop client for GNOME environment supporting a variety of protocols | |
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"slimmed down" terminal emulator |
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screen manager that multiplexes a terminal between processes |
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remote desktop viewing application |
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calendar |
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calculator |
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clock |
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displays samples and information about available fonts |
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load gauge |
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| xlock | screen saver, locks display | |
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calendar |
Athena calendar |
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creates new, empty terminal window |
Communication
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Electronic Mail |
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text mail client; alpine is the successor to pine |
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standard Athena GUI mail client; user guide |
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mail program; author Web pages |
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| Outlook Web App | Web-based Exchange mail system | |
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mail client and newsgroup reader based on Mozilla engine |
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allows decoding attachments in MS winmail format files |
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Conferencing/ |
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standard Athena message board system |
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on the Web |
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| pan | lightweight news reader | |
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mail client and newsgroup reader based on Mozilla engine |
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Dialup/ |
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serial data transfer program |
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| Mosh | secure remote login terminal application | |
| openconnect | Virtual Private Network (VPN) application | |
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remote login application; access via Web |
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secure remote login, file transfer program; OpenSSH Web page; local Web page, ssh on Athena dialups |
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program to transfer files via Email |
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IBM 3270 terminal emulator |
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Real-Time |
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multi-protocol instant message client; information |
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standard Athena instant messaging system; local online docs |
Text Software
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Text/HTML |
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word processor |
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utility that converts dvi files to PostScript |
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standard UNIX text editor; local online docs |
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utility that prints text files on PostScript printers |
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lightweight text editor |
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utility that converts html to PostScript; author Website |
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spelling checker |
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text editor with many syntax highlighting modes and built-in scripting language |
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standard UNIX text formatting system; local online docs |
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utility that converts latex files to html; online docs |
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html editor component of LibreOffice office suite |
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word processor component of LibreOffice office suite |
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structured document authoring application |
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utility that converts MS Word docs to html, other formats; author Website |
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text editor |
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utility that converts tex and latex files to pdf |
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simple text editor |
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utility that converts PostScript files to pdf |
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texmacs |
"scientific" word processor, allowing embedded math formulas; author site |
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| Texmaker | texmaker | LaTeX editor that integrates many tools needed to develop documents with LaTeX |
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text formatting application |
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utility that converts latex math equations to html |
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standard UNIX modal text editor |
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vim_v8.0 |
vi editor variants |
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| Visual Math Editor | editor for math/scientific formulas that supports LaTeX, AsciiMath and MathML in HTML web pages | |
| Visual Studio Code | vscode | source code editor with built-in support for various languages; many plugins are available |
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editors |
text editor |
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GUI emacs variant |
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Text Previewers |
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pdf file viewer by Adobe |
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| evince | pdf file viewer | |
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PostScript file viewer |
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Ghostscript front end |
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chm (compiled html help) file viewer |
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dvi file viewer |
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pdf file viewer |
Graphics Software
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Graphics (drawing) |
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bitmap file editor |
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utility to convert to/from various image formats |
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drawing program for creating diagrams; author Website, with documentation |
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toolset for manipulating DjVu image files; author Web pages |
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ds9 |
astronomical image analysis application supporting FITS image format |
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eaglecad |
circuit board design application; provider site, MIT distributor |
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image file viewer |
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| FreeSurfer | freesurfer | software suite for processing and analyzing human brain MRI images |
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VRML2/VRML97/X3D file viewer |
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| FSL | fsl | library of analysis tools for FMRI, MRI and DTI brain imaging data |
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fwtools |
utilities for viewing and manipulating GIS image data; supports multiple formats including jpeg2000 |
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3d image viewer; author Web pages |
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Gerber circuit board design file viewer |
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image manipulation application; author Web page |
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language for generating 2d graphics |
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toolkit for building OpenGL graphics applications |
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utility for plotting graphs in various image formats |
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| Graphviz, xdot | layout programs and viewer for graph visualization | |
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GUI editor for Scalable Vector Graphics (SVG) drawing files |
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extensible drawing editor that interfaces to LaTeX |
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VRML1/Inventor file viewer |
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drawing component of LibreOffice office suite |
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presentation graphics component of LibreOffice office suite |
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utility for presenting slide shows |
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utility to convert to/from various graphic formats |
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3d graphics libraries |
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3d image generation system; local Web page |
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orbisnap |
VRML2/VRML97 file viewer |
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povray |
ray-tracing image renderer |
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utility to convert PostScript files to editable formats |
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rayshade |
ray-tracing image renderer |
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page layout application |
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| Seismic Unix | cwpsu | command-line utilities for analysis and visualization of seismic data |
| slicer | package for biological and medical image visualization and analysis | |
| SPM | spm | MATLAB-based utilities for analysis of brain imaging data sequences |
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structured drawing program |
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| TrackVis | trackvis | software tool that can visualize and analyze fiber track data from diffusion MR imaging |
| trimage | lossless image file compressor and metadata remover | |
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drawing program for circuit diagrams; Author Website |
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drawing program |
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drawing program |
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graphics |
image file viewer; online manual |
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utility that saves window images to files |
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Graphics (CAD) |
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ac3d |
3d image modeler |
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3d modeling, animation, rendering, post-production and playback application |
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| FreeCAD | parametric 3d CAD modeler | |
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2d CAD application |
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Graphics (video) |
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video media file player that can handle multiple formats |
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| totem | GNOME video media player based on GStreamer | |
| vlc | video media file player that can handle multiple formats | |
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video media file player that can handle multiple formats |
Audio Software
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media player |
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utility that controls audio settings |
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| gxmms2 | xmms2-based media player with playlists | |
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mp3 player |
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utility that plays various audio formats |
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RealAudio/Video player |
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| rhythmbox | audio player |
Numerical/Math Software
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Analysis/Plotting Software |
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| Axiom | axiom-math | symbolic math system |
| CoCoA | cocoa | specialized computer algebra system |
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desk calculator |
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interactive numerical analysis language with notebooks, graphics capabilities |
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| Fermat | fermat | specialized computer algebra system |
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imj-fiji |
multifeatured image analysis tool for life sciences |
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fits curves to experimental data points |
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| Gephi | gephi | interactive graph visualization and exploration application |
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data plotting utility; FAQ |
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2d numerical plotting; Web page, user's guide |
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maple |
symbolic math system; local Web page |
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math |
symbolic math system |
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matlab |
digital signal processing & data analysis system; local Web page, online docs for latest release, FAQ |
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freely distributable symbolic algebra system; documentation |
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desk calculator, prototyper for numerical algorithms |
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digital signal processing & data analysis system |
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3d data analysis and visualization |
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computer algebra system designed for fast computations in number theory |
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r |
statistical analysis and graphics system |
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reduce |
symbolic math system with many add-on packages |
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| ROOT | root | software framework for data analysis |
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pure and applied mathematics system incorporating notebooks and interfaces to other mathematics applications |
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sas |
statistical analysis system; local Web page |
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scientific software for numeric computation, digital signal processing & data analysis |
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| singular | computer algebra system for polynomial computations | |
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splus |
statistical analysis system; local Web page |
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stata |
statistical analysis system |
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tecplot |
sophisticated data plotting system; local Web page |
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Spreadsheets |
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GNU spreadsheet |
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spreadsheet component of LibreOffice office suite |
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simple spreadsheet |
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xess |
sophisticated, programmable spreadsheet; local Web page |
Languages/Debuggers
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C |
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sunsoft_v12.6 |
Oracle C compiler |
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| gcc-6plus |
gnu C compiler; gcc Web page |
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sunsoft_v12.6 |
Oracle C code checker |
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C++ |
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sunsoft_v12.6 |
Oracle C++ compiler |
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| gcc-6plus |
gnu C++ compiler; gcc Web page |
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FORTRAN |
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sunsoft_v12.6 |
Oracle FORTRAN 77 compiler |
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| f90/f95 | sunsoft_v12.6 |
Oracle FORTRAN 90/95 compiler |
| gcc-6plus |
gnu FORTRAN 77/90 compiler |
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| g95 | g95 | FORTRAN 95 compiler, supports some FORTRAN 2003 and FORTRAN 2008 features |
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lint-like utility for checking FORTRAN code |
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Other Languages |
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mlisp (Allegro Common Lisp) |
acl |
Common Lisp compiler/interpreter |
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ampl |
modeling language for mathematical programming ; limited availability (see detail description) |
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pattern scanning language interpreter |
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| Ceylon | ceylon | Open Source language from Red Hat targeted for JavaScript and Java virtual machines |
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Common Lisp compiler/interpreter |
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LISP-like dynamic programming language based on Java |
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mono |
Cobra language compiler, running within Mono environment |
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| 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 |
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eiffel |
IDE and command-line compiler for Eiffel programming language |
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compiler and runtime for Erlang functional programming language |
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fabric |
federated, distributed language for securely and reliably storing, sharing and computing information | |
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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 |
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fsharpc (F# compiler, mono) |
mono |
F# compiler, running within Mono environment |
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IDE for Visual Basic-like language |
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gcc-6plus |
gnu Java compiler |
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gdc (D language compiler) |
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D language native compiler, based on gcc |
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GDL (IDL clone) |
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interpreter, incremental compiler for GNU Data Language |
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ghc (Glasgow Haskell Compiler) |
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compiler, interpreter for Haskell functional programming language |
| GNAT | gcc-6plus | GNU Ada compiler |
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ggo, gcc-6plus |
compilers for Go system programming language |
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interpreter, compiler for Prolog programming language |
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| 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 |
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Hugs 98 (Haskell) |
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interactive programming environment for Haskell 98 programming language |
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j |
mathematical programming language related to APL with full graphics capabilities |
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java |
Java programming language tool suite; local Web page |
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| Julia | julia | high-level dynamic programming language for technical computation |
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python interpreter that allows direct access to Java classes |
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| Kotlin | kotlin | statically typed programming language that compiles to JVM bytecodes and JavaScript |
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interactive, graphics based language interpreter |
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extensible, general- purpose scripting language designed for speed and ease of use |
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mcs (C# compiler, mono) |
mono |
C# compiler, part of Mono computing environment |
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80x86 assembler, supports range of object formats and macros |
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newlisp |
extensible, embeddable lisp-like scripting language |
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| Nim | nim-lang | systems programming language with extensive metaprogramming support, generics and exceptions tracking built in |
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compiler, interpreter for Caml functional programming language |
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multi-purpose scripting language interpreter; online docs |
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| Picat | picat | logic-based, multi-paradigm programming language for general-purpose applications |
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processing |
Java-based language for programming images, animation and interactions |
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general purpose scripting language interpreter; also NumPy numeric package |
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racket |
Scheme interpreter, development environment |
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object-oriented scripting language interpreter |
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| rust | rust-lang | block-structured expression language oriented towards creating and maintaining boundaries |
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object-oriented, functional language that interoperates with Java and .NET |
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scheme |
MIT Scheme language interpreter |
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Scheme interpreter and library |
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visual scripting language that allows automated generation and testing of graphical user interfaces |
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compiler and development environment for ML functional programming language |
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Prolog language compiler, development environment |
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interpreted scientific language with graphics support |
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Debuggers/Development Environments |
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Java build tool, conceptually similar to "make" |
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| antlr, antlrworks |
antlr |
language tool and IDE for developing recognizers, interpreters and compilers for languages specified in grammatical description files |
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cross-platform build system generator |
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| Cscope | cscope | developer's tool for browsing source code |
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sunsoft_v12.6 |
Oracle debugger for a variety of languages |
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eclipse-sdk |
open, extensible IDE with Java implementation |
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gnu debugger |
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| IntelliJ IDEA | kotlin | Java development environment with support for Kotlin programming language |
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jbuilder |
Borland Java development environment |
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netbeans |
Oracle integrated development environment |
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sunsoft_v12.6 |
Oracle Integrated development environment |
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totalview |
C, C++ and Fortran debugger for multiprocessor and multithreaded systems |
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profiler, Linux/i386 dynamic memory allocation debugger |
Programming Libraries
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Graphics Libraries |
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3d data visualization system |
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graphics library toolkit for 3d image visualization; author Web page |
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Math Libraries |
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numerical analysis library; online docs |
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mathematical and digital signal processing library; online docs |
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numeric linear algebra libraries |
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| Netlib | archive containing Lapack, other code; runs on Web | |
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recipes |
numerical analysis library; online books |
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User Interfaces/Widgets |
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multipurpose additions to the C++ Standard Library |
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cross-platform C++ GUI builder and widget toolkit |
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version of the Scheme programming language that can be used as an embedded scripting language |
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dynamic and static libraries of 2d X Windows graphics "widgets" |
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C++ based GUI builder and "widget" set |
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programming environment for creating GUI interfaces |
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dynamic and static libraries of 2d X Windows graphics "widget" components |
Simulation & Modeling
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Bioinformatics |
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seven |
viewing & analysis of functional MRI brain images |
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seven |
gene sequence processing and analysis tools |
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application for finding regions of local similarity between molecular sequences |
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clcbio |
tool suite for bioinformatics analysis |
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general purpose multiple sequence alignment program for DNA or proteins |
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| COPASI |
copasi |
application for simulation and analysis of biochemical networks and their dynamics |
| Cytoscape | cytoscape | application for visualizing molecular interaction networks and biological pathways |
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collection of tools for molecular analysis of genomic data |
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geneious |
integrated bioinformatics tool suite for manipulating, finding and exploring biological data |
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seven |
tool for predicting locations and exon-intron structures of genes |
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set of tools that profile hidden Markov models for protein sequence analysis |
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| Integrative Genomics Viewer | igv | visualization tool for interactive exploration of large integrated genomic datasets |
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meme |
meme: tool for discovering motifs in a group of related DNA or protein sequences. mast: tool for searching biological databases for known motifs |
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neuron |
simulator of neurons and networks of neurons; Web page |
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osprey |
tool for visualization of biological interaction networks |
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collection of tools for inferring phylogenies |
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| primer3 | program for designing Polymerase Chain Reaction primers | |
| SnapGene | snapgene | program for planning, visualizing and documenting molecular biology procedures |
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ugene |
bioinformatics application that integrates multiple biological tools and algorithms. These can be arranged in a workflow scheme using UGENE Workflow Designer |
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Finite Element Analysis |
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COMMENT |
| Abaqus | abaqus | software suite for finite element analysis and computer-aided engineering |
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calculix |
3d structural analysis finite-element program, with pre- and post-processor |
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easymesh |
2d Delaunay mesh generator |
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multiphysics finite-element application |
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finite-element analysis, partial differential equation solver |
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| 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 |
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libraries and tools for computational fluid dynamics and multiphysics applications |
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3d tetrahedral mesh generator and Delaunay triangulator |
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2d mesh generator and Delaunay triangulator |
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Geographic Information Systems |
LOCKER |
COMMENT |
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arcims |
Geographic Information System file viewer; docs |
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Molecular Modeling & Dynamics |
LOCKER |
COMMENT |
| AIMAll | aimall | package for performing quantitative and visual analyses of molecular systems |
| Avogadro | molecule editor and visualizer | |
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utility that converts molecular description files to/from other formats |
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cambsd |
database of chemical and crystallographic information for small organic and metal-organic compounds |
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cpmd |
parallelized plane wave/pseudopotential implementation of Density Functional Theory |
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deepview |
structural analysis and display of protein molecular chemistry models; online docs |
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| DINO | dino | realtime 3D visualization program for structural biology data |
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dsvisualizer |
visualization and analysis of molecular images and sequences |
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espresso |
programs for quantum-mechanical simulations based on Density Functional Theory |
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| GAMESS, MacMolPlt | gamess | computational molecular chemistry modeler |
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gaussian |
computational molecular chemistry modeler |
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3d molecule image viewer in Java |
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cambsd |
crystal structure visualization tool |
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molden |
application that computes and displays molecular density patterns |
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molekel |
3d molecule image viewer |
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molscript |
tool for generating 3d molecular images |
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| 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) |
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platon |
crystallographic computational chemistry tool |
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| Psi4 | psi4 | suite of ab-initio quantum chemistry programs |
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pymol |
multi-featured molecular structure viewer |
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| 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 |
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3d molecule image viewer |
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|
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3d Java molecular viewing application, accessible on Web |
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vmd |
VMD: 3d molecule image viewer, supports animation, rendering; local docs; NAMD: molecular chemistry computational dynamics; local docs |
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xcrysden |
crystalline and molecular structure visualization program |
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2d chemical formula drawing program |
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Other Simulations |
LOCKER |
COMMENT |
| Alloy | alloy | language and tool for describing and exploring structures |
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aeroutil |
applications for the design and analysis of subsonic aircraft and airfoils |
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chemkinpro |
advanced gas phase chemical kinetics analysis simulation |
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| Coq | formal proof management system based on an internal formal language | |
| Dakota | dakota | software for design optimization and uncertainty quantification |
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|
VLSI circuit design and simulation application |
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| FORTE | forte | computational fluid dynamics package that incorporates CHEMKIN PRO's solver technology |
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suite of of electronic design tools, currently offering schematic capture and simulation tools |
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solver/library routines for solving linear programming problems |
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ipopt |
large-scale nonlinear optimization package |
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| 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 |
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lpsolve |
Mixed Integer Linear Programming solver |
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|
|
interactive editor for VLSI layouts |
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meep_v1.3 |
utilities for analysis of time-domain signals |
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|
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mixed-level/mixed-signal circuit simulator |
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|
oof |
computation of macroscopic material properties from images of microstructure |
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| 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 |
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sketch |
software synthesis tool for rapid development of tuned, bug-free algorithm implementations |
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| SmartSim | smartsim | digital logic circuit design and simulation package |
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snopt |
general-purpose solver for constrained optimization |
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spin |
LTL model checking system in asynchronous software systems design; local online docs |
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su2 |
software tools for performing Partial Differential Equation analysis and solving PDE constrained optimization problems |
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| 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 |
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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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|
LOCKER |
COMMENT |
|---|---|---|
| aptitude | command-line package manager | |
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Moira list maintenance utility; Web version (MIT only) |
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| brasero | records data on CD-R, DVD-R and R/W drives | |
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records data on CD-R, CD-R/W drives |
||
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consult |
removes control characters from text files (converts DOS to UNIX newlines) |
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| CrashPlan | network backup system | |
|
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version control system |
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| dos2unix, unix2dos | converts text file newline between UNIX/DOS formats | |
| dosemu | simulates a DOS computer | |
|
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utility to search Discuss meetings for text strings |
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AFS file system commands; online docs |
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extracts numeric data values from graphs published in image format |
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|
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fast, scalable distributed version control system |
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|
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personal finance manager |
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tool for encrypting and digitally signing files; Web page |
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consult |
utility that helps deal with "over quota" problems |
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|
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Hesiod information utility (users, filesystems..) |
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|
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Macintosh disk access utility |
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consult |
utility that tells when servers of a given type were last updated |
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|
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Moira list maintenance utility; Web version (MIT only) |
|
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consult |
utility to find server a locker is on |
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lists open files on computer |
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mailing list maintenance utility |
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|
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distributed source code management system |
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|
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interface to Moira database; also on Web (MIT only) |
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|
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PC/ZIP disk access utility suite |
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| OpenRefine | refine | tool for cleaning and transforming messy data |
|
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mail encryption utility; quickstart guide |
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|
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lists processes running on computer |
|
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consult |
utility for recursively listing members of mailing lists |
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|
|
utility that converts files between character sets and "surfaces" |
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|
|
renews user's Kerberos tickets and AFS tokens |
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|
|
utility that attaches lockers, performs initialization commands |
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|
|
version control system |
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| synaptic | GUI package manager | |
| Tabula | tabula | utility for extracting data tables from text-based (non-scanned) pdfs |
|
|
converts physical quantities between different units |
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| xmoira | utility for managing user's Email forwarding, finger information and default shell | |
|
infoagents |
deletes damaged or expired browser certificates |
|
|
|
data compression utilities |