Only those that have survived the test of usefulness find a place here...
Software is open-source or free to use unless indicated [commercial].
See elsewhere for source code and programs of mine and for Whisker and related programs.
Debian Linux quick install
Automated install
See:
Manual install:
Also:
# ============================================================================
# Install additional software (as Debian packages, or manually to /opt)
# ============================================================================
cd /tmp
# ----------------------------------------------------------------------------
# Google Chrome
# ----------------------------------------------------------------------------
# https://www.google.com/intl/en_uk/chrome/browser/
wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
sudo dpkg -i google-chrome-stable_current_amd64.deb
# ----------------------------------------------------------------------------
# PDFEdit
# ----------------------------------------------------------------------------
# http://pdfedit.cz
# http://sharadchhetri.com/2013/12/29/install-pdfedit-for-editing-pdf-file-in-ubuntu/
wget http://us.archive.ubuntu.com/ubuntu/pool/main/q/qt-x11-free/libqt3-mt_3.3.8-b-8ubuntu3_amd64.deb
sudo dpkg -i libqt3-mt_3.3.8-b-8ubuntu3_amd64.deb
wget http://us.archive.ubuntu.com/ubuntu/pool/universe/p/pdfedit/pdfedit_0.4.5-2_amd64.deb
sudo dpkg -i pdfedit_0.4.5-2_amd64.deb
# ----------------------------------------------------------------------------
# Zotero
# ----------------------------------------------------------------------------
# http://www.zotero.org/
wget https://download.zotero.org/standalone/4.0.20/Zotero-4.0.20_linux-x86_64.tar.bz2
sudo tar xjvf Zotero-4.0.20_linux-x86_64.tar.bz2 -C /opt
# (and then it will run as e.g. /opt/Zotero_linux-x86_64/run-zotero.sh)
# ----------------------------------------------------------------------------
# Briss
# ----------------------------------------------------------------------------
# http://sourceforge.net/projects/briss/
wget http://downloads.sourceforge.net/project/briss/release%200.9/briss-0.9.tar.gz
sudo tar xzvf briss-0.9.tar.gz -C /opt
# see /opt/briss-0.9/README.txt for instructions
# run with e.g. java -jar /opt/briss-0.9/briss-0.9.jar [options]
# ... options e.g. -s sourcefile -d destfile for automatic use
# ----------------------------------------------------------------------------
# RStudio
# ----------------------------------------------------------------------------
# http://www.rstudio.com/products/rstudio/download/
wget http://download1.rstudio.org/rstudio-0.98.507-amd64.deb
sudo dpkg -i rstudio-0.98.507-amd64.deb
# ----------------------------------------------------------------------------
# Sage
# ----------------------------------------------------------------------------
# http://www.sagemath.org/
wget http://www.mirrorservice.org/sites/www.sagemath.org/linux/64bit/sage-6.3-x86_64-Linux-Ubuntu_14.04_x86_64.tar.lzma
sudo tar --lzma -xvf sage-6.3-x86_64-Linux-Ubuntu_14.04_x86_64.tar.lzma -C /opt
# run with /opt/sage-6.3-x86_64-Linux/sage
# ----------------------------------------------------------------------------
# Truecrypt
# ----------------------------------------------------------------------------
# Was http://www.truecrypt.org/ -- but dead as of end May 2014
# See http://www.truecrypt.ch/
wget http://truecrypt.ch/download/current/truecrypt-7.1a-linux-x64.tar.gz
tar xzvf truecrypt-7.1a-linux-x64.tar.gz
./truecrypt-7.1a-setup-x64
# ----------------------------------------------------------------------------
# Wine (with NVidia drivers, fixing a distribution bug in other packages)
# ----------------------------------------------------------------------------
# See http://askubuntu.com/questions/449507/nvidia-libopencl1-331-has-to-be-removed-before-installing-wine
sudo apt-get install nvidia-cuda-toolkit
sudo apt-get install ocl-icd-opencl-dev
sudo apt-get install wine
# ----------------------------------------------------------------------------
# Make 16-bit Wine programs work on 64-bit kernels (Aug 2014)
# ----------------------------------------------------------------------------
# See https://lkml.org/lkml/2014/5/7/508
# http://stackoverflow.com/questions/84882/sudo-echo-something-etc-privilegedfile-doesnt-work-is-there-an-alterna
echo 1 | sudo tee --append /proc/sys/abi/ldt16 > /dev/null
echo 0 | sudo tee --append /proc/sys/vm/mmap_min_addr > /dev/null
And:
# ----------------------------------------------------------------------------
# HARDWARE
# ----------------------------------------------------------------------------
# Canon MX-870: http://ubuntuforums.org/showthread.php?t=1475336
# ----------------------------------------------------------------------------
# SYSTEM/NETWORK
# ----------------------------------------------------------------------------
# FIX cups-pdf bug:
# https://bugs.launchpad.net/ubuntu/+source/cups-pdf/+bug/1236120/comments/12
# Strange "device not accepting address" / "device descriptor read/64" errors:
# try an alternative USB port: http://paulphilippov.com/articles/how-to-fix-device-not-accepting-address-error
# OLD:
# google-chrome-stable
sudo dpkg-reconfigure gdm # gives option to restore gdm as the default window manager
# Fixing GIMP 2.8 saving behaviour: http://askubuntu.com/questions/332994/gimp-2-8-doesnt-allow-to-save-usual-image-file-formats-jpg-png-via-save-dial
wget https://github.com/akkana/gimp-plugins/raw/master/save-export-clean.py -O ~/.gimp-2.8/plug-ins/save-export-clean.py
chmod a+x ~/.gimp-2.8/plug-ins/save-export-clean.py
# XFCE ribbon (add in reverse order, then re-sort)
# Places (via Thunar) | Firefox | Terminal | Komodo | Thunderbird | Chrome | Write | Calc | Impress | Zotero | MySQL Workbench | RStudio | X2Go | VirtualBox
BELOW HERE: not up to date.
Open source and free software archives
Operating systems (and desktop environments)
Major applications
-
Wordprocessing, spreadsheet, presentations
- [commercial] The ubiquitous MS Office 97 Professional (Word, Excel, Powerpoint).


- OpenOffice (open source). Main weakness at present is lack of good bibliography support.


-
Database
-
Statistics, mathematics, graphing
-
Bibliographies
- Zotero; runs under Firefox; excellent; integration with Word and OpenOffice. Can import exported EndNote libraries.



- [commercial] EndNote 5, from Niles Software. UK distributor is Cherwell Scientific.

-
CD recording
-
PDF creation
- [commercial] Acrobat 4.0, from Adobe. The PDFzone WebRing is a handy information service. Adobe UK download section.


- PDFCreator is one; download from the SourceForge PDFCreator page.

- To remove PDF security, print the PDF and distil it (using Acrobat Distiller or a third-party utility such as PDFCreator). If this fails, load it into GhostView/GhostScript


, print it as PostScript, and distil that. GhostScript comes with a file called pdf_sec.ps, which deals with PDF security.
- To convert PostScript and PDF to other vector-graphics formats, use pstoedit.


-
Illustration
- [commercial] Adobe Illustrator 8.0. Unrivalled.

- For 2D illustration, choices include Inkscape (open source;


) and Sodipodi (open source; 
), which are both open-source illustration packages that edit .SVG (scalable vector graphic) format files.
- For converting Illustrator (.AI) files to .SVG format, use ILL2SVG, a Perl script (open source;


). This script also requires ImageMagick (see below) to be installed for Perl. However, it doesn't convert text properly.
- For 3D illustration, which I haven't done much of, Blender (open source


); a 3D scanner
for convex hulls; Anim8or (
); Amira, a very powerful (but expensive) suite.
-
Research apparatus and experimental control
- [commercial] Whisker, by me and Mike. Does better software exist on this planet? (Don't answer that.) Not free, but if you buy the program, you get the source code. See www.whiskercontrol.com.

- PsyScope, should one be faced with the unpleasant need to use Mac OS 9 machines.

-
Music (composing)
Network applications
-
WWW browser
-
E-mail client
-
HTML editor
- Textpad, as above. DIY HTML is better.
- NVU (open source;

). Includes a site manager as well as an excellent WYSIWYG HTML editor based on Mozilla's Composer (open source; 

).
-
FTP/SFTP client
- [commercial] FTP Voyager. Powerful and will do mirroring.

- [commercial] GoodSync. Does decent SFTP file synchronization.

- Unison (for two-way synchronization) and rsync (for one-way synchronization; under Windows use cwrsync) are fast and reliable.


- WinSCP. Supports FTP and SFTP. Does file moves.

- FileZilla
Hasn't yet got a "move up/down" feature; otherwise excellent.
- KBear, perhaps.

-
WWW/FTP server
- Xitami, from Imatix. The sign of good software: you never notice it.

- Also, of course, Apache.


-
SFTP server
- Part of SSHD, which is native on Linux and runs on Windows under Cygwin
.
-
Web site log analyser
- There are lots of web log analysers. I use Webtrax occasionally, which is a Perl script.
-
WWW capture
- GNU WGET downloads files and sites via HTTP, HTTPS, and FTP. Other, GUI, tools include Getleft
, HTTrack 
.
- Acrobat 4.0, from Adobe (captures web pages as PDF files).



-
TCP/IP diagnostics
-
Remote control
-
Time synchronization
-
Firewall
- GNU/Linux has firewalling built in (ipchains, and the proxy server squid).

- tdi_fw

- To configure firewalls, the IP port list is useful, as is Seifried's more extensive set of IP port explanations.
Programming
-
C/C++ compiler
-
BASIC
-
Perl
- Perl for Win32; from ActiveState. Perl is supplied by default with most Linux distributions. Perl FAQ.


-
Python
-
Installation
- Inno Setup. Fast, and capable of command-line operation; superb.

-
Source code control
-
Source code formatting/beautifying
- [commercial]
For C++, SourceStyler C++
seems to be about the best, though it's not cheap. I use a variant of the Stroustrup layout style, but to be honest I've not found this sort of formatting tool terribly useful.
- CodeOrganizer.com reviews source code formatting tools.
- Arachnophilia


is a Java-based HTML editor that cleans up HTML code nicely.
-
File/folder comparison and merging
-
Help file and documentation system
- [commercial] Help & Manual 3.4. Excellent conceptually and fast; one edits a central project and the program can produce all sorts of help including HTML Help and PDF documentation of a very high standard. Even has a command-line interface. Caveat: Problem running it with MS Word open (conflict to do with a rich-text-editor DLL?).

-
Specific C++ libraries
- [commercial]
Some hardware-specific drivers; for touchscreens, the Touch-Base UPDD driver (not without bugs).

- For multithreading, the MCL and MCL4MFC libraries (from Cohen & Woodring, 1998, Win32 Multithreaded Programming, O'Reilly).

- See CodeProject.com for a wide range of source code.



- See also the Boost libraries.



-
Cross-platform tools
- [commercial]
QT, from Trolltech (open source for some releases and commercial for others, including all Windows editions). Cross-platform C++ development framework for Windows, UNIX, and Mac OS.



- Cygwin (lets you run UNIX programs under Windows: a UNIX function call library for Windows and Windows ports of GNU development tools)

- Wine (lets you run Windows programs under UNIX: open source implementation of the Windows API for UNIX)

Utilities
-
Postscript viewer
-
PDF viewer
- Adobe Acrobat Reader, from Adobe.



-
Compression tool
-
Text editor
-
Image manipulation
-
Photo album software
- [commercial] Paint Shop Photo Album, from Jasc.

- Picasa.

-
Anti-virus software
- [commercial] McAfee VirusScan.

- Spybot-S&D (for removing spyware)

- [in Linux, achieved primarily by securing the operating system]
-
DVD player
- [commercial] InterVideo WinDVD.

- Ogle (Note that open-source DVD players have been the subject of much legal attention, since to play most DVDs they required reverse engineering of the encrypted DVD format.)

-
Video processing
-
Sound/audio processing
-
Disk tools
-
Font processing
-
Printing tools
Information sources
-
Dictionary
- [commercial] The New Shorter Oxford English Dictionary on CD.

-
Neuroanatomy
- [commercial] Paxinos & Watson, The Rat Brain in Stereotaxic Coordinates, CD edition. Supplied as a set of PDFs.



-
Books
-
Music
- Mutopia, a free collection of scores, with links to others.
-
Encyclopaedia