Here is a list of installed software in OSX mountain lion machine.
I leave this as a memo, mostly for myself.

• google chrome
• chrome app
  • simplenote
  • evernote
  • dropbox
  • google japanese input
  • google calender
  • google tasks
  • diigo
  • white spaces
• Google Notifier
  • For setting gmail as default mail client.
• DropBox, desktop
• Evernote, desktop
• istat pro (dashboard gadget)
• BetterZipQL
  • This allows quick view (command-space) to automatically show ZIP contents
• Xcode
  • launch xcode once, then agree to the licensing
  • from preference, download and install command line tools (151 Mb)
• Homebrew:
  • install Git
  • add /user/local path to the .bash_profile
  • install python (2.7.3)
    • followed instruction here
    • then with python pip, install numpy, scipy, matplotlib
    • IPython (instruction)
      • brew install pyqt
  • macvim
    • brew install macvim –override-system-vim
    • instruction
  • maven
  • jython
    • ln -sf ../Cellar/jython/2.5.3/libexec/jython /usr/local/bin/jython
      • this is required for interactive shell.
    • M2_PATH=~/.m2/repository
      JYTHONPATH=`find $M2_PATH -name “*.jar” | tr “\\n” “:“`
      export JYTHONPATH
  • scala
    • sbt
  • brew linkapps
  • R
    • brew install R
      • sudo mv /Library/Frameworks/R.framework /Library/Frameworks/native_R.framework
      • sudo ln -s ”/usr/local/Cellar/r/2.15.1/R.framework” /Library/Frameworks
      • defaults write org.R-project.R force.LANG en_US.UTF-8
  • ffmpeg
  • wget
  • openCV
    • brew install opencv
  • bash-completion
  • ctags
    • ln -s ~/<>/config/dotfiles/ctags ~/.ctags
  • newsbeuter
• XQuarz
• iTerm2
  • alternative of Terminal.app, more functionalities.
  • colorscheme Solarized HIgh-Contrast
• Eclipse
  • IDE, I use this for Java coding and latex editing.
  • plugins
    • (vwrapper http://vrapper.sourceforge.net/home/)
    • (texlipse http://texlipse.sourceforge.net/)
    • pydev http://pydev.org/download.html
• RStudio (linked to homebrew R)
  • IDE for R
  • http://rstudio.org/
• Fiji & ImageJ
• Tex related (instructions)
  • http://www.tug.org/mactex/
  • brew install ghostscript
  • brew install imagemagick
  • MacTeX.pkg > double click, in “customoize” select only text live 2012 and GUI package
  • ln -s /usr/local/Cellar/r/3.0.1/R.framework/Versions/3.0/Resources/share/texmf/tex/latex ~/Library/texmf/tex/
    • this is to link sweave style file to tex.
• Mendeley Desktop
  • http://www.mendeley.com/
  • sync reference pdf and database via dropbox
    • instructions
      • ~/Library/Application Support>cp -r Mendeley\ Desktop ~/Dropbox/Mendeley/db/
      • ~/Library/Application Support>mv Mendeley\ Desktop _backup_Mendeley\ Desktop
      • ln -s ~/Dropbox/Mendeley/db/Mendeley\ Desktop
• skim
  • PDF viewer, that could be in sync with texlipse (tex editor)
• VLC
  • Universal video viewer.
  • addons
    • TuneIn, an internet radio tuner.
• pandoc
  • swiss army knife for document conversion.
• AppCleaner
  • osx application uninstaller
• Sophos Anti-Virus
• CyberDuck
  • SFTP. I sometime use this for transfering many files across servers
• Copy File Path
  • customize a Finder service,, that adds a shortcut key (command-shift-c) to copy full path into clipboard.
  • Instruction
• LibreOffice
• Skype
• Fonts
  • Inconsolata
  • brew install fontforge
    • generate ricty font
      • instruction
• IgorPro (Wavemetrics, not free)
• Mou
• Parallel (not free)
  • Windows7 (not free)
  • Chrome OS
• MS office standard (not free) + endnote (not free)
• Adobe CS package (not free)
• pending: some adjustments needed needed
  • wake-on-LAN