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From OS X Scientific Computing

Footnotes

... UFS ^1.1: UFS stands for unix file system, the typical disk formatting for computers employing unix operating systems
...http://arstechnica.com/reviews/os/macosx-10.4.ars. ^1.2: http://arstechnica.com/reviews/os/macosx-10.4.ars
...http://www.apple.com/downloads/macosx/apple/x11formacosx.html. ^1.3: http://www.apple.com/downloads/macosx/apple/x11formacosx.html
... consider.^1.4: I changed three default settings in X11 by issuing these unix commands in a terminal window:
defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 wm_click_through -bool true defaults write com.apple.x11 no_quit_alert true The first two of these get rid of the annoying, non-canonical click-to-focus property, and the third gets rid of a warning window that pops up and prevents you from logging out if X11 is running. man Xquartz and man quartz-wm for more information and other possibilities.
...http://iterm.sourceforge.net/)^1.5: http://iterm.sourceforge.net/
... mouse ^1.6: Apple provides a one-button mouse by default. I strongly recommend replacing this lobotomized mouse with a standard third-party multi-button mouse with a scroll-wheel. Apple provides the driver for such mice by default, and these mice tend to work better if one does not install the third-party drivers that come with multi-button mice. Just plug in the mouse to any USB port on your computer and it simply works.
...http://smultron.sourceforge.net/,^1.7: http://smultron.sourceforge.net/
...http://www.barebones.com/products/textwrangler/index.shtml ^1.8: http://www.barebones.com/products/textwrangler/index.shtml
...http://www.codingmonkeys.de/subethaedit/^1.9: http://www.codingmonkeys.de/subethaedit/
...http://www.barebones.com/products/bbedit/index.shtml ^1.10: http://www.barebones.com/products/bbedit/index.shtml
... interchangeably.^1.11: This behavior is only pathological on OS X and is a result of the unusual ``rootless'' mode of running X11. On other unix systems, a root xterm session is always run first, and this always reads the .bash_profile file; subsequent invocations of xterm will inherit the settings found in .bash_profile, allowing finer control.
...http://zsh.sourceforge.net/^1.12: http://zsh.sourceforge.net/
...http://zsh.sourceforge.net/Guide/^1.13: http://zsh.sourceforge.net/Guide/
... Shell ^1.14: Oliver Kiddle, Jerry Peek and Peter Stephenson, From Bash to Z Shell: Conquering the Command Line, Apress (2005).
...http://chemistry.ucsc.edu/ wgscott/xtal/unix.html ^1.15: http://chemistry.ucsc.edu/~wgscott/xtal/unix.html
... Kleywegt ^1.16: an X-ray crystallographer
... Tickle ^1.17: an X-ray crystallographer
...http://docs.info.apple.com/article.html?artnum=152218 ^1.18: http://docs.info.apple.com/article.html?artnum=152218
... website ^1.19: http://discussions.info.apple.com/
...http://www.tcf.vt.edu/systemX.html ^2.1: The most famous example is at Virginia Tech. http://www.tcf.vt.edu/systemX.html
...http://developer.apple.com/hardware/ve/quickstart.html ^2.2: http://developer.apple.com/hardware/ve/quickstart.html
...http://developer.apple.com/performance/g5optimization.html ^2.3: http://developer.apple.com/performance/g5optimization.html
...http://developer.apple.com/hardware/ve/^2.4: http://developer.apple.com/hardware/ve/
...http://hpc.sourceforge.net/index.php ^2.5: http://hpc.sourceforge.net/index.php
... properly,^2.6: Python uses a GUI called Tkinter, which in turn relies upon Tk being present. Normally, this is an X-windows based GUI environment, and is thus absent from a default OS X installation. Recently, most of the functionality of Tcl and Tk has been ``ported'' to an Aqua environment, and this is provided with the default installation of OS X 10.4.x in /System/Library/Frameworks. If for example you have installed the X-windows version of Tcl Tk with the package management system Fink, the Python compilation will use the X-windows version of Tkinter unless you ensure that /usr/bin is prepended to the PATH.
...http://babyurl.com/C0xY8p ^2.7: http://developer.apple.com/documentation
... variables ^2.8: It is best to leave these unset as they tend to mask problems and occasionally will create problems for the user and the system as well.
...http://fink.sourceforge.net/^2.9: http://fink.sourceforge.net
... website ^2.10: http://fink.sourceforge.net/pdb/section.php/sci
... use ^2.11: http://fink.sourceforge.net/about.php
...http://www.chemistry.ucsc.edu/ wgscott/xtal/pkgdiff.html ^2.12: http://www.chemistry.ucsc.edu/~wgscott/xtal/pkgdiff.html
...http://fink.sourceforge.net/download/index.php ^2.13: http://fink.sourceforge.net/download/index.php
... page ^2.14: http://darwinports.opendarwin.org
...http://babyurl.com/4vsTGx ^2.15: http://babyurl.com/4vsTGx
... website ^2.16: http://gnu-darwin.sourceforge.net
... general ^2.17: http://gnu-darwin.sourceforge.net/index.php?page=about
... quit ^3.1: When this string is embedded in the argument of an osascript command, the double quotes required by the AppleScript programming language to be around the name of the application must each be escaped with a backslash as shown.
... program ^3.2: AppleScript is a syntactically brain-damaged monstrosity of a programming language. There are several books devoted to explaining its Kafkaeqsue syntax, but none have managed to impart their wisdom unto me. It tries to have an ``English-like'' syntax, resulting in a verbose, confusing language that is difficult to use.
... medium ^3.3: It is often quite helpful to think of these sorts of interactions in terms of analogies having to do either with occult paranormal phenomena or else intermediary vector bosons, for purposes of absolute clarity.
...http://www.chemistry.ucsc.edu/ wgscott/xtal/terminal_finder_interactions.html ^3.4: http://www.chemistry.ucsc.edu/~wgscott/xtal/terminal_finder_interactions.html
...http://fink.sourceforge.net/pdb/package.php/pos ^3.5: http://fink.sourceforge.net/pdb/package.php/pos
...http://www.pyehouse.com/lynn/termopen.php ^3.6: http://www.pyehouse.com/lynn/termopen.php
...http://www.tco.net/ dscott/software/itermhere/ ^3.7: http://www.tco.net/~dscott/software/itermhere
...http://www.chemistry.ucsc.edu/ wgscott/mystuff/zsh_files.html ^3.8: http://www.chemistry.ucsc.edu/~wgscott/mystuff/zsh_files.html
...http://www.chemistry.ucsc.edu/ wgscott/mystuff/gdirs.html ^3.9: http://www.chemistry.ucsc.edu/~wgscott/mystuff/gdirs.html
...http://www.chemistry.ucsc.edu/ wgscott/mystuff/zsh_files.html ^3.10: http://www.chemistry.ucsc.edu/~wgscott/mystuff/zsh_files.html
...http://fink.sourceforge.net/pdb/package.php/zsh-templates ^3.11: http://fink.sourceforge.net/pdb/package.php/zsh-templates
... TeXShop ^7.1: http://www.uoregon.edu/~koch/texshop/texshop.html
... TexFog ^7.2: http://homepage.mac.com/marco_coisson/MacOSXsoftware.html
... Editor ^7.3: http://evolve.lse.ac.uk/software/EquationEditor/
... files!)^7.4: OS X, and at least some GNU/Linux systems, assigns uid numbers sequentially to each new user, starting with 501. Other systems assign large random numbers, which makes the appearance of this sort of security anomaly (or hole) statistically much more unlikely.
... Manager ^7.5: http://www.bresink.de/osx/NFSManager.html

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