Other software and file transfer information

SSH software

	# to connect to various computers

	ssh user_name@biophysics.med.jhmi.edu
	ssh user_name@jedi1.med.jhmi.edu
	ssh user_name@jedi2.med.jhmi.edu
	ssh user_name@flea.med.jhmi.edu
	ssh user_name@tick.med.jhmi.edu
	ssh user_name@nit.med.jhmi.edu

	# to run X11 programs, use -X or -Y as in the following example.

	ssh -X user_name@jedi2.med.jhmi.edu xlogo

	# various commands to copy files
	# the scp syntax is identical to ssh and cp.  just add a colon.

	scp user_name@biophysics.med.jhmi.edu:file_name .
	scp -r user_name@biophysics.med.jhmi.edu:directory_name .
	
	# rsync employs ssh with it's syntax to copy files and directories.
	# rsync is the recommended program for copying.  The man page is beautiful

	rsync -rvlpt user_name@biophysics.med.jhmi.edu:file_name .
	rsync -rvlpt user_name@biophysics.med.jhmi.edu:directory_name .

	# it is also highly recommended to study and use the following programs.
	# read the man pages.

	ssh-keygen
	ssh-add
	ssh-agent
	

1. putty for Microsoft Windows
2. nifty telnet for Apple Macintosh
3. OpenSSH is included with Mac OS X. Use the above instructions with the X11 or terminal window utilities.

Mail software

1. mail mail_att, simple but more difficult to use
2. Mail mail_bsd, not quite so bad as mail_att
3. elm menu-driven but cursor-based program, much easier than the above. "Cursor-based" means that it can run on any terminal.
4. pine simple menu-driven but cursor-based program, commonly used here. Looked down upon for being not free.
5. mutt the best (in my not so humble opinion!) of the cursor-based, menu-driven e-mail programs, similar in appearance to elm but with many improvements making it much more powerful.
6. mozilla

   Both mutt and elm can be extensively customized, including choice of editor when composing messages, sorting of the displayed messages, etc. Your mail (to be read by any of the above programs) can also be pre-filtered to remove junk mail or to direct mail from certain people or on certain subjects into specific mailboxes or folders. See man filter or man procmail.)

7. procmail e-mail filtering into separate folders and/or to remove spam. A sample .procmailrc file to put in your home directory can be found here

Editors

1. vi the quintessential UNIX editor, now free software
2. vim a vi-like editor distributed with GNU/Linux
3. emacs the 2nd (?) most popular UNIX editor - extremely extensible and customizable
4. jed an emacs clone that includes syntax highlighting (modes for using colour for emphasis and automatic formatting of programs.
5. nedit
6. pine a simple editor. It is recommended to learn vi instead of pine.

Web browsing software

1. firefox
2. mozilla
3. konqueror
4. links
5. dillo
6. lynx (for character-based terminals - no graphics, and therefore fast)

Graphic design, image display and image manipulation software

Graphic design and drawing, Batch image manipulation and display

1. The Gimp, the most powerful image manipulation program on the planet.
2. ImageMagick powerful command-line batch tools, such as mogrify, and a speedy menu-driven image manipulation program called display