Two of the basic functionalities that date back to the beginning of the Internet are remote shells and file transfer. Initially, these were implemented as the TELNET and FTP protocols which are still with us today. However, more secure methods of doing remote shells and file transfer are now available and so we're phasing out TELNET immediately and FTP in the near future.
The protocols we plan to support and recommend are SSH, secure shell, (preferably SSH2) for remote shells and SCP, secure copy, (based on SSH) for file transfer. These are available for Unix, Macintosh and Windows in various command line and GUI variants. Another secure file transfer protocol that will likely be supported is SFTP, secure FTP.
A few systems may not have SSH and/or SCP available. If necessary you may have to go through an outside account that has SSH capability, such as Stanford's Leland systems.
Here is a list of Macintosh & Window software that supports SSH.
The Unix (including Macintosh OSX) command line utilities that implement the SSH suite are ssh for executing a remote command securely and opening a remote, secure terminal session, and scp for transfering files securely.
The SSH suite of command line utilities are designed to be secure replacements for, the Unix RSH suite of of programs, rsh, rcp and rlogin and so emulate their behavior, not that of TELNET and FTP.
Here are some usage examples for the SSH suite of utilities.
The older TELNET protocol will be blocked for all genome machines at our firewall. It will still work within the department, but it will no longer be possible to TELNET directly to any machines inside the department from outside. FTP will still be available for a while, until some older systems are replaced. After that, SCP or SFTP will be required. This is also true of other non-secure protocols like Unix RSH and RCP -- they are available between department machines but blocked at the firewall from outside use.
Independent of our local policy, for your own security on the Internet, you should only use FTP for anonymous login sessions from a public FTP site, not for your own files on your own ISP.
Some desktop X windows packages (like older copies of Reflection X for the PC) don't implement SSH. However you don't need to use the package's own TELNET option to make the initial connection. As long as the X windows package is running, any X clients you start will show up, using an independent SSH connection, as long as your DISPLAY environment variable is set correctly.
To use this properly, you will need an SSH client that does X forwarding (as TeraTerm does on the PC with the TTSSH extension.) Then you can log in through your separate SSH client and any X clients you start will show up through your X windows package and be fully encrypted. (The lastest Reflection X 10.0 includes SSH capabilities.)