MBG 8680: Computer Applications in Molecular Genetics

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FILE TRANSFER METHODS


It is often necessary to copy files from one computer to another.  
Here are some methods to copy files using the Internet.

1. FTP (file transfer protocol)

One of the most useful tools available for computers is the ability 
to transfer files from one machine to another.  You may use FTP to 
copy files from one computer to another through the Internet.

There are 2 basic kinds of files that you can transfer: text (or 
ascii) and binary (or image).  Text files can be read by humans.  As 
an example, most of the results of GCG programs are written out to
text files.  Binary files can only be read by a machine.  Examples 
include computer programs, images, compressed files, and word processor 
files (such as from WordPerfect or MS Word).

There are 2 kinds of FTP logins: user account and anonymous.  You can 
login to most computers by either method.  If you login with your user 
account, you have the same permissions you have with your regular telnet
login.  For an anonymous login, you will usually only be allowed access
to the public areas.

An easy way to use FTP is with a graphical client program, so you don't
have to learn any FTP commands.   WS_FTP is a graphical FTP program 
for Windows.  A graphical FTP program for the Mac is called Fetch.  Both
are available on the WSU Internet Toolkit CD, or at the WSU Download Center
at: 

http://computing.wayne.edu/download/index.php

NB: Under Session Options, make sure that you are not using Passive
Transfer Mode - the reason is that most firewalls will not allow the
use of passive transfer mode, and most FTP servers today are protected by
firewalls.

I have written a basic manual on using FTP, available at:

http://www.genetics.wayne.edu/dwomble/ftp.html


2.  E-MAIL

You can attach ascii or binary files to your E-mail messages.  The 
recipient can then detach the file on the other end.  This is a 
convenient way to exchange word processor documents with a colleague, 
such as manuscripts or grant proposals.  The E-mail program must 
first encode the file into a text format so that it can be sent.  It 
must then be decoded on the other end.  Methods include MIME, uuencode, 
and binhex.  Read the online documentation in the PINE E-mail program 
on Genetics for additional information.

Eudora, Outlook, and Netscape Mail are also easy ways to attach files to 
E-mail messages, or to receive messages with attached files and
automatically detach and decode the attachments into a temporary 
directory on your PC.

NB: The practical limit for size of an attachment is about 1 MB.  If you 
need to transfer files larger than that, it is much better to use FTP.

3. World Wide Web

You can use Netscape to download files such as computer programs
and sequence data from various sites on the Internet.  For example, 
you could use Netscape to read the GCG Manual at:

http://www.genetics.wayne.edu/gcg/gcgmanual.html

You could then choose to print the manual, or you could save it as 
a file on your PC's hard disk and then read it or print it later.

You may also use Netscape as an FTP client, instead of WS_FTP or Fetch.
To use Netscape to log into an anonymous account on an FTP server, use 
an "ftp" URL like this:

       ftp://ftp.whatever.com

You can also use a full path pointing directly to a specific file on the
ftp server:

       ftp://ftp.whatever.com/path/filename

To log into a specific user account on the FTP server, you can include
your username in the URL.  The syntax is:

       ftp://username@genetics.wayne.edu

Don't ever type your password into a URL, because everyone can read
it.

NB: Web browsers may have difficulties distinguishing text and binary
file types, with unpredictable results.
Send comments to: dwomble@genetics.wayne.edu
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