Computer Class Home Page

Below are the lecture notes; note that the C programs may be strangely formatted;

The University of Florida Soda Shoppe: place to get some free software (i.e. FTP program) and a lot of cheap software (i.e XWindows for PC, Hummingbird Exceed for PC, both allow you to run Xwindows on a PC). http://www.software.ufl.edu/

A few words about FTP; FTP stands for File Transfer Protocol and is the first important program designed for the ARPA net, basically to allow military establishments to rapidly transfer documents around. It was designed to transfer files seamlessly between any kind of computer regardless of what operating system it was using. Initially most ARPA net computers used IBM, DEC and other proprietary operating systems. Later UNIX, DOS, Windows and Mac OS programs were developed. The program for each of this types of computer is different, but the transfer protocol is the same, so files go from one kind of computer to another without problems. FTP is still an extremely useful program today and is widely used to transfer files around buildings, across campus, across the country and across the world. Often an FTP command is embedded in Web pages, so you actually activate an FTP program to move images, movies, protein and nucleic acids sequence databases etc. from the web. You might also want to use it to transfer sequence files to your GCG accounts. First you need an FTP program. Windows actually includes an FTP program, usually in the Windows subdirectory but it is rather clunky to use. It is one of those command line programs which works O.K. and is actually quite versatile but you have to remember the various commands. You can get a free Windows based FTP program called WS_FTP from the University of Florida Soda Shoppe at http://www.software.ufl.edu/ which is much more user-friendly. Download this, install it and run it. You'll see a "session properties" menu appear. Look into the "Profile name" box by selecting the down arrow and you can see the various places you can download files by FTP. Most computer related and other hi-tech companies, universities, research institutes etc. have public access FTP sites from which anyone can download a variety of files. There are two ways you can do this. One is called "anonymous FTP", and allows anyone in the world to get to file without any restriction. However, for obvious reasons, anyone using anonymous FTP cannot rename, delete or modify files or run actually programs on the host machine. It may be possible to upload files, but usual this not allowed either. To do this you enter some sort of name that will remind of what the site you are connecting to is in the "Profile Name" box, then enter the "host name/address", which is generally the same or similar to the internet HTTP address. In the "Host_Type" window select "Automatic detect" (this usually works) and tick the "Anonymous" box. Then press "Apply" to save that profile so you don't have to type it again; next time you can select it from the menu. For example enter "UFBI" in "Profile Name", "ufbi.ufl.edu" in the "Host Name/Address" box, and select the "anonymous" box, the "Apply". Finally click "OK", and you should connect to the public access part of the UFBI computer. You'll see a bunch of subdirectories on the right, which are on the UFBI server. Click on the "Pub" subdirectory and you can see more subdirectories, one of which is called "Shaw". If you look in there you'll see all the files that are linked from the http://www.ufbi.ufl.edu/~shaw/computer.htm page. This is where I put these files and when you select them from that page they are automatically downloaded to your computer by anonymous FTP. The other kind or FTP is, well, nonanonymous FTP, and is used when you have an account on a particular computer. In this case you transfer things in basically the same way but you enter your username and password, and you are then directed to your own subdirectory which in theory anyway no-one else can get to, so this is not public access. For example enter "GCG" or something similar in the Profile Name box, "gcg.biotech.ufl.edu" in the "Host Name/address" box, but don't click the "Anonymous" box this time. Then enter your username and password, click the "Save pwd" box (if you want to) and press "Apply", so all this will appear in the "Profile Name" menu, so you don't have to type all that stuff again. Then press "OK" and you should be off to your subdirectory. You can then migrate about your computer using the menu on the left and upload to the GCG computer using the left arrow, or get stuff off the GCG computer using the right arrow. Since you have an account you are allowed to rename files, upload new files, delete files and so on, but you can't actually execute a program on the host machine by FTP. To do that you need to use a Telnet program, or else Xwindows or the Web interfaces. The only other thing to watch is the three boxes labeled "ASCII", "binary" and "Auto". Select "ASCII" for simple sequence files, MSDOS text files, HTML documents and stuff like that, which will include most protein and nucleic acid sequence data, structural data files and sequence libraries. Select "binary" for images, movies, word files, PDF documents etc, and select "auto" if you're not sure. The Mac has an FTP program built in which I somewhat less familiar with which is called "Fetch". If anyone is interested or has problems with this I have an old Mac at home and can write similar instructions for that program/computer combination.

c1.c	c2.c	c3.c	c4.c	c5.c	c6.c	c7.c
c8.c	c9.c	c10.c	c11.c	c12.c	c13.c	c14.c
c15.c	c16.c	c17.c

If Motifer and Fasta don't print out the sequence names correctly, try FTP downloading in Binary format, or, alternately, translate from Unix to PC format using the simple program: Unix-pc.exe

Link to a Web page quite like the one Richard Rathe made on Friday 13th April: Press here