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The primary purposes of this facility are analysis of molecular biological data, electronic communication, and graduate training. The CMB UNIX Biocomputing Workstation is sponsored by the Center for Molecular Medicine and Genetics (CMMG) at Wayne State University. It operates on a Sun SPARCStation 20 that is connected to the WSU network and the Internet.
This guide presents basic information that will help you to use the CMB computer. More detailed information on various subjects can be found in other links at the CMMG Web Site. Detailed help can also be obtained "online" as described below.
2. ACCESS ACCOUNTS
To obtain access to the CMB computer, you must have a user account with a
username and a password. WSU scientists may contact
David Womble to
request information on how to obtain a user account. Once you are signed
up, you will receive one page of
information for new users, including your username and password, and
brief instructions on how to connect to the computer for the first
time.
3. INTERNET ADDRESS
The Internet (IP) address of the CMB computer is cmb.biosci.wayne.edu .
This stands for Center for Molecular Biology, BIOlogical SCIences building,
WAYNE state university, EDUcational institution (The Center for Molecular
Biology became the Center for Molecular Mecidine and Genetics on
October 1, 1994). The numerical equivalent address is 141.217.51.7
4. CONNECTING TO CMB
To connect to the CMB computer, you must have a terminal emulator program
(e.g. telnet) on your PC or Mac and either an ethernet/Internet connection
or a modem connected to a phone line. Once you are connected to the
network, use telnet to open a connection to cmb.biosci.wayne.edu or to
141.217.51.7 (both ways are equivalent).
Dialin network service is available through
MichNet. Use your
WSU AccessID and password to set up a PPP connection to MichNet. Set your
modem to 8 data bits, 1 stop bit, parity none.
5. LOGIN
After connecting to the CMB computer with telnet, you will see:
6. LOGOUT
To disconnect (or log out) from the CMB computer, at the cmb% prompt type
exit and press enter (or type logout and press enter, either way works).
If you connected by dialup through MichNet, be sure to also disconnect the
phone.
7. ONLINE HELP
Online Help Guides for the CMB computer are available at the CMMG Web
site at:
http://cmmg.biosci.wayne.edu/dwomble/guides.html
Also, when you login to CMB with telnet, the CMB welcome screen reminds
you where to find online help during your login.
8. ARROW KEYS
Some programs require use of the arrow (cursor) keys. On most UNIX
computers, such as CMB, you can also use the keys H, J, K, L for left,
down, up, and right arrow keys.
9. TERMINAL TYPE
If a program refuses to work because of improper terminal type, set your
terminal type to vt100 by typing:
10. UNIX FILE SYSTEM
Information is stored in files on the hard disk of the CMB computer, much
as it is on your PC or Mac. The hard disk is divided into directories.
Each user has a "home directory" in which to store files. When you first
login, you are located in your home directory. Your home dirctory is
called /home/username. For example, my username is dwomble, and my home
directory is /home/dwomble
You can create subdirectories below your home directory. For example, I
have created a subdirectory called Folder, in which I store certain files.
The complete name of the subdirectory is /home/dwomble/Folder . By
convention (but not by requirement) subdirectory names often begin with an
upper case letter, as in Folder. Upper and lower case are important in
UNIX, so you must type exactly as shown.
11. USING UNIX
You use UNIX commands to control the operation of a UNIX computer such as
CMB. However, there are easy ways to do that without having to learn too
much UNIX. You may also use the HYBROW menus to control the CMB computer,
or you may use X Windows. More information on using UNIX and X Windows is
available here.
12. HYBROW MENUS
HYBROW (Hypertext Browser) is a menuing and browsing program for UNIX.
HYBROW is easy to use even if you are unfamiliar with UNIX, because you do
not need to know UNIX commands. You can navigate between programs,
directories, and files with the arrow keys. The DIRECTORY BROWSER allows
you to view, copy, delete, rename, or edit your files. A companion
program, HYGCGMENU, is available to help guide you through the GCG
sequence analysis programs.
Here is the HYBROW main menu:
13. X WINDOWS
UNIX computers such as CMB support X Windows, a Graphical User Interface
for controlling programs. X Windows server
software is available for your PC or Mac so that you can use your
mouse to control the programs on CMB and display graphics on your screen.
Using X Windows is an excellent way to manage your files on CMB with the X
File Manager (filemgr) and Text Editor (textedit). Click here to see the File Manager Window. You
can also use X Windows to operate the GCG programs through SeqLab
(seqlab), and to view the graphical results of many GCG programs. Click here to see the main SeqLab screen. A
guided tour on using the X File Manager and Text Editor is available here.
14. FILE TRANSFER (FTP)
You may use FTP (File Transfer Protocol) to copy files from one computer
to another through the Internet. Detailed information on using FTP is
available here.
You may install simple-to-use graphical FTP programs on your PC or Mac,
such as WS_FTP (PC) or Fetch (Mac). With those programs, you can use your
mouse to select which files to transfer, without having to learn any FTP
commands. You can also use these programs as a remote "file manager",
since they usually allow you to copy, delete, rename, or view the contents
of your remote files. See USEFUL SOFTWARE below for information on how to
obtain free copies of these programs.
You may also use ZMODEM or KERMIT to transfer files to or from CMB if your
terminal software supports those methods.
Using E-mail file attachments is also a convenient way to share files with
others. If you share files with others by any means, be sure to use an
up-to-date VIRUS CHECKING PROGRAM on all files that you receive.
15. E-MAIL
You can send and receive Internet E-mail on the CMB computer. Your E-mail
address is username@cmb.biosci.wayne.edu (substitute your own username).
You may use either the PINE email program or a POPMail program such as
Eudora or Netscape Mail for sending or receiving E-mail with the CMB
computer.
To start the PINE email program, from the cmb% prompt type pine and press
enter. Functions are listed in a menu at the bottom of the screen. Here
is the PINE main menu:
You may use a POPmail program on your own
PC or Mac, such as Eudora or Netscape mail. Your address is
the same, i.e. username@cmb.biosci.wayne.edu, and the CMB computer serves
as the Postmaster as usual. The difference is that you manage all of your
mail activities, including storing the messages, from your PC or Mac.
Click here to see the Eudora main
screen. Eudora and Netscape mail are free programs for educational users
such as us. See the USEFUL SOFTWARE section for
information on how to obtain free copies of these programs. In the
Preferences menu of your POPMail program, set both POP3 Server and SMTP
Server to cmb.biosci.wayne.edu
FILE ATTACHMENTS are a very powerful feature of E-mail. You can attach
any file to your message, including binary files such as Word Processor
files or executable computer program files. Your recipient will then
detach the file on the other end, where it can be used just as it had
been on your own computer before you sent it. This is a good way to
share drafts of manuscripts or grant proposals. Pine and Eudora both
have easy methods to attach or detach files from messages.
16. SEQUENCE ANALYSIS
The
GCG sequence analysis programs (Wisconsin Package) are
available on the CMB computer, including the GenBank and
EMBL databases. To use these programs, you must first activate
them by typing gcg and pressing enter. You will then be able to use the
GCG programs either from the cmb% prompt, from HYBROW, or with X
Windows using SeqLab.
The coolest way to operate the GCG programs is through
SeqLab, a Graphical User Interface that
allows you to control the GCG programs through Windows with your mouse.
For that, you will need to install an X Windows
server program on your PC or Mac.
An new and experimental method to operate the GCG programs through the WWW
is available with BioPortal. Try
it and let me know how you like it.
All GCG documentation is available at the CMMG Web site. You may read the
manuals or print out copies for your own use. To read the GCG docs, click
here. Please read the special online
held guides about the GCG Programs for
additional information.
Online help is also available from the cmb% prompt by typing genhelp or
genmanual and pressing enter (after first activating GCG as above).
Here is the HYGCGmenu main menu:
17. MEDLINE
Traditional Medline searches can be done at the Shiffman
Medical Library. For an account to access Medline at Shiffman, contact
Mohammed Ali at 577-0705
(
mali@shiffman.med.wayne.edu). There is a link
to Medline on the main HYBROW menu, including detailed instructions on how
to get connected.
Also, Medline in now available by WWW at
http://www.ncbi.nlm.nih.gov/PubMed/
18. USENET NEWS
You may subscribe to and post to the UseNet News with the rtin newsreader
program. There are many molecular biology-oriented newsgroups under the
heading bionet. The rtin newsreader is available both from the cmb%
prompt and within HYBROW. If you are using Netscape on campus, you can
read the newsgroups by setting preferences for your NNTP server to
news.wayne.edu
19. USEFUL SOFTWARE FOR PC AND MAC
You can download many programs from the Internet with FTP or Netscape. I
have some useful programs in subdirectories below my home directory on CMB
(Mac, Win95) that you are free to retrieve. Useful Internet programs are
available for PC and Mac at the WSU Software Center at:
http://support.wayne.edu/down/
20. FILE BACKUPS
The complete file systems of CMB are backed up regularly to tape. If you
lose an important file, for example by accidentally deleting it, it can
probably be retrieved from the taped backups. The version of the file
retrieved would be up-to-date as of the most recent backup (nightly). You
can also back up your important files on your own PC or Mac hard disk or
in your own floppy drives by using FTP to transfer the files. It is wise
to regularly backup your important files on your own. Click
here
for instructions on using FTP to transfer files. If it is necessary to
retrieve files from tape, please contact me for help.
21. HIDDEN (DOT) FILES
There are several files in your home directory, called dot files, that are
used to configure programs that you use. For example, .cshrc
and .login are read by the system each time you login to CMB
(these are similar to DOS config.sys and autoexec.bat files), and
.pinerc is read by pine each time you start it up. These files
are required, so don't delete them. However, you may edit these files to
customize the way various programs operate. The man pages for the various
programs explain how to do this. This is entirely optional, of course.
22. TEXT EDITING
There are 3 text editors available on CMB: vi, pico, and textedit. The vi
editor is the standard UNIX text editor available on most UNIX computers.
vi is more powerful than pico, but is more difficult to use. You can edit
preexisting files or create new files with vi or pico. HYBROW and PINE
use pico for editing, whereas vi is used by most UNIX programs. Textedit
is the X Windows text editor.
More details on how to edit text on CMB are available
here.
23. ADDITIONAL INFORMATION
If you need additional information about any of the above topics, there
are reference books available in libraries and book stores. The magazine
"MichNet News" is sent to most WSU faculty and staff. It contains
information on the network, including how to get connected and how to get
help (phone 313-764-9430; E-mail mnn-request@merit.edu). The WSU C&IT
newsletter "Information Technology" contains information on computing,
networking, and communicating on the WSU campuses (phone 7-3614; E-mail
mjfitz@cms.cc.wayne.edu). The
WSU WWW Server has information about Wayne
State University, including computing resources and how to get help.
24. ADMINISTRATION
The CMMG Biocomputing Facility is sponsored by the Center for Molecular
Medicine and Genetics at Wayne State University. WSU researchers may use
the CMB computer free of charge at this time. If you have questions,
please contact David Womble at:
Phone: 7-2374
[ CMB Computer |
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Send comments to:
dwomble@cmb.biosci.wayne.edu Copyright © 1997, David D. Womble.
UNIX(r) System V Release 4.0 (cmb.biosci.wayne.edu)
login:
Type your CMB username and press enter. Then you will see:
Password:
Type your CMB password and press enter. Your password will not appear on
screen. Next, the welcome screen appears:
Last login: Sun Apr 14 12:39:02 from pm004-23.dialip.
Sun Microsystems Inc. SunOS 5.5.1 Generic May 1996
################################################
Welcome to the CMB Biocomputing Facility
CMMG, Wayne State University
http://cmmg.biosci.wayne.edu
################################################
For an index of available HELP: type help
To start the GCG programs: type gcg
To activate the HYBROW menu system: type hy
**** Instructions for using CMB programs are in the HYBROW menus ****
E-mail questions/comments to root@cmb.biosci.wayne.edu
Finally you will see:
cmb%
This is referred to as the cmb% prompt. It awaits your command.
setenv TERM vt100
and press enter.
+---------------------------------------+
| HYBROW 1.3 |
| Hypertext-like Unix Browser/Interface |
| Copyright 1992 D. Kiong, T. W. Tan |
| Menus for CMB by D. Womble |
+---------------------------------------+
Current working directory: /home/dwomble/cmb
MAIN MENU CHOICES:
HYBROW Info [program summaries] Please read this first.
HYBROW Browser [directory browser]
GOPHER [cmb gopher]
USENET News [tin newsreader]
E-MAIL [pine]
PILOT Browser [pilot directory browser]
MEDLINE [OVID MedLine]
LYNX [World Wide Web]
GCG Programs [HYGCGmenu]
CMB Info [CMB information files]
Use arrow keys to navigate, ? for help, q to quit
-- press SPACE BAR for more --
Start HYBROW by typing hy and pressing enter from the cmb%
prompt. Use the arrow keys to make a selection from the menu. For help,
type ? from the main menu. General information about HYBROW and other
programs available on CMB is in HYBROW Info, including a tutorial on how
to use HYBROW. Instructions on how to use many of the programs on CMB can
be found in the CMB Info or the Network Information sections of HYBROW.
You can also send and read E-mail from within HYBROW.
PINE 3.93 MAIN MENU Folder: INBOX 0 Messages
? HELP - Get help using Pine
C COMPOSE MESSAGE - Compose and send a message
I FOLDER INDEX - View messages in current folder
L FOLDER LIST - Select a folder to view
A ADDRESS BOOK - Update address book
S SETUP - Configure or update Pine
Q QUIT - Exit the Pine program
Copyright 1989-1996. PINE is a trademark of the University of Washington.
[Folder "INBOX" opened with 0 messages]
? Help P PrevCmd R RelNotes
O OTHER CMDS L [ListFldrs] N NextCmd K KBLock
Additional information on the Pine E-mail program is available
here.
+-------------------------------+
| Welcome to HYGCGmenu for Unix |
+-------------------------------+
Editing Sequences [edseq]
Fragment Assembly [fragas]
Restriction Mapping [restmap]
Sequence Comparison [seqcomp]
Database Searching / Retrieval [dbsearch]
Multiple Sequence Analysis [multseqan]
DNA Sequence Pattern Recognition [patrecog]
RNA Secondary Structure [rnasecstr]
Protein Sequence Analysis [protan]
Translation [trans]
Manipulation [manip]
Display / Graphics [disp]
Convert Sequence Format [seqconv]
File Management Utilities [util]
System Manager's Utilities [sysutil]
What is GCGmenu? [whatisgcgmenu] Request for help [mailforhelp]
Right arrow or RETURN to go into an option. Arrow keys up and down navigate.
Left arrow to get out of an option. "?" for help
"q" to quit program Directory browser []
FAX: 7-6200
E-mail:
dwomble@cmb.biosci.wayne.edu
