Example of using USENET (LONG message)

Dave Kristofferson kristoff at GENBANK.BIO.NET
Wed Jul 31 16:32:31 EST 1991


Rob Harper's BIOBIT encouraged me to snip out the following section
from the GenBank On-line Service Manual because I think that it will
give a feel for using an actual USENET system.  "Freenet" mentioned by
Rob has a system of menus layered over their system which may be nice
for the first couple of times but would get onerous to anyone who uses
the system regularly.  Also the messages on-line there (at least when
I looked some time ago) would not be of much interest to biologists.

We chose to use the vnews software on GenBank a couple of years back
but would probably make a different recommendation today (possibly nn
but this depends on the system in use).  Much of what is illustrated
below for vnews holds true for other USENET software packages.  More
experienced users may still find it worth their while to read the
following because it contains several useful software "tricks" that
they may not know.

Please note that this section was written some time ago and some of
the newsgroups mentioned no longer exist while new ones have been
added.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff at genbank.bio.net

----------------------------------------------------------------------

		     USENET and USENET Newsgroups

On the GenBank computer system bulletin boards are accessed as USENET
newsgroups through the UNIX netnews software (vnews, rn, readnews, and
postnews). USENET is short for users network.  It consists largely of
UNIX-based computers which run the netnews software and which are
connected by communications links to exchange information.  (Note,
however, that GenBank can also still exchange messages with sites that
do not run UNIX.)  The communications links can be over the Internet,
other networks, and even over direct dial-ups (modem-to-modem) between
two sites that use UUCP (unix-to-unix communications protocol).

A large number of newsgroups related to scientific, computer, and
other subjects are carried over USENET and are also available on the
GenBank on-line service in addition to the regular BIOSCI newsgroups.
USENET newsgroups usually have segmented names separated by periods,
e.g., comp.sys.ibm.pc. The newsgroups are named in a hierarchical
manner with the most general part of the newsgroup name on the left.
For example, the IBM PC newsgroup comp.sys.ibm.pc is in the computing
newsgroups section, then in the computing systems subsection, then
specifically in the ibm systems subsection and finally in the pc
niche.  On USENET all of the BIOSCI newsgroups are in the bionet
grouping at the top level.  A sample list of newsgroups follows
together with the Internet and BITNET mailing list names. The most
current list can be seen on-line by entering help genbank
communications bulletins bb-list at the genbank% prompt.

(NOTE added 31 July 1991 - the following list of newsgroups is current
- D.K.)

NEWSGROUP NAME             Mailing Address       USENET Newsgroup Name
--------------             ----------------      ---------------------
AGEING                     AGEING                bionet.molbio.ageing
AGROFORESTRY               AG-FORST              bionet.agroforestry
ARABIDOPSIS                ARAB-GEN              bionet.genome.arabidopsis
BIONAUTS                   BIO-NAUT              bionet.users.addresses
BIONEWS                    BIONEWS               bionet.general
BIO-JOURNALS               BIO-JRNL              bionet.journals.contents
BIO-MATRIX                 BIOMATRX              bionet.molbio.bio-matrix
BIO-SOFTWARE               BIO-SOFT              bionet.software
CHROMOSOME-22              CHROM-22              bionet.genome.chrom22
COMPUTATIONAL-BIOLOGY **   COMP-BIO              bionet.biology.computational
EMBL-DATABANK              EMBL-DB               bionet.molbio.embldatabank
EMPLOYMENT                 BIOJOBS               bionet.jobs
GENBANK-BB                 GENBANKB              bionet.molbio.genbank
GENETIC-LINKAGE            GEN-LINK              bionet.molbio.gene-linkage
GENOMIC-ORGANIZATION       GENE-ORG              bionet.molbio.gene-org
HUMAN-GENOME-PROGRAM       GNOME-PR              bionet.molbio.genome-program
METHODS-AND-REAGENTS       METHODS               bionet.molbio.methds-reagnts
MOLECULAR-EVOLUTION        MOL-EVOL              bionet.molbio.evolution
NEUROSCIENCE               NEUR-SCI              bionet.neuroscience
POPULATION-BIOLOGY         POP-BIO               bionet.population-bio
PROTEIN-ANALYSIS           PROTEINS              bionet.molbio.proteins
SCIENCE-RESOURCES          SCI-RES               bionet.sci-resources

** Note that newsgroups flagged with ** are moderated, i.e., postings
are directed to a moderator (editor) who later forwards messages
(possibly edited or condensed) to the newsgroup.


Reading Specific Newsgroups with Vnews

USENET newsreading software is in the public domain and has evolved at
different sites over a period of time.  Two good reference books on
the netnews software are:

Anderson, B., B. Costales, and H. Henderson. UNIX Communications.
(1987) The Waite Group. Howard W. Sams & Company. Indianapolis,
Indiana.

Todino, G., T. O'Reilly, and D. Doughtery. Using UUCP and USENET.
(1987) A Nutshell Handbook. O'Reilly & Associates, Inc. Newton,
Massachusetts.

Three programs are commonly used for reading USENET news: readnews, rn
and vnews. On GenBank we intend to support the vnews program, but the
other two are available as options to those experienced UNIX users who
may already be accustomed to them.  Foreign users who operate in half
duplex mode may not be able to use vnews.  We recommend the use of
readnews for these users.  Readnews is simpler, but by and large
similar to vnews, the main difference being the "visual" interface used
by vnews which does not work well in half duplex mode.

To read the latest news, simply enter vnews after the genbank% prompt.
For those who prefer to see the latest news at login, the command
vnews can be added as the last line in your .login file with an
on-line editor such as Emacs or vi.  This will automatically run vnews
each time that you log in to GenBank.


EXAMPLE:

genbank%vnews

If no news is available one will simply see the message "No news".
Otherwise the screen blanks and something like the following
information might come up.

Article <12486874925.28.SOKATCH.BURNS at BIONET-20.BIO.NET> Apr 17 15:32
Subject: affinity purification of DNA-binding proteins
From: SOKATCH.BURNS at BIONET-20.BIO.NET (P. Gayle Burns)
(15 lines)



















0%                  bionet.molbio.meth 1/3      Jun 2 5:12

If you wish to read this article, simply press your spacebar. If you
wish to skip the article, press the n key. If you wish to stop reading
news, press the q key. More options are considered below. Note that at
the bottom of the screen is a % indicator which displays how much of
the current message has been seen, then the name of the newsgroup
(slightly truncated in this case, bionet.molbio.methds-reagnts), then
a 1/3 indicating that this is the first of three new messages, and
finally the current date and time (not the time the message was
sent; that information is in the header). Assuming that the spacebar
is pressed to read the message , one would see the following.

Article <12486874925.28.SOKATCH.BURNS at BIONET-20.BIO.NET> Apr 17 15:32
Subject: affinity purification of DNA-binding proteins
From: SOKATCH.BURNS at BIONET-20.BIO.NET (P. Gayle Burns)
(15 lines)

Thanks! Yes, the Promega GRAB kit was the one I was thinking of.  The
original method on which this kit is based is from Levens and Howley,
Mol.  Cell Biol. Vol 5, 2307-2315 (1985).  Also see Gimble, Levens,
and Max, Mol Cell Biol Vol. 7, 1815-1822 (1987).

        Another affinity method that was brought to my attention is
this: The DNA fragment is affinity labeled with biotin-deoxynucleotide
by filling in the end using Klenow.  This binds to
streptavidin-agarose (BRL) and you have your affinity matrix! After
binding of the repressor from a crude celllysate, the protein can be
eluded by high salt concentration, inducer, or as acomplex with the
bound DNA fragment by restriction digestion. The authors claim a
3400-fold enrichment.  This method is by Leblond-Francillard, Dreyfus
and Rougeon, Eur. J. Biochem vol 166, 351-355 (1987).

        I'd like to hear of successes and failures with these methods.

Gayle Burns
-------



100%                bionet.molbio.meth 1/3      Jun 2 5:13

Note that the % indicator now reads 100% which means that all of the
message has been displayed. The display will pause at the end of each
page when longer messages are encountered and one must press either
the spacebar to continue reading or n to skip to the next message or q
to quit reading news. Other options can be displayed by pressing a ?
which leads us into the next section.


Common Vnews Commands

The list of vnews commands follows. These can be displayed by pressing
a ? anytime while reading news.

Commands:vnews

Vnews commands:    (each may be preceded by a non-negative count)

SP  Next page or article                D   Decrypt a rot 13 joke
n   Go to next article                  CR  Go to article numbered count
e   Mark current article as unread      <   Go to article with given ID
+   Go forwards count articles          p   Go to parent article
b   Go to previous article              ug  Unsubscribe to this group
^B  Go backwards count pages            ud  Unsubscribe to discussion
^N  Go forward count lines              ^L  Redraw screen
^P  Go backwards count lines            v   Print netnews version
^D  Go forward half a page              c   Cancel the current article
a   Switch to/from article index        q   Quit
H   Display article header              ^\  Quit without updating .newsrc
!   Escape to shell
r   Reply to article
f   Post a followup article
l   Display article (use after !, r, f, or ?)
s   Save article in file
w   Save without header
N   Go to newsgroup (next is default)

Here we will discuss the b,a,r,f,s,CR,p, and ug commands which are the
most useful besides the space (SP above), n and q commands (mentioned
earlier).

Note that BEFORE pressing any of these commands one can enter a number
("a non-negative count") which indicates how many times to execute
the command.  For example, if you see that there are 1059 news
messages to read because you haven't looked at the news in ages,
you could use the command 1059n to mark them all as seen (but see the
a command below for a quick method of skimming the contents!!!). Using
q in this case would simply exit the vnews program, and these same
messages would be presented to you next time because they have not yet
been marked as seen.  Messages are marked only by either reading them
or skipping them with n.

b.  Pressing b will move you back one message in the list (unless you
are at the first message in the list).

a.  The a command is particularly useful when you are presented with a
large number of messages. Suppose, for example, you were confronted by
the following screen which indicates that the message is the first of
nine.

EXAMPLE:

Article <12439493589.49.GORDON.BRADSHAW at BIONET-20.BIO.NET> Oct 18
21:39
Subject: Commercial sources of database on floppies
From: GORDON.BRADSHAW at BIONET-20.BIO.NET (Toby Bradshaw)
(9 lines)

















0%                  bionet.molbio.pir 1/9       Jun 2 5:51

By pressing a, the screen is blanked and the following index of titles
is displayed.

 IND FILE LINES Newsgroup bionet.molbio.pir, 9 articles

>  1    1    9 Commercial sources of database on fl GORDON.BRADSHAW at BIONET-20.B
   2    2    5 Database currency		    GORDON.BRADSHAW at BIONET-20.B
   3    3    6 database statistics		    GGREENBERG.HILFINGER at BIONET
   4    4   26 Response to Hilfinger		    GEORGE at gunbrf.bitnet
   5    5   19 Accession numbers		    g_barton at icrf.ac.uk
   6    6   20 accession numbers		    g_barton at icrf.ac.uk
   7    7  113 PIR Accession numbers		    g_barton at icrf.ac.uk
   8    8   49 PIR Accession Numbers		    BARKER at gunbrf.bitnet
   9    9   49 (none)		    		    GEORGE at gunbrf.bitnet

The > symbol in the left hand column indicates that one is poised to
read the first message which can be done simply by pressing return.
Otherwise one can skip messages by pressing the n key, possibly
preceded by a number. For example, pressing 3n would change the index
to look like the following

 IND FILE LINES Newsgroup bionet.molbio.pir, 9 articles

D  1    1    9 Commercial sources of database on fl GORDON.BRADSHAW at BIONET-20.B
D  2    2    5 Database currency		    GORDON.BRADSHAW at BIONET-20.B
D  3    3    6 database statistics		    GGREENBERG.HILFINGER at BIONET
>  4    4   26 Response to Hilfinger		    GEORGE at gunbrf.bitnet
   5    5   19 Accession numbers		    g_barton at icrf.ac.uk
   6    6   20 accession numbers		    g_barton at icrf.ac.uk
   7    7  113 PIR Accession numbers		    g_barton at icrf.ac.uk
   8    8   49 PIR Accession Numbers		    BARKER at gunbrf.bitnet
   9    9   49 (none)		    		    GEORGE at gunbrf.bitnet

The first three messages are marked as seen (or Deleted) and one is
now set to read the fourth message by pressing a return.  If one
wishes to review quickly a newsgroup after a long absence, use of the
index display and the n command preceded by an appropriate number is
the quickest way to go through the group without possibly missing
information of interest.

Note that two columns of numbers are displayed on the left hand side
of the index. The leftmost column is simply the message order in the
index and the order in which the messages are displayed. The next
column to the right indicates the order in which the messages were
actually received. In this case the two columns are identical, but one
should note that the vnews software groups new messages together that
are related by subject.  Thus the second column numbering (order of
receipt) may differ from the order in the index.

For multipage indexes one must push the spacebar to see the next page
of the index. One can toggle between the index display and the
single-message-at-a-time display by repeated use of the a command.

r.  The r command is used to reply only to the author of the bulletin
and NOT also to the newsgroup. More details on replying are given in a
following section below.

f.  The f command is used to reply to the newsgroup for everyone to
see. More information on this command is provided below.

s.  The s command can be used to save a bulletin into a file in your
directory. After pressing s one sees a file: prompt.  One can then
enter a filename for the file in which the message will be stored.
Note that message can also be mailed to electronic mail addresses
(including your own) through the use of the s command. After pressing
s and seeing the "file:" prompt, simply enter "| mail address" where
address is the electronic mail address to which you wish to send the
posting. Use your own mail address if you wish to put the bulletin
into your own mail file and then forward it on to someone else
together with your comments through the use of the MM mail program.

RETURN.  Indicated by CR in the list above, this command lets you
select a message. Preceding the command by a number selects the
message with that number.

p.  Skips one back from a message to its "parent," i.e., the one to
which the message was a response. This allows one to back up to the
beginning of a discussion and then review it in the forward direction
again.

ug.  The ug command allows one to unsubscribe to a newsgroup. After
pressing these two keys sequentially, not simultaneously, one will no
longer be presented with messages from the newsgroup in question when
vnews is run. See below for more information about adding and deleting
newsgroup subscriptions in your .newsrc file.


Replying to messages

As noted in the section above on common vnews commands, there are two
commands to reply to a message depending upon your intent.  If you
think that your reply contains information that will be of interest to
more than just the author of the original message, use the f
(followup) command to post to the newsgroup. If you wish to send your
response only to the author of the original message and not to the
newsgroup, use the r (reply) command. These commands can be used after
reading a message or at any point while paging through a message.
After pressing f or r, the screen is blanked and one is placed into
one's default editor. Note that the screen (VT100 terminal using
Emacs here) is split into an upper and a lower window. The upper
window contains the message to which you wish to reply and the lower
window is where you compose your reply. The cursor is initially
positioned in the lower window.



Path: bionet!net.bio.net!kristoff
From: kristoff at NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: J. Biol. Chem. now on BIO-JOURNALS!
Message-ID: <CMM.0.88.611348084.kristoff at NET.BIO.NET>
Date: 16 May 89 18:54:44 GMT
Sender: kristoff at NET.BIO.NET
Lines: 12

The Journal of Biological Chemistry is a new addition to the
--%%-Emacs: 287                    [(Text Fill)]----Top------------------------
Command: reply
Newsgroups: bionet.general
To: kristoff at NET.BIO.NET
Subject: Re: J. Biol. Chem. now on BIO-JOURNALS!
Distribution:
References: <CMM.0.88.611348084.kristoff at NET.BIO.NET>

_  <= (the cursor is placed here)



-----Emacs: repa17122              [(Vnews Fill)]----All-----------------------
Loading vnews...done

For purposes of illustration we will use Emacs here although
experienced UNIX users might use, e.g., vi. The use of Emacs is
described in Chapter 13, but we remind you here of the following basic
commands (^B below means press the Ctrl and B keys simultaneously).

Basic Emacs Commands

^F	Move cursor Forward one space
^B	Move cursor Backwards one space
^N	Move cursor to the Next line
^P	Move cursor to the Previous line
^X O	Move cursor to other window

^X^S	Save text
^X^C	Exit Emacs

If one wishes to learn no more than the above and the use of the
backspace key for editing, one can manage one's way through the use of
Emacs (of course, learning more about the editor in Chapter 13 is
preferable).

After composing one's message, to post it press ^X^S followed by ^X^C.
After a slight delay you will exit from the editor and your message
will be posted. Should you change your mind part way through a reply,
you can exit without posting anything by pressing only ^X^C.

Please note that postings are distributed worldwide and that a few
scientists in foreign countries must pay to receive bulletins. For
these reasons we ask that you use the bulletin boards only for
legitimate scientific purposes.  One problem area involves the
mentioning of commercial products. While commercial scientific
products can be discussed on the appropriate newsgroup (usually
bionet.molbio.methds-reagnts), this should usually involve people with
no financial interests in the products (and this should be noted
explicitly in the messages).  Commercial advertising is not allowed
and can be grounds for the termination of network access privileges.

Posting new messages

While vnews is used for reading and responding to bulletins, the UNIX
hacker cabal decided for some unknown reason to use a separate program
called postnews to post new messages. Postnews is a very simple
program to use as illustrated in the following example.

EXAMPLE:

genbank%postnews
Is this message in response to some other message? n
Subject: 1989 ASCB Meeting GenBank Presentation
Keywords: ASCB, GenBank
Newsgroups (enter one at a time, end with a blank line):

The most relevant newsgroup should be the first, you should
add others only if your article really MUST be read by people
who choose not to read the appropriate group for your article.
But DO use multiple newsgroups rather than posting many times.

For a list of newsgroups, type ?
This list is long!
> bionet.general
> <cr>
Distribution (default='bionet', '?' for help) : ?
Display the help text on this (optional).
How widely should your article be distributed?

local	Local to this site
bionet	All sites carrying bionet newsgroups
ba	Sites in the San Francisco Bay Area
ca	California sites
usa	United States
na	North America
world	Everywhere on Usenet in the world (same as net)

Enter the word that specifies the distribution that you require.
Distribution (default='bionet', '?' for help) : <cr>

Choose the bionet default distribution mode which is essentially
worldwide, not just to users on the GenBank computer.  The system now
calls your default editor which is Emacs in this example.  The screen
will go blank and the following will be displayed.

Subject: 1989 ASCB Meeting GenBank Presentation
Newsgroups: bionet.general
Distribution: bionet
Keywords: ASCB, GenBank


This is where text is entered using Emacs (or your default editor).
Finish by pressing ^X^S^X^C.














--**-Emacs: posta17720             [(Vnews Fill)]----All-----------------------

What now?  [send, edit, list, quit, write, append] s


Accessing Particular Newsgroups and Older Information

Detailed on-line information about vnews can be seen by entering man
vnews at the genbank% prompt. We mentioned above that one can start
vnews simply by entering vnews after the genbank% prompt. As with
most other UNIX programs one can also use various command line options
(flags) together with the vnews command. Here we discuss the -n
flag used for reading only newsgroups with a particular name and the
-x flag which is used to access older messages in a group.

For example, vnews -n bionet.general can be used after the genbank%
prompt to read only new messages in the bionet.general newsgroup.
Remember that newsgroup names are arranged hierarchically from left to
right.  One can use the command vnews -n bionet to read all of the
bionet groups or vnews -n comp to see new messages on all of the
computer groups.

The -x flag allows you to see all of the messages currently archived
in a newsgroup. Normally when one runs vnews, one sees only new
messages. If one enters vnews -x one will be confronted with all of
the stored messages in every newsgroup in which one participates.
Obviously this is less useful than looking at old messages in a single
newsgroup. To do this one can combine the -x and -n flags with a
particular newsgroups, e.g., vnews -xn bionet.general to see all
saved messages on bionet.general. Note that the hyphen need only be
used once on the command line although vnews -x -n bionet.general
will also work.


Tracking your news Subscriptions - the .newsrc file

By now you might be wondering how vnews keeps track of what newsgroups
you read and what messages in these groups have been seen. The
mechanism used for this purpose is the .newsrc file in your directory
(visible only via the ls -a command). This file is created the first
time that you run vnews, and it contains the names of the various
USENET newsgroups and a tally of the messages that you have seen.
Part of a sample .newsrc file might look as follows:

options -n bionet,sci.bio,sci.chem,comp
bionet.general: 1-294
bionet.jobs: 1-117
bionet.molbio.news: 1-69
bionet.molbio.methds-reagnts: 1-111
bionet.molbio.genbank: 1-31
bionet.molbio.embldatabank: 1-4
bionet.molbio.bio-matrix: 1-79
bionet.molbio.evolution: 1-40
bionet.molbio.gene-org: 1-4
bionet.molbio.proteins: 1-13
bionet.software: 1-44
bionet.sci-resources: 1-63
bionet.molbio.pir: 1-10
bionet.molbio.swiss-prot: 1-7
bionet.technology.conversion! 1-138
bionet.molbio.ageing! 1-13
bionet.population-bio: 1-60
bionet.journals.contents: 1-12
sci.bio: 1-801
sci.bio.technology: 1-97
sci.chem: 1-297

You can display your own .newsrc file by entering the command more
.newsrc after the genbank% prompt.

The first line in the .newsrc file above is called the options
line. This line (as named) is optional and can be added if desired
with an editor such as Emacs or vi. It overrides the default vnews
settings which on GenBank allow you only to read the bionet
newsgroups. The options line in the example above lets one read all of
the bionet groups (the top level bionet domain is listed), the sci.bio
groups (includes sci.bio and sci.bio.technology), the sci.chem group,
and finally all comp computer groups. As further examples, one could
see all bionet, sci, and comp groups with the line

options -n bionet,sci,comp

or even every single USENET group (WARNING: a few hundred!!) with

options -n all

Also in the sample .newsrc file above one sees

bionet.technology.conversion! 1-138
bionet.molbio.ageing! 1-13

where these lines differ from the others in the use of a ! instead of
a :. This substitution prevents the reading of messages in the !'ed
newsgroup. Use of the ug (unsubscribe group) command in vnews
automatically effects this change in the .newsrc file.
Alternatively, one can directly edit the .newsrc file with, e.g.,
Emacs or vi and make these changes manually. Note that if one
unsubscribes from a newsgroup using the ug command then the only way
to resubscribe to the group is by editing .newsrc and changing the !
after the newsgroup name back to a :.

The last three newsgroups listed in the sample .newsrc above are in
the USENET sci (scientific) domain. These groups were established
independently of GenBank and are not connected with the GenBank
Resource. Nonetheless, we provide them along with the other USENET
newsgroups for use at your convenience.

If any new newsgroups are formed that are within the limits of your
vnews options (new bionet groups if no options are specified or else
new groups in whatever is used on the options line at the top of your
.newsrc file), you will be presented with these new groups
automatically when messages first appear in them. You can
participate in these new groups or use the ug command to remove your
subscription.   New newsgroups are automatically appended to
your .newsrc file after they appear for the first time.

Finally, the newsgroups are presented to you in the order in which
they appear in the .newsrc file. One can edit the file and change the
order of presentation simply by reordering the lines to suit your
preferences.


Viewing Messages at Login

On the GenBank On-line Service newsgroups are not viewed automatically
at login except for the newsgroup bio.announce which will be used only
by the GenBank staff to announce important changes in the Service.  To
read the news, you will have to explicitly use the vnews command after
the genbank% prompt.



Should you desire to see bulletins at login, this can be done by
adding the line

vnews 

with an editor to the end of your .login file. The .login file
contains commands that are run automatically each time that you log in
to GenBank.  While not absolutely required, it is safest if the vnews
line in the .login file is the last line in the file.




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