dbd%benden@LANL.GOV (Dan Davison) (03/11/89)
The Bio-Matrix archive server (archive-server@genome.lanl.gov) has been
expanded. It now includes all the BIONET MOLECULAR-EVOLUTION discussions,
divided into three parts. The TDALIGN sequence alignment program has
also been added, and the tRNA database is also in this directory.
This is the new top-level index. The standard help message about using
the archive-server follows the index.
If you have trouble with the server, send a message as described in the
HELP message. The only outstanding problem that I know of is some mailers
do not correctly handle messages longer than 64K bytes. Be sure to
request the latest index in case the longer files have to be split up.
dan davison
bio-matrix-request@bionet-20.bio.net
molecular-evolution@bionet-20.bio.net
goad.davison@bionet-20.bio.net
============================================================================
TOP-LEVEL INDEX for the BIO-MATRIX ARCHIVE SERVER
(last change 3/10/89 8:30PM PST)
I. matrix - The Matrix of Biological Knowledge archives
(Bio-matrix-request@bionet-20.bio.net for info)
file name Description and size
------------ ----------------------------------------------------------
87matrix. (NOTE THE "." IN THE NAME!) 1987 Bio-Matrix postings
88matrix. (NOTE THE "." IN THE NAME!) 1988 Bio-Matrix postings
matrixreport. (NOTE THE "." IN THE NAME!) 1987 draft Matrix report
("matrixreport" (no ".") will now work too.
limb1.1of4 The Listing of Molecular Biology Databases, version 1.0
limb1.2of4 broken into four pieces of about 30K each. You must
limb1.3of4 get all four files and assemble them (use cat(1)) for
limb1.4of4 the complete database.
limb.index index of the LiMB database
limb.note a "read this first" for LiMB
questions. questions about the Matrix concept
answers. answers to those questions
II. molevol - Molecular Evolution mail list archives
(Molecular-evolution-request@bionet-20.bio.net for info)
file name Description and size
------------ ----------------------------------------------------------
msg1-40 Molecular-Evolution bulletin board messages 1-40 90K bytes
msg41-80 Molecular-Evolution bulletin board messages 41-80 111K bytes
msg81-98 Molecular-Evolution bulletin board messages 81-98 47K bytes
III. tdalign - Thompson and Davison sequence alignment program
file name Description and size
------------ ----------------------------------------------------------
tdalign.shar The Thompson and Davison alignment program, shar format
69Kbytes
trna.seq The NAR tRNA sequence collection 119K
trna.lst The directory of the tRNA sequence collection 47K
==============================================================================
The HELP message:
This message comes to you from the archive server at genome.lanl.gov,
archive-server@genome.lanl.gov. It received a message from you asking for
help.
The archive server is a mail-response program. That means that you mail it a
request, and it mails back the response.
The archive server is a very dumb program. It does not have much error
checking. If you don't send it the commands that it understands, it will just
answer "I don't understand you".
The archive server has 3 commands. Each command must be the first word on a
line. The archive server reads your entire message before it does anything,
so you can have several different commands in a single message. The archive
server treats the "Subject:" header line just like any other line of the
message. You can use any combination of upper and lower case letters in the
commands.
The archives are organized into a series of directories and subdirectories.
Each directory has an index, and each subdirectory has an index. The
top-level index gives you an overview of what is in the subdirectories, and
the index for each subdirectory tells you what is in it.
---------------------------------------------------------------------------
If you are bored with reading documentation and just want to try something,
then send the server a message containing the line
send index matrix
When you get the index back, it will give you the names of all of the files
in the archive; send the server another message asking it to send you the
files that you want:
send matrix 87matrix.
etc.
If you are using a mailer that understands "@" notation, send to
archive-server@genome.lanl.gov. If your mailer deals in "!" notation, try
sending to {someplace}!genome!archive-server, e.g.
ihnp4!cmcl2!lanl!genome!archive-server. Less intelligent mailers may like
archive-server%genome@lanl.gov; from BITNET,
archive-server%genome.lanl.gov@CUNYVM
For other mailers, you're on your own. Good luck!
---------------------------------------------------------------------------
Here is some more documentation. The server has 3 commands:
"help" command: The command "help" or "send help" causes the server to
send you the help file. You already know this, of course, because
you are reading the help file. No other commands are honored in a
message that asks for help (the server figures that you had better
read the help message before you do anything else).
"index" command: if your message contains a line whose first word is "index",
then the server will send you the top-level index of the contents of
the archive. If there are other words on that line that match
the name of subdirectories, then the indexes for those subdirectories
are sent instead of the top-level index. For example, you can say
index
or
index matrix
You can then send back another message to the archive server,
using a "send" command (see below) to ask it to send you the files
whose name you learned from that list.
(Footnote: "index matrix" and "send index matrix" mean the
same thing: you can use the "send" command instead of the "index"
command, if you want, for getting an index.
If your message has an "index" or a "send index" command, then all
other "send" commands will be ignored. This means that you cannot
get an index and data in the same request. This is so that index
requests can be given high priority.)
"send" command: if your message contains a line whose first word is "send",
then the archive server will send you the item(s) named on the
rest of the line. To name an item, you give its directory and its
name. For example
send matrix matrixreport.
Once you have named a category, you can put as many names as you
like on the rest of the line; they will all be taken from that
category. For example:
send matrix 87matrix. 88matrix. matrixreport.
Each "send" command can reference only one directory. If you
would like to get one recipe and one program, you must use two
"send" commands, one beginning "send recipe" and the other
beginning "send program".
You may put as many "send" commands as you like into one message
to the server, but the more you ask for, the longer it will take
to receive. See "FAIRNESS", below, for an explanation. Actually,
it's not strictly true that you can put as many "send" commands
as you want into one message. If the server must use uucp mail
to send your files, then it cannot send more than 100K bytes
in one message. If you ask for more than it can send, then it
will send as much as it can and ignore the rest.
The archive server is relatively resistant to
case-sensitivity. Matrix, MATRIX, and matrix will all work
in the "send" command, as in
SEND MATRIX filename
but the filename still has to be in the proper case.
Similarly, TDALIGN, Tdalign, and tdalign all work, as do
MOLEVOL, Molevol, and molevol.
EXAMPLES:
1) Get the list of what's in the archive-server. Send this message:
To: archive-server@genome.lanl.gov
Subject: hi there
send index
2) Get the Bio-matrix report from the archive (you have learned
the file name from the list that was sent to you in step 1).
To: archive-server@genome.lanl.gov
Subject: send matrix matrixreport
send matrix limb1.1of4 limb1.2of4 limb.note
send matrix limb1.3of4 limb1.4of4 questions answers
NOTES:
The archive server acknowledges every request by return mail. If you don't
get a message back in a day or two (depending on how close you are to genome
on the network) you should assume that something is going wrong. If you
aren't getting anywhere and you don't know a wizard to help you, try
sending mail to dd@lanl.gov with a subject of "Matrix Server Help Needed".
Anything else may be ignored!
The delays in sending out large items from the archives are intentional, to
make it difficult to get copies of everything in the archives. If you are new
to the network and would like to get all back issues of everything, you
should post a request to a regional newsgroup asking whether someone who is
geographically near you can provide them.
Don't send mail with long lines. If you want to ask for 20 recipes in one
request, you don't need to put all 20 of them in one "send" command. The
archive server is quite able to handle long lines, but before your mail
message is received by the archive server it might pass through relay
computers that will choke on long lines.
The archive server does not respond to requests from users named "root",
"system", "daemon", or "mailer". This is to prevent mail loops. If your name
is "Bruce Root" or "Joe Daemon", and you can document this, I will happily
rewrite the server to remove this restriction. Yes, I know about Norman
Mailer and Waverley Root. Norman doesn't use netmail and Waverley is dead.
FAIRNESS:
The archive server contains many safeguards to ensure that it is not
monopolized by people asking for large amounts of data. The mailer is set up
so that it will send no more than a fixed amount of data each day. If the
work queue contains more requests than the day's quota, then the unsent files
will not be processed until the next day. Whenever the mailer is run to send
its day's quota, it sends the requests out shortest-first.
If you have a request waiting in the work queue and you send in another
request, the new request is added to the old one (thereby increasing its
size) rather than being filed anew. This prevents you from being able to
send in a large number of small requests as a way of beating the system.
If you request 10 recipes together, you will get substantially higher
priority than if you make 10 requests for 1 recipe each.
The reason for all of these quotas and limitations is that the delivery
resources are finite, and there are many tens of thousands of people who
would like to make use of the archive.