Bionet hierarchy

Dave Kristofferson kristoff at GENBANK.BIO.NET
Tue Apr 21 16:47:31 EST 1992


> Re the suggestion that someone write a FAQ sheet for the
> bionet hierarchy, I hereby volunteer myself to do the job,
> with a little help (and final approval from the bionet.general
> crowd).  So, while I finish up some other urgent business out 
> in reality-land, you can help me get started.
> 
> Please send me your favorite frequently asked (pertinent)
> question, and its answer, by either e-mail or bionet.general.
> E-mail would probably be better.
> -- 
> 
> Una Smith   una at phy.duke.edu    School of the Environment
>                                 Duke University
>                                 Durham, NC  27706
> 
> 

I include below what I had finished as of several months ago.  There
were only a few topics left, but the FAQ must also be revised in light
of the changeover from IRLEARN to Daresbury.  When completed, please
send it back to me for review and I will install it for automatic
posting each month.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff at genbank.bio.net

P.S. - After scanning through this I see there are several other
things that have changed, and I am not sure that it's such a good idea
to have someone else do this.  Una, if you still want to take a crack
at it, go ahead, but my feeling is that this can wait one more month.
I would have got to this fairly soon if the floppy disk release hadn't
just blown up in my face.

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

               BIOSCI Frequently Asked Questions (FAQ)
               ---------------------------------------

What is BIOSCI and bionet?
--------------------------

We'll spare you the fascinating historical details and say simply that
BIOSCI is a series of freely accessible electronic communication
forums (i.e., electronic bulletin boards or "newsgroups") for use by
biological scientists worldwide.  No fees are charged for the service.
The system is intended to promote communication between professionals
in the biological sciences.  All postings to the newsgroups should be
made in that spirit.  BIOSCI messages are distributed without
editorial intervention in most cases.  Dissemination is by normal
electronic mail and also over USENET in the form of the "bionet"
newsgroups (see below for USENET details).  The contents of the
electronic mail distribution is identical to the USENET news
distribution, but we encourage BIOSCI users to access the system
through USENET news software whenever possible.  E-mail distributions
may eventually be phased out.


What newsgroups are available on BIOSCI/bionet?
-----------------------------------------------

This is the list of the mailing lists as of 12/21/91.  USENET
newsgroups are described further below.

NEWSGROUP NAME               TOPIC
--------------               -----
AGEING                       Scientific Interest Group
AGROFORESTRY                 Scientific Interest Group
ARABIDOPSIS                  Newsgroup for the Arabidopsis Genome Project
BIOLOGICAL-INFO-THEORY       Discussions about biological information theory
BIONAUTS                     Address & other info about biologists on networks
BIONEWS                      General announcements of widespread
                                interest to biologists
BIO-JOURNALS                 Tables of Contents of biological journals
BIO-MATRIX                   Applications of computers to biological databases
BIO-SOFTWARE                 Information on software for the
                                biological sciences
CHROMOSOME-22                Mapping and Sequencing of Human Chromosome 22
COMPUTATIONAL-BIOLOGY **     Mathematical and computer applications in biology
EMBL-DATABANK                Messages to and from the EMBL database staff
EMPLOYMENT                   Job opportunities
GENBANK-BB                   Messages to and from the GenBank database staff
GENETIC-LINKAGE              Newsgroup for genetic linkage analysis
GENOMIC-ORGANIZATION         Scientific Interest Group
HIV-MOLECULAR-BIOLOGY        Discussions about the molecular biology of HIV
HUMAN-GENOME-PROGRAM         NIH-sponsored newsgroup on human genome issues
METHODS-AND-REAGENTS         Requests for information and lab reagents
MOLECULAR-EVOLUTION          Scientific Interest Group
NEUROSCIENCE                 Scientific Interest Group
POPULATION-BIOLOGY           Scientific Interest Group
PROTEIN-ANALYSIS             Scientific Interest Group
SCIENCE-RESOURCES            Information from/about the funding agencies

** 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.


What is USENET?
---------------

USENET (short for Users Network) is an electronic bulletin board
network which utilizes various public domain versions of the "netnews"
software for message transmission.  The software can operate over
physical networks ranging from as simple as a telephone UUCP link (via
modem) to networks as sophisticated as the Internet.  Netnews has been
optimized to tranmit messages without loss and also to avoid possible
mail loops and other errors which plague simple electronic mail
"broadcasting."  It is for this reason that we strongly encourage our
users to adopt netnews software at their sites as soon as possible.
News software also keeps messages segregated into their respective
newsgroups, making it easier to follow the thread of a discussion.  If
you only use e-mail, messages from all of the newsgroups to which you
subscribe will be sent to your one personal e-mail address and will be
mixed in with each other and with other personal messages.  This is
obviously a suboptimal way to keep messages organized.

Here is the list of the mailing lists with their corresponding USENET
newsgroups:

NEWSGROUP NAME             Mailing Address       USENET Newsgroup Name
--------------             ----------------      ---------------------
AGEING                     AGEING                bionet.molbio.ageing
AGROFORESTRY               AG-FORST              bionet.agroforestry
ARABIDOPSIS                ARAB-GEN              bionet.genome.arabidopsis
BIOLOGICAL-INFO-THEORY     BIO-INFO              bionet.info-theory
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
HIV-MOLECULAR-BIOLOGY      HIV-BIOL              bionet.molbio.hiv
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.


How can I get news software at my site?
---------------------------------------

Contact kristoff at genbank.bio.net for a compliation of assorted
messages on this topic.  News software can be obtained free of charge
from anonymous FTP sources.


How do I request or cancel e-mail subscriptions to BIOSCI newsgroups?
---------------------------------------------------------------------

If you have access to USENET news software, then YOU DO NOT NEED AN
E-MAIL SUBSCRIPTION!  Only those people who need to receive postings
by e-mail must request to be added to the mailing lists.  USENET users
can simply read the various bionet newsgroups using their news
software.  If your site has USENET news but does not get the bionet
newsgroups, please request them by sending a message to
biosci at genbank.bio.net.

For those who need e-mail subscriptions or who want to cancel current
e-mail subscriptions, please send a request to one of the following
addresses.  Choose whichever site that you can reach most
conveniently.  Simply pick the newsgroup(s) from the list above that
you wish to subscribe to and request that your address be added to the
appropriate mailing lists.  Please use plain English; no special
message syntax is required in your subscription or cancellation
request.

Address                               Location        Network
-------                               --------        -------
biosci at genbank.bio.net                U.S.A.          Internet/BITNET
biosci at irlearn.ucd.ie                 Ireland         EARN/BITNET
biosci at uk.ac.daresbury                U.K.            JANET

****If you are changing e-mail addresses****, please be sure to send a
message to your appropriate biosci address above and request that your
subscriptions be changed or canceled!!


Why are there three BIOSCI sites?
--------------------------------

Although 99% of you never have to pay for any BIOSCI messages, rest
assured that network resources are not free and should not be
squandered.  We established one BIOSCI distribution site on each major
network in the Western Hemisphere and in Europe to minimize network
e-mail traffic.  For example, if a message is posted to the U.S. site,
only one copy is sent on to the other two sites before being
"exploded" for distribution to all of the final e-mail destinations.
This is more efficient than sending hundreds of copies of the same
message across the Atlantic.  A trade-off for this efficiency is
increased complexity in the distribution network.  This has caused
sporadic problems with bounced mail, but we have so far lived with
these occasional inconveniences in order to minimize waste of
resources.  Everyone would be better served if USENET news was used
exclusively, and we have the eventual elimination of e-mail
subscriptions as a long term goal.  Currently, however, too many
biologists still have no other means of access to BIOSCI other than
through e-mail.


How do I know to which newsgroup a message was posted?
------------------------------------------------------

If you use USENET news software, all messages are sorted by newsgroup
so there is no problem identifying the source.  If you receive BIOSCI
postings in your mail file, all postings are funneled into one mail
file and you must be a little discerning.  The best way to determine
the news forum is to look at the line in the mail header that starts
with "To:".  For example, if you see "To: arab-gen at genbank.bio.net"
then you can tell by refering to the list of mailing addresses above,
that the message was sent to the ARABIDOPSIS newsgroup.  The "From:"
line in the mail header indicates who sent the message.  If you want
to reply only to the author of the message, use the address on the
"From:" line.  If you want to reply to everyone on the newsgroup, use
the address on the "To:" line.


What is the BIOSCI-REQUEST address?
-----------------------------------

The BIOSCI-REQUEST at genbank.bio.net address was established to trap
mailing error messages.  The address is not normally seen by BIOSCI
readers in the messages that they receive.  Unfortunately some
proprietary (read VMS) and other oddball mail systems misread the
information used to transmit Internet e-mail messages and may end up
putting the BIOSCI-REQUEST address on the From: line in the mail that
you may receive.  If this happens at your site and you want to reply
to a message, please use either the newsgroup address on the To: line
of the message or try to find the author's e-mail address elsewhere in
the message (people often append this at the end of their text in
their "signature").  If you send a message back to
BIOSCI-REQUEST at genbank.bio.net, the BIOSCI managers at GenBank will be
the only ones who will see it (we will try to forward it to the
appropriate newsgroup).


How do I post a message?
------------------------

If you use USENET, run your posting program (e.g., postnews, please
check with your local systems administrator) and follow the prompts.
Enter the appropriate newsgroup from the list of USENET names (below)
when prompted.  Be sure to set your news distribution to "world" (or
"bionet" if the option is available) if you want your message to be
seen by others.  Some USENET systems may default to "local" which
means that only people on your local computer will see the message.

If you are using e-mail, first select the newsgroup that you wish to
post to from the following list and find the mailing address.  For
example, the address for the BIO-SOFTWARE newsgroup is BIO-SOFT (but
there is more to it below, of course!):

----------------------------------------------------------------------
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.
----------------------------------------------------------------------

Once you have the mailing address, you also need to decide which of
the three BIOSCI sites to mail your message to.  For example, if you
are in the U.S. your site is genbank.bio.net, so to mail to
BIO-SOFTWARE, use the address BIO-SOFT at genbank.bio.net.  The same
mailing addresses are in use at all BIOSCI sites.  Copies of mail
posted to any one of the sites are distributed to the other sites
automatically, so you should NOT send to more than one site.  The
following table lists the possible addresses for BIO-SOFTWARE.  To
post to other newsgroups, simply replace BIO-SOFT with the appropriate
mailing address from the list above:

Address                               Location        Network
-------                               --------        -------
bio-soft at genbank.bio.net              U.S.A.          Internet/BITNET
bio-soft at irlearn.ucd.ie               Ireland         EARN/BITNET
bio-soft at uk.ac.daresbury              U.K.            JANET



How can I get a list of newsgroups or my subscriptions?
-------------------------------------------------------

As with any other subscription correspondence, simply send a request
to your appropriate BIOSCI distribution site:

Address                               Location        Network
-------                               --------        -------
biosci at irlearn.ucd.ie                 Ireland         EARN/BITNET
biosci at uk.ac.daresbury                U.K.            JANET
biosci at genbank.bio.net                U.S.A.          Internet/BITNET

The most recent list of BIOSCI newsgroups and the latest revision of
this message is posted the first of each month on the
BIONEWS/bionet.general newsgroup.  You should save these postings for
future reference.


Why have I stopped getting messages?
------------------------------------

If your computer or network connection is down, mail sent to your
address will "bounce" back to the sender of the message and often to
the BIOSCI-REQUEST address at GenBank.  Given the number of people
using BIOSCI around the world, this can become quite a problem, so we
have to take prompt action to eliminate troublesome addresses from our
mailing lists.  If your system is down there may be no way to reach
you, so it is your responsibility to contact your BIOSCI distribution
site and request reinstatement if you notice a lapse in distribution.
We do not have the resources to be able to send out reminders.


I posted a message and got back an error message from a daemon!!
----------------------------------------------------------------

Don't panic!!  The devil is not in the employ of BIOSCI!  It is a rare
day when every single computer and e-mail address on the BIOSCI
mailing lists is functional.  Mail systems are programmed to alert you
if mail does not go through to a particular address which could be on
any of our lists around the world.  Rest assured that your message was
received by the vast majority of readers.  You may either just delete
these bouncers or send them on to your local BIOSCI distribution node
(in most cases we will probably be aware of them already).  It is not
uncommon to receive one or two bouncers for any e-mail posting that
you make.  Note once again that if everyone used news software and if
we didn't have to bridge so many incompatible e-mail networks to bring
the biology community together, we wouldn't have to deal with this
problem.

Note that the BIOSCI-REQUEST address at GenBank was established to
trap daemon bouncers instead of passing them back to the person who
posts a message.  Unfortunately due to network incompatibilities,
the BIOSCI-REQUEST trapping mechanism is often disabled when the bad
address is not on the Internet.


Where (and how many times) should I post my messages?
-----------------------------------------------------

The list of newsgroups above gives a brief description of the purpose
of each newsgroup.  Please select the appropriate forum for your
posting with the newsgroup's purpose in mind.  The groups designated
as "Scientific Interest Group" are for discussions of professional
interest in the area designated by the newsgroup name, i.e.,
population biology issues should obviously be directed to the
POPULATION-BIOLOGY newsgroup.  

A few guidelines on some of the other newsgroups:

BIONAUTS:  This newsgroup was designed to help biologists "voyaging"
into the new world of electronic networking.  This is the appropriate
forum for requesting electronic mail addresses of other biologists (no
guarantees they'll respond, of course, but someone might;  e-mail
directory services still leave much to be desired).  In addition, this
forum can be used for asking questions if you need any help with mail
and news software or other aspects of electronic networking.

BIONEWS: At the time of this writing (Dec. 91) a vote is taking place
among the readership to possibly change the prupose of this newsgroup.
It is currently supposed to be a place for general announcements such
as for scientific meetings, courses, etc., but it has also served as a
forum for discussions on other topics that do not fit in to any of the
specialty newsgroups.  Watch this space in latter versions of the FAQ
sheet for new developments.

BIO-JOURNALS:  This newsgroup is not for postings by readers.  It is
used to distribute the Table of Contents for the following journals
approximately a week or two in advance of publication:

Applied and Environmental Microbiology
CABIOS
EMBO Journal
Journal of Bacteriology
Journal of Biological Chemistry
Journal of Virology
Molecular and Cellular Biology
Molecular Microbiology
Nucleic Acids Research

BIO-SOFTWARE: For USENET users only, please note that there is an
accompanying newsgroup bionet.software.sources used for distributing
biological software source code and binaries.  This service is not
available by e-mail.

COMPUTATIONAL-BIOLOGY: This newsgroup is moderated, i.e., postings
made to the group are reviewed by a moderator before being
distributed.  You can post messages without editorial intervention to
other BIOSCI/bionet newsgroups.

EMPLOYMENT: Because of network regulations (many of our distribution
routes are subsidized at taxpayer expense) commercial job postings are
not allowed on this newsgroup.  Please post only non-profit jobs in
the biological sciences.

SCIENCE-RESOURCES: This newgroup is used solely to distribute funding
agency announcements such as the "NIH Guide for Grants and Contracts"
and is not to be used for postings by readers.

Most other BIOSCI newsgroups are dedicated to professional discussions
in the area defined by the name of the newsgroup.  You are free to
post anything of interest within the specialty.  Please note that the
lack of face-to-face contact often emboldens some of our readers.
While we can wish that everyone learned manners in grade school or at
home, please be aware that discussions can sometimes become a bit more
heated than a new user might be used to (our readership is usually
composed of "sober" Ph.D.s, or so I used to think 8-).  NOTE: To
understand what 8-) means tilt your head to the left; other variants:
:-) and :-(.  These symbols try to add emotional conotations to the
electronics such as "that's a joke, son!"


How do I find back issues of BIOSCI postings?
---------------------------------------------





How to start a new newsgroup

What journals are available on BIO-JOURNALS?

Why didn't my USENET posting show up elsewhere?

My messages are going to bionet.followup.



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