IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

BIOSCI/bionet Frequently Asked Questions

BIOSCI Administrator biosci-help at net.bio.net
Fri Jan 1 04:04:03 EST 1999

         BIOSCI/bionet Frequently Asked Questions (FAQ)

This document supplements the BIOSCI Newsgroups Information Sheet and
provides details on how to participate in BIOSCI forums. Both
documents are available for anonymous FTP and gopher retrieval (port
70) from net.bio.net []. The text version of the FAQ is
found in pub/BIOSCI/doc/biosci.FAQ. This document is also available
using the World Wide Web at
"http://www.bio.net/BIOSCI/biosci.FAQ.html". This document may also
be requested by e-mail by sending the command

     info faq

in the body of an e-mail message addressed to the Internet address

             biosci-server at net.bio.net

Any text placed on the Subject: line of your message is ignored, so
please be sure to put the "info faq" command in the main body of your
e-mail message. The FAQ is posted the first of each month to the
BIONEWS/bionet.announce newsgroup along with the BIOSCI information
sheet and the list of changes to the newsgroups during the preceding



  * What is BIOSCI and bionet?
  * What newsgroups are available on BIOSCI/bionet?
  * Where should I post my messages?
  * What are the restrictions on commercial activities in the
    BIOSCI/bionet newsgroups?
  * How does one post a message?
  * Should I post my message to more than one newsgroup?
  * Sorting out mail - which newsgroup did an e-mail message come
  * Why do all of my postings come from "BIOSCI-REQUEST?"
  * How do I reply to a BIOSCI posting?
  * What is Usenet?
  * How can I get news software at my site?
  * How can I test my news or mail software?
  * I hear that a new bionet newsgroup was created but why isn't it at
    my site yet?
  * A new bionet Usenet group has been created at my site but there
    are no messages in it. However, I see that messages are being
    sent out to the mailing list. Why do the contents differ?
  * How do I request or cancel e-mail subscriptions to BIOSCI
  * How can I get a list of newsgroups or my subscriptions?
  * How do I find back issues of BIOSCI postings?
  * Is there a summary of METHODS-AND-REAGENTS postings?
  * What journals are available on BIO-JOURNALS? How can one locate
  * Why are there two BIOSCI sites?
  * Why have I stopped getting messages?
  * What should I do about mail error messages that come back when I
  * How does one start a new BIOSCI newsgroup/mailing list?
  * How can I list my address information in the BIOSCI user
  * Why didn't my Usenet posting show up elsewhere?
  * Why are my messages are going to bionet.followup?

  * What are all of these references to FTP, WAIS, Gopher, and WWW?
  * Please help me find the e-mail address for Dr. ...
  * How do I report a problem in a biological data base?
  * What about submitting sequence data to GenBank, EMBL, DDBJ or PIR?

Other questions to add to this list??? Please send them to
biosci-help at net.bio.net. We would also appreciate your sending the
answer to the question if possible. All contributions will be
gratefully acknowledged by including the author's name along with the
answer provided.


Common Questions about BIOSCI/bionet usage


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. While the general public may "listen in" to the
discussions, these newsgroups are intended primarily for
communications between researchers. There are other forums on Usenet
such as sci.bio for the asking and answering of biological questions
from lay persons.

BIOSCI messages are distributed without editorial intervention in most
cases. Dissemination is by both electronic mail and 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. As of October 1992, 59% of
our readers used Usenet news software instead of e-mail.

You may find much more detailed and up to date information concerning
Usenet in the news.announce.newusers newsgroup. These articles are
also available using anonymous FTP from rtfm.mit.edu [, but
please always reference the hostname rtfm.mit.edu, as IP addresses and
canonical names will change in the future, but rtfm.mit.edu will
remain correct], in the /pub/usenet/news.announce.newusers directory.
You may be specifically interested in the following articles:
  * What_is_Usenet?
  * What_is_Usenet?__A_second_opinion.
  * Usenet_Software:_History_and_Sources
  * How_to_Get_Information_about_Networks
  * How_to_become_a_Usenet_site
  * Answers_to_Frequently_Asked_Questions_about_Usenet
  * Emily_Postnews_Answers_Your_Questions_on_Netiquette
  * Hints_on_writing_style_for_Usenet

Detailed starting information on how to get your site connected to the
Internet can be found the file



the latest list of newsgroups, e-mail posting addresses, and other
information about subscribing/unsubscribing, etc., to BIOSCI is posted
the first of each month on the BIONEWS/bionet.announce newsgroup along
with this FAQ posting.

Two versions of the BIOSCI info sheet are available, one for the
Americas and the Pacific Rim countries, and the second for Europe,
Africa, and Central Asia. The former may be requested by e-mail to
biosci-help at net.bio.net, while the latter may be requested from
biosci at daresbury.ac.uk.



The list of newsgroups in the BIOSCI info sheet 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 specific newsgroups:

BIONAUTS/bionet.users.addresses: This newsgroup was designed to help
biologists "voyaging" into the new world of electronic networking.
This is also the appropriate forum for requesting electronic mail
addresses of other biologists if you can not find them in the BIOSCI
user address directory (the address directory is described elsewhere
in this FAQ). Regarding address requests to BIONAUTS, there are no
guarantees that the people in question will respond personally, of
course, but someone else might. 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, e.g. "What is WAIS, gopher,
and all of these other newfangled things that I have been hearing
about?" (see another FAQ section for answers to this last question!).

BIONEWS/bionet.announce: This is a moderated newsgroup designed to be
low-volume, high content and intended primarily for announcements of
interest to most users on the network, e.g., for general announcements
such as for scientific meetings, courses, etc. We recommend that *ALL*
participants subscribe to this newsgroup to keep up with the items
above and also to receive the latest information about changes to

BIOFORUM/bionet.general: BIOFORUM is intended for discussions on
topics that do not fit in to any of the specialty newsgroups. If you
want to start a new newsgroup, you might begin by trying to raise
interest through a discussion in this forum. Be aware that this
newsgroup is by design one of the most "chatty" forums in the BIOSCI

BIO-JOURNALS/bionet.journals.contents: This newsgroup is not for
postings by readers. It is used to distribute the Table of Contents
for over 30 biological research journals approximately a week or two
in advance of publication (see the latest listing of journals in the
FAQ section about the BIO-JOURNALS newsgroup).

BIO-SOFTWARE: Intended for discussions about software in the
biological sciences. There are other Usenet newsgroups and mailing
lists for questions about word processors, etc., i.e., for general
purpose software. BIO-SOFTWARE is intended for discussions about
software for biologists. 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

EMPLOYMENT: These are the posting regulations for
EMPLOYMENT/bionet.jobs as formulated by the U.S. National Science
Foundation. Readers outside of the U.S. should check with their local
network authorities to determine what rules apply to their usage.
EMPLOYMENT/bionet.jobs is to be used for the posting of job openings
in the biological sciences or professional level jobs that support the
work of biological scientists (such as for computer/systems
programming/support). There are no restrictions on the content of the
postings if these jobs are in the non-profit sector. Individuals
regardless of their place of employment may post their CVs/resumes to
this newsgroup or simply place a request for work if they are looking
for jobs in this area of endeavor. Commercial companies can post jobs
intended for professional people in the areas just mentioned provided
that the postings are limited to the format described below. Extended
commercial job/benefit descriptions and promotional material are not
allowed, nor may commercial firms post openings for non-professional
positions (if in doubt about the appropriateness of a posting, please
check with biosci-help at net.bio.net *before* proceeding).

 Commercial job posting format

The posting should include
  * job title
  * one or two line factual description of the position
  * an e-mail contact address for further information; a regular
    surface mail address and contact telephone number is also

To repeat, commercial job postings that do not comply with the above
format or that are for jobs in areas outside of the range described
above are not permissible in this newsgroup. Your cooperation is
greatly appreciated.

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 served by the newsgroup.
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 accustomed
to (our readership is usually composed of "sober" Ph.D.s, or so we
used to think, but it appears that perhaps economic hard times have
taken their toll on sobriety 8-).

NOTE: To understand what 8-) means tilt your head to the left; other
variants: :-) and :-(. These symbols try to add emotional connotations
to the electrons such as "that's a joke, son!"



BIOSCI is funded in part by the National Science Foundation (NSF)
which supports the Internet in the U.S. with U.S. taxpayer dollars.
NSF is responsible for setting Acceptable Use Policy (AUP) for the the
NSFNet backbone section of the Internet of which BIOSCI makes
extensive use. Because of these reasons, BIOSCI users should adhere to
the following guidelines.

Commercial activities on BIOSCI are in general prohibited except as
noted below. People at for-profit organizations are free to read all
postings made to the BIOSCI/bionet newsgroups, but must ensure that
their postings to the newsgroups do not violate our guidelines.

Commercial organizations may post job openings on
EMPLOYMENT/bionet.jobs subject to the format restrictions for that
group. Commercial job posting format restrictions for the
EMPLOYMENT/bionet.jobs newsgroup are described above under the
question "Where should I post my messages?" Users who violate these
format restrictions consciously risk losing their network access.

BIOSCI readers without any financial connections to a company or a
product may discuss and/or post endorsements of a commercial product.
However, it is standard Internet practice to include in the posting a
disclaimer of any financial interest in the product/company. Note that
postings to newsgroups are subject to libel laws. BIOSCI advises
readers to think twice before taking potshots at products that they do
not like.

BIOSCI users often post general questions about problems that might be
solved through the use of a commercial product. It is EXTREMELY
IMPORTANT, however, that such general questions *not* be answered by
people affiliated with the product or company that might stand to gain
a sale as a result. For example, user X may ask, "Is there a product
that will allow me to separate protein A from protein B given the
following properties ...?", but, if user Y works at company Z which
sells a product that can accomplish this task, user Y does *NOT* have
permission to respond to the question. Responses can only be posted by
other scientists who might have experience in solving the problem in
question and who do not stand to gain financially by promoting the
product in question, i.e., they are not employees, consultants, or
connected to the company via other financial ties. As noted above,
postings endorsing commercial products should contain a customary
disclaimer stating the absence of financial ties of the poster to the

Commercial companies MAY RESPOND to a public BIOSCI newsgroup if a
BIOSCI user asks a question directly about one of their products,
e.g., mentions it by name. The response should be limited to a factual
answer of the question posed and should avoid any hint of advertising
hype. Comparisons with competitors' products should be avoided

Finally, as a general rule, if you are unsure about the
appropriateness of your posting, before you post anything please send
a copy of what you propose to post to the BIOSCI adminstrator at
biosci-help at net.bio.net for review.

BIOSCI will takes steps to terminate network access to any reader who
willfully violates our commercial use policies.



If you use Usenet, run your posting program (e.g., postnews or e.g.,
use the ":post" command in nn) and follow the prompts. Please check
with your local systems administrator for details on using your local
news software; general information on Usenet and how to get news
software is provided further below but each news program is different.
When prompted, enter the appropriate newsgroup name from the list of
Usenet names in the BIOSCI info sheet. 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. You can limit the extent of distribution of your
message by choosing other distribution options, e.g., "usa"
distributes only to the U.S.A. (sometimes! - on occasion these
distribution limiting features don't work for a variety of reasons).
Usually pressing "?" or "h" at the Distribution: prompt will show you
your options. After entering your options, you are usually placed in
an editor to compose your message. After saving it and exiting the
editor, one typically enters a "send" command to complete the posting

If you are using e-mail, first select the newsgroup that you wish to
post to and find the mailing address in the BIOSCI info sheet for your
region. For example, to post to the METHODS-AND-REAGENTS newsgroup you
would use one of the following two addresses depending upon your

Address                            Serving
-------                            -------
methods at net.bio.net                The Americas and Pacific Rim
methods at daresbury.ac.uk            Europe, Africa, and Central Asia

Once you have entered the newsgroup mailing address on the To: line of
your mail message, the rest of the process is the same as composing
and sending any e-mail message. Your message will be automatically
distributed to all mail recipients on the list and also distributed by
Usenet news.

The BIOSCI information sheet containing the latest list of e-mail
addresses for each of the above regions can be requested from
biosci at net.bio.net or biosci at daresbury.ac.uk respectively.



Generally only *ONE* copy of a message should be posted to the most
appropriate forum. Crossposting the same message to multiple
newsgroups can aggravate readers who participate by e-mail. These
people will receive multiple copies of a message if they are on the
mailing lists for the groups that receive the crosspostings.

Please note that software safeguards in our system which prevent
mailing loops also make it difficult to use news software to both
crosspost to different newsgroups AND simultaneously mail to all
associated mailing lists. If you *absolutely must* distribute a
message to different newsgroups AND their associated mailing lists,
the way to do this is to e-mail a *separate* copy of your message to
each newsgroup e-mail posting address. Including multiple mailing
addresses on a single e-mail message will not crosspost to all mailing
lists. Please be aware that many people read multiple groups by mail
and be assured that, if two groups are related, many people who are
interested in one will obviously sign up for the other group, too.
Before crossposting, be certain that your message is so important that
it really warrants sending multiple copies to a large number of



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 your one
mail file merely by chronological order of posting and you must be a
little discerning to follow discussions.

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 net.bio.net" or "To: arab-gen at daresbury.ac.uk" then you know
that the address for sending a reply to everyone on the newsgroup is
"arab-gen at net.bio.net" or "arab-gen at daresbury.ac.uk." The "From:" line
in the mail header indicates who sent the message. In most cases, if
you want to reply only to the author of the message, use the address
on the "From:" line, and, if you want to reply to everyone on the
newsgroup, use the address on the "To:" line (but please read the
following sections on the BIOSCI-REQUEST address and replying to
BIOSCI postings for additional information).

Please note that replies to BIOSCI messages are *not* automatically
sent back to the newsgroup address. The default reply on most mail
systems (your local mail configuration may differ) will be to reply to
the address that you see on the "From:" line, i.e., only to the person
who posted the original message. You must consciously decide to send a
copy of your reply to the newsgroup by including the newsgroup posting
address in your e-mail response. This default reply (to the original
sender only) is an Internet newsgroup standard and is the opposite of
that used by the BITNET LISTSERV software (for those who may be
familiar with the latter; the Internet standard is designed to
minimize wasted network bandwidth, i.e., to avoid the *automatic,
unthinking* posting by many people of the same answer to a particular



Unfortunately some mail systems make all BIOSCI postings appear to
come from someone named "BIOSCI-REQUEST." The
BIOSCI-REQUEST at net.bio.net address was established to trap mailing
error messages ("bouncers"). 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 net.bio.net, the BIOSCI managers at net.bio.net will be
the only ones who will see it (we will try to forward it to the
appropriate newsgroup, but would appreciate it if you would determine
the correct address yourself first).



If you are using news software, there are usually two types of reply
commands. One command sends a private reply to the author of the
original posting; the second sends a "followup" posting to everyone on
the newsgroup. Press ? or h in your news software to find these
commands. They are often noted by "r" and "R" or "r" and "f"

If you are replying to an e-mail message from BIOSCI, be sure to look
carefully at the To: and Cc: lines of your reply message *before*
sending it off. If you want the reply to be PRIVATE, only the address
of the person who posted the original message (and perhaps your
address and/or that of other individuals) should be on the To: and Cc:
address lines. If you want the reply to be PUBLIC, be sure that the
newsgroup posting address appears on either the To: or Cc: line of
your response. If your mail system is a bit unorthodox and puts the
"BIOSCI-REQUEST" address in your response (see the section about
BIOSCI-REQUEST above), please be sure to correct this *before* sending
your message (ask your systems administrator how to edit the To: and
Cc: lines of your mail messages before sending if you do not know how
to do this).

Now that you have read about all of these problems with using e-mail
to participate in BIOSCI, why don't you get news software installed at
your site and make life easy for yourself instead of using e-mail
8-)!! Let's look at Usenet news next!



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 transmit messages without loss and also to avoid possible
mail loops and other errors which plague simple electronic mail
"broadcasting." 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 your other personal messages. This is obviously a suboptimal
means of organizing messages. With news software, you can browse the
discussion topics easily, read what you want and discard the rest. Why
subject yourself to having to page through a disorganized mail file
message-by-message unless you really have no other choice?? News
software makes the use of BIOSCI pleasant and efficient. It's time to
get your organization "into the 20th Century" before it turns into the
21st Century!



Contact biosci-help at net.bio.net for information on getting started
with Usenet. News software can be obtained free of charge from
anonymous FTP sources. Note, however (yes, here's the unfortunate
catch), that news software should be installed and maintained by a
trained systems administrator in most cases; it is not a task for a
computer novice. You can find detailed information about Usenet using
anonymous FTP from rtfm.mit.edu [, but please always
reference the hostname rtfm.mit.edu, as IP addresses and canonical
names will change in the future, but rtfm.mit.edu will remain
correct], in the /pub/usenet/news.announce.newusers directory. You may
be specifically interested in the following articles:
  * What_is_Usenet?
  * What_is_Usenet?__A_second_opinion.
  * Usenet_Software:_History_and_Sources
  * How_to_Get_Information_about_Networks
  * How_to_become_a_Usenet_site



Please DO NOT post test messages to any of the BIOSCI/bionet Usenet
newsgroups. If you are unsure about whether or not your mail is
working, please send test mail messages to either of our two
administrative addresses, but NOT to newsgroup mailing addresses:

Address for tests                 Location
-----------------                 --------
biosci at daresbury.ac.uk            Europe, Africa, and Central Asia
biosci at net.bio.net                Americas and the Pacific Rim

If you need to test your Usenet news software, please post test
messages to the Usenet newsgroup misc.test which was created solely
for this purpose.



This could happen for a variety of reasons. When we create a new
Usenet newsgroup, a "newgroup" message is sent out from net.bio.net to
news administrators at Usenet sites around the world. Many sites are
configured so that such newgroup messages are acted upon automatically
and the group is established without human intervention. However, due
to the growing volume of Usenet newsgroups, many sites have turned off
automatic newgroup creation and require human intervention to create a
new Usenet group in response to a newgroup message. If you know from
reading BIONEWS/bionet.announce or from contacting the BIOSCI staff at
biosci-help at net.bio.net that a new bionet newsgroup should be in
existance, please contact your local news administrator and ask them
if they acted on the newgroup message. Newgroup messages can sometimes
be simply overlooked by the news administrator and sometimes they may
not be received if a Usenet site upstream on the net from you had a
problem and did not pass on the message. Please let your news
adminstrator know that a bionet "checkgroup" message is posted on the
first of each month to bionet.announce. Your news administrator can
use the contents of that message to update your local list of bionet
Usenet newsgroups.

Please note that all new BIOSCI/bionet newsgroups are announced on
BIONEWS/bionet.announce as soon as they are ready for use. If you see
this announcement, this means that the BIOSCI staff has tested the
group and is (1) sure that it works, and (2) knows that it has
propagated to at least some other sites in both North America and
Europe. We obviously can not check for propagation to the thousands of
sites on Usenet. Depending upon your source of Usenet news, there may
be a delay of several days before the newgroup message reaches your
site. The announcement of the newsgroup availability, however, is
always sent to bionet.announce *after* the newgroup message has been
sent and after system tests have been run.



If you experience the problem above, please contact your local news
administrator and have them check with the site that sends you your
bionet Usenet news feed. We explained in a question above that new
Usenet newsgroups are created in response to a "newgroup" message
which is sent out to all Usenet news administrators. It is possible
that your news administrator acted on the message to create the group,
but that the site which sends you bionet Usenet news did not. Having
your Usenet news administrator contact the administrator at the
upstream site can usually resolve the problem. If you have a problem
getting a reliable bionet Usenet news feed, please contact
biosci-help at net.bio.net.



Instructions for subscribing and unsubscribing to the BIOSCI
newsgroups by e-mail are included in the BIOSCI info sheet which can
be obtained from either of the following two addresses:

Administrative Address            Location
----------------------            --------
biosci at daresbury.ac.uk            Europe, Africa, and Central Asia
biosci at net.bio.net                Americas and the Pacific Rim



Simply send a request to your appropriate BIOSCI distribution site:

Administrative Address            Location
----------------------            --------
biosci at net.bio.net                The Americas and Pacific Rim
biosci-help at daresbury.ac.uk       Europe, Africa, and Central Asia

The most recent list of BIOSCI newsgroups/mailing addresses and the
latest revision of the BIOSCI/bionet FAQ are posted the first of each
month on the BIONEWS/bionet.announce newsgroup. You should save these
postings for future reference.



The BIOSCI node at net.bio.net maintains the entire collection of
BIOSCI/bionet messages. They are available via WAIS (biosci.src and
biology-journal-contents.src), Gopher (net.bio.net port 70),
anonymous ftp from net.bio.net [], and Mosaic/WWW (URL is
gopher://net.bio.net/). Contact biosci-help at net.bio.net for further
help. If you are on the Internet but do not have WAIS software running
locally, try

     telnet quake.think.com

and login in as "wais" to experiment with the software. All of our
WAIS sources (biosci.src, biology-journal-contents.src, and
biologists-addresses.src) may be selected from the menu for searching.
Please also refer to the FAQ section below entitled "Please help me
find the e-mail address for Dr. ..." for additional uses of our WAIS

If you are not on the Internet you may search the BIOSCI WAIS archives
by e-mail using our WAISMAIL e-mail server. For instructions on using
WAISMAIL, please send the message


in the body of a mail message addressed to the Internet address

     waismail at net.bio.net

and be sure to leave the Subject: line of your message blank. Detailed
instructions will be returned to you automatically.

The SERC Daresbury BIOSCI node runs a BIOSCI newsgroups WAIS source
called BIOWAIS. This source can also be searched through their gopher
client at host s-crim1.dl.ac.uk, port 70.

All the Bionet newsgroup postings since December 1991 are stored for
Gopher searching and retrieval and anonymous ftp at
ftp.bio.indiana.edu, the IUBIO Archive maintained by Don Gilbert. The
directory in the anonymous FTP account is usenet/bionet. This gopher
site also contains an outstanding collection of biological software
and databases.

Another excellent gopher server is maintained by Dan Jacobson at
merlot.gdb.org, port 70. In addition to newsgroup archives, many
other information sources of use to biologists are available.

In Europe, Rob Harper runs a full-featured Gopher for biologists at
gopher.csc.fi and Reinhard Doelz maintains a biology gopher at
gopher.embnet.unibas.edu. The number of "gopher holes" on the
network is expanding too rapidly to list them all here.



Yes. A FAQ for the METHODS newsgroup was created by Paul Hengen of
Frederick Cancer Research and Development Center. It can be obtained
via anonymous FTP from net.bio.net in
pub/BIOSCI/METHDS-REAGNTS/METHODS.FAQ or from ftp.ncifcrf.gov in

Note, however, that maintaining such a FAQ is a gargantuan task. We
also recommend searching the METHODS archives for keywords through the
use of the WAIS and Gopher software as described in the "archives"
question above.

In each issue of "Trends in Biochemical Sciences" since November 1993,
Dr. Hengen writes a monthly digest column of the METHODS newsgroup.
This column highlights topics of special interest which were discussed
recently on the newsgroup.



The following journals appear regularly as of 6/28/94. This list is
constantly expanding and the latest copy can be requested from
biosci-help at net.bio.net.

  * Anatomy & Embryology
  * Applied Microbiology and Biotechnology
  * Applied and Environmental Microbiology
  * Binary
  * Cell and Tissue Research
  * Chromosoma
  * Clinical Chemistry
  * Current Genetics
  * EMBO Journal
  * European Journal of Biochemistry
  * European Journal of Physiology
  * Experimental Brain Research
  * Histochemistry
  * Human Genetics
  * IEEE Engineering in Medicine and Biology
  * Immunogenetics
  * Journal of Bacteriology
  * Journal of Biological Chemistry
  * Journal of Comparative Physiology B: Biochemical, Systemic, and
    Environmental Physiology
  * Journal of Membrane Biology
  * Journal of Molecular Evolution
  * Journal of Virology
  * MGG - Molecular and General Genetics
  * Mammalian Genome
  * Microbial Releases
  * Molecular Microbiology
  * Molecular and Cellular Biology
  * Nucleic Acids Research
  * Plant Cell Reports
  * Planta
  * Protein Science
  * Roux's Archives of Developmental Biology
  * Seminars in Cancer Biology
  * Seminars in Cell Biology
  * Seminars in Developmental Biology
  * Seminars in Immunology
  * Seminars in the Neurosciences
  * Seminars in Virology
  * TAG - Theoretical and Applied Genetics

Table of Contents for the journals above are available for FTP from
net.bio.net in pub/BIOSCI/BIO-JOURNALS and also for searching and
retrieval by Gopher from net.bio.net, port 70. One can use either
gopher or WAIS to search the WAIS source biology-journal-contents.src
at net.bio.net and retrieve individual article references from the
journals above. This can be accessed through WAIS, WAISMAIL, gopher,
and Mosaic as described in the FAQ section entitled "How do I find
back issues of BIOSCI postings?"



Originally there were *four* BIOSCI distribution sites (nodes), but
due to administrative complexities, the number of nodes was scaled
back to two. 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 BIOSCI distribution sites on each
side of the Atlantic 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 U.K. site *via netnews software, not by mail* before being
"exploded" for mail distribution to all of the final e-mail
destinations on the "other side of the pond." This is more efficient
than sending hundreds of copies of the same message across the
Atlantic. A trade-off for this efficiency is slightly increased
complexity in the distribution network, i.e., the mailing lists for
each newsgroup are split between two sites. In the past BIOSCI
experienced sporadic problems with "bounced" mail, but the reduction
in the number of BIOSCI distribution sites and the implementation of
U.S. to U.K. message transfer via news rather than by e-mail has
eliminated this problem. 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.



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 net.bio.net. 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. Offending addresses are "commented out" of the 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. There is
an automatic reminder system at net.bio.net in the U.S. that sends a
message to all "commented out" addresses on the mailing lists at
net.bio.net each Monday for three weeks. After that if no response is
received to biosci-help at net.bio.net, the bad addresses are completely
removed from the mailing lists.



It is not uncommon when posting a mail message to a newsgroup to
receive an error message from a "mailer 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 in the world 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 BIOSCI lists. 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 net.bio.net 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.



BIOSCI's goal is to promote the use of electronic communications among
biologists and we are here to assist you in establishing new forums at
no charge. There are currently two options - create a full newsgroup
or a prototype (mailing lists only):

 For full-fledged BIOSCI newsgroup status (also see "prototype" rules below)

Proposals for new groups must contain a statement of purpose for the
group and the name of a person designated as discussion leader unless
the group is in the service category such as METHODS, EMPLOYMENT, etc.
Discussion leaders are responsible for ensuring that a reasonable
level of activity is sustained on the newsgroup (see Newsgroup
Termination Policy below). The discussion leader can also propose the
creation of moderated newsgroups if he/she agrees to serve as
moderator (this requires access to Usenet news software at the
moderator's site). Proposals should be sent to
biosci-help at net.bio.net.

When a proposal is received it will be posted on
BIONEWS/bionet.announce. A ten day period for discussion on
BIOFORUM/bionet.general will follow and precede the call for votes.
After the discussion, the person proposing the newsgroup may modify or
withdraw the proposal prior to the call for votes. The modified
proposal will then be included in a call for votes on
BIONEWS/bionet.announce. The proposal must collect 80 YES votes in 30
days and the number of YES votes must exceed the number of NO votes by
at least 40 to pass.

BIOSCI management must be informed in advance of any intended efforts
to advertise the newsgroup proposal in other forums. While BIOSCI
wishes to inform potential users of the creation of newsgroups that
might be of interest to them, promotional efforts should be focussed
in forums likely to be utilized by professionals in the subject area
covered by the newsgroup proposal, and should seek participation in
the discussion of the proposal within bionet.general/BIOFORUM rather
than promoting separate discussions in other forums to which portions
of the BIOSCI readership may not have ready access.

If a proposal is not passed by the readers, there will be a three
month period before it can be brought up for another vote.

   Newsgroup Termination Policy

Any group with less than 52 msgs in the previous calendar year will be
put on notice by posting an announcement to the newsgroup (not to
bionet.announce) that it faces cancellation. It can be reprieved if 80
readers respond within two weeks (this policy will be stated in the
termination announcement). It then has two months to reach a usage
level of one message per 3 days or else it will be abolished. Appeals
to the BIOSCI management about high content albeit low volume on the
group will be considered.

   Newsgroups for Professional Societies in Biology

BIOSCI will create a moderated newsgroup in the bionet.prof-society
domain without voter approval for any professional society in the
biological sciences which has a membership of at least 500. Smaller
groups must go through the regular BIOSCI/bionet newsgroup creation
process. Because these groups are not discussion forums, they will be
exempted from the 52 message per year minimum posting limit and would
only be discontinued if the society in question no longer wishes to
use them. If usage seems extremely low on any group in the
bionet.prof-society domain, the BIOSCI/bionet staff will contact the
society in question and ensure that the newsgroup is still wanted.

 BIOSCI "prototype" newsgroup creation policy

We will be happy to establish and administer a straight *mailing* list
*without* an associated Usenet newsgroup for a six month trial period
for anyone that wants to try to form a new electronic community in the
biological sciences (We stress that the topics are limited to
professional communications though.).

The mailing lists will be maintained *initially* only at net.bio.net
instead of at both BIOSCI sites. It will be the responsibility of the
person who proposes the list to get it up and running within the six
month period. They will have to handle promotion; our involvement at
BIOSCI at net.bio.net will be limited to creating the list, putting
out one announcement about it, and handling subscription requests.

After six months, the list will be put out for discussion and a vote
according to our procedures for full-fledged newsgroups above (unless
the organizer decides to bow out). If it passes it will become a
full-fledged BIOSCI newsgroup at both net.bio.net and daresbury.ac.uk
and will also have a parallel Usenet newsgroup. If it fails, the
prototype mailing list at net.bio.net will be shut down.

Note that this service does not preclude people who have an idea that
has widespread appeal from following our current newsgroup creation
policy and going to a vote after a 10 day discussion.

If you have an idea for a prototype newsgroup, please send it to
biosci-help at net.bio.net.



Below is the address form that we would like each reader of the
BIOSCI/bionet newsgroups to complete and return if you would like to
be listed in our database. The database serves as a directory that
enables biologists, who are currently using (or even just reading) the
BIOSCI newsgroups, to look up e-mail addresses and other information
about our users.

The address database is reindexed nightly for WAIS, waismail, and
gopher access. If you have access to gopher, connect to net.bio.net to
search the database. If you have access to WAIS, please use our WAIS
source biologists-addresses.src. If you are not on the Internet,
please use our waismail server (send the word "help" to
waismail at net.bio.net to get instructions; any text on the Subject:
line of your message will be ignored, so put the help command in the
body of the mail message.).

Please carefully follow the instructions for completing the form below
and return it to either of the following two addresses (whichever is
more convenient for you). Thanks in advance for taking the time to
complete and return the form.

Addresses for returning forms      Location        Network
-----------------------------      --------        -------
biovote at net.bio.net                U.S.A.          Internet/BITNET
biovote at daresbury.ac.uk            U.K.            JANET

 Making Sure That Your Information Is Current

This notice will be mailed bimonthly to each newsgroup. You should
check your database entry from time-to-time to see if your address
information is still up-to-date.

   Using Gopher to complete the form

If you don't want to use a text editor, you can also use Dan
Jacobson's gopher site to fill out the address database form as
follows. Otherwise skip this section on gopher and proceed to the
instructions for filling out the form below.

> To add yourself to the database just point your
> gopher client at merlot.gdb.org and select the following:
> -->  15. Searching For Biologists/
>  -->  9.  E-mail Addresses of Biosci-Bionet Users/
>-->  1.  Add (or Correct) Your Address to the BIOSCI User Address
> Data..
> And fill out the form.

or Rob Harper's gopher site in Europe as follows:

> Europeans can point their gopher client at gopher.csc.fi and add their
> information to the database. All entries will be mailed directly to
> Dave for incorporation in a wais source.
> The path to the questionare is as follows.
> ---> 10. Finnish EMBnet BioBox/
>      ---> 8.  FAQ Files/
>                            FAQ Files
>    1.  EMBnet: Information.
>    2.  EMBnet: Internet resources guide.
>    3.  A Biologist's Guide to Internet Resources/
>    4.  All FAQs (Frequently Asked Questions) Searches and Archives/
>--->5.  Bionauts Address Database (questionaire) <TEL>

 Important Instructions - Please Read Carefully

Please enter all responses after the : on each line, leaving one (1)
blank space after the : (i.e., before the start of your text).

Please do NOT extend your responses past the end of each line (80

PLEASE DO NOT alter any of the field identifiers such as "first
name:". If you have nothing to enter after a field identifier, PLEASE
LEAVE IT - do not delete it even if there is no data on the line in

Several lines are provided at the end of the form for comments, but,
please adhere to the line length restriction.

On the date: line, please enter the date in the DD-MM-YY format, e.g.,
15-05-93 for 15 May 1993. This line will tell others when the
information was last updated. Please be sure to include the 0's for
single digit days or months, e.g., 15-05-93, not 15-5-93.

Note that the "e-mail network:" line below is for specifying, e.g.,
"Internet," "BITNET," "EARN," "JANET," or whatever other network that
your computer may be on.

If you are uncertain about any field, please feel free to leave it
blank, but please DO NOT DELETE the field identifier from the form!

In the first field below, "New information or Update ...", please
enter "N" if this is the first time that you have registered in the
directory or "U" if you are correcting a listing that you sent to us

The comment: lines may be used for anything that you like but PLEASE
to list the names of the newsgroups in which you participate. Please
use the MAILING LIST name (see below - the latest version of the list
can be requested from biosci at net.bio.net) instead of the Usenet name
even if you don't participate by e-mail. WAIS might get confused by
the periods in the Usenet names. This allows one to retrieve via WAIS
or waismail the list of participants in a particular group.

For example:


On the comment: lines
use these names below  --  NOT the Usenet names below

MAILING LIST NAME       Usenet Newsgroup Name
-----------------       ---------------------
ACEDB-SOFT              bionet.software.acedb
AGEING                  bionet.molbio.ageing
AGROFORESTRY            bionet.agroforestry
ARABIDOPSIS             bionet.genome.arabidopsis
BIOFORUM                bionet.general
BIO-INFORMATION-THEORY  bionet.info-theory
BIONAUTS                bionet.users.addresses
BIONEWS                 bionet.announce
BIO-JOURNALS            bionet.journals.contents
BIO-MATRIX              bionet.molbio.bio-matrix
BIOPHYSICAL-SOCIETY     bionet.prof-society.biophysics
BIOPHYSICS              bionet.biophysics
BIO-SOFTWARE            bionet.software
BIOTHERMOKINETICS       bionet.metabolic-reg
CELL-BIOLOGY            bionet.cellbiol
CHLAMYDOMONAS           bionet.chlamydomonas
CHROMOSOMES             bionet.genome.chromosomes
COMPUTATIONAL-BIOLOGY   bionet.biology.computational
CYTONET                 bionet.cellbiol.cytonet
DROSOPHILA              bionet.drosophila
EMBL-DATABANK           bionet.molbio.embldatabank
EMPLOYMENT              bionet.jobs
GDB                     bionet.molbio.gdb
GENBANK-BB              bionet.molbio.genbank
GENETIC-LINKAGE         bionet.molbio.gene-linkage
GRASSES-SCIENCE         bionet.biology.grasses
HIV-MOLECULAR-BIOLOGY   bionet.molbio.hiv
HUMAN-GENOME-PROGRAM    bionet.molbio.genome-program
IMMUNOLOGY              bionet.immunology
INFO-GCG                bionet.software.gcg
JOURNAL-NOTES           bionet.journals.note
METHODS-AND-REAGENTS    bionet.molbio.methds-reagnts
MOLECULAR-EVOLUTION     bionet.molbio.evolution
MYCOLOGY                bionet.mycology
NEUROSCIENCE            bionet.neuroscience
N2-FIXATION             bionet.biology.n2-fixation
PARASITOLOGY            bionet.parasitology
PHOTOSYNTHESIS          bionet.photosynthesis
PLANT-BIOLOGY           bionet.plants
POPULATION-BIOLOGY      bionet.population-bio
PROTEIN-ANALYSIS        bionet.molbio.proteins
PROTISTA                bionet.protista
RAPD                    bionet.molbio.rapd
SCIENCE-RESOURCES       bionet.sci-resources
STRUCTURAL-NMR          bionet.structural-nmr
TROPICAL-BIOLOGY        bionet.biology.tropical
VIROLOGY                bionet.virology
WOMEN-IN-BIOLOGY        bionet.women-in-bio
YEAST                   bionet.molbio.yeast

Listing newsgroups on the comment: line is optional, of course.

Thanks again for your cooperation!

--------------- please cut here and return portion below ---------------

New information or Update to old record (enter N or U):
date (DD-MM-YY):
first name:
middle initial:
family name:
job title:
e-mail address:
e-mail network:
phone number:
FAX number:
postal code:
research interest:



Your local Usenet software may have defaulted to "local" distribution.
If this option is selected, only other readers of the bionet
newsgroups on your local computer will see your posting. If you want
your message to be delivered to all BIOSCI/bionet readers, please be
sure to specify "world" or "bionet" when prompted for the
Distribution:. Generally, if you press "?" or "h" when prompted, you
will see your options for controlling the distribution of your
messages on Usenet. If your message does not reach one of the two
BIOSCI nodes in the U.S. or the U.K. it will not be distributed to
people who participate in BIOSCI by e-mail.



This is a problem that might plague users of older versions of the
"rn" newsreading program when they try to reply to messages on
BIOFORUM/bionet.general. bionet.followup is a non-existent newsgroup.
In the "good old days" there was a newsgroup called "net.general" and
replies to net.general were posted to "net.followup." Unfortunately
the Usenet name of the BIOFORUM newsgroup, bionet.general, contains
the text "net.general" as a subset. Older versions of news software
can latch on to this text string and redirect replies to
bionet.general messages to bionet.followup. If you are plagued by this
problem, please call the following fixes, provided by Roy Smith and
Wayne Rindone, to the attention of your local systems manager:

+++++++++++++++++++++++ The problem is indeed in the rn sources,
specifically in intrp.c. In the version I have (intrp.c,v
90/12/31 11:47:44 sob Exp), It's the following code at lines 664-670:

if (h = instr(s,"net.general")) { off = h-s; strncpy(scrbuf,s,off+4);
safecpy(scrbuf+off+12,h+11,sizeof(scrbuf)); s = scrbuf; } What's going
on is that there used to be the convention that followups to articles
in the newsgroup net.general (which doesn't exist anymore and hasn't
for something like 5 years) should be placed in net.followup. For
better or for worse, the rn code attempted to enforce this convention.
What's going on in the above code is that the string "net.general" in
the Newsgroups line of an article being follow-ed-up to gets changed
to "net.followup". Unfortunately, that means "bionet.general" gets
changed to "bionet.followup". I would suggest simply deleting the
above code entirely. I'm not even sure why it's still there, other
than nobody bothered to take it out, and until bionet.general came
around, it never bit anybody. Old code never dies. It simply gets
integrated into the host genome of the program it's part of waiting
for the right environmental conditions to appear. --
roy at alanine.phri.nyu.edu (Roy Smith) Public Health Research Institute
455 First Avenue, New York, NY 10016, USA "Arcane? Did you say arcane?
It wouldn't be Unix if it wasn't arcane!" +++++++++++++++++++++++
From: Wayne Rindone <wrindone at BBN.COM> Subject: Another source of
bionet.followup problem Thought you might like to know that there are
other potential reasons for the appearance of the bogus
bionet.followup group name. A couple of months ago, I installed rn 4.4
on my workstation, expecting that to fix the bionet.followup problem,
among other things. I was very surprised to discover that I still had
bionet.followup appearing, even though it was quite clear there was
nothing in the new rn sources to account for that. It turned out that
the following lines were included in /usr/local/news/rn/Pnews.header:
case $ng in *net.general*) follow=`echo "$ng" | sed
's/net\.general/net.followup/g'` ;; *) follow="" ;; esac Once these
were removed the problem disappeared. I have no idea if this logic was
created locally at BBN or not, or if it came from elsewhere or had
wider dissemination beyond BBN. Although the problem is solved for me,
I have a bad feeling that it will turn up many places around the world
for many years to come. Feel free to mention Pnews.header as another
potential source of the problem the next time someone asks if you
think that helpful. Wayne Rindone, BBN +++++++++++++++++++++++ -------

Common questions posted to BIOSCI/bionet newsgroups



FTP stands for File Transfer Protocol and is a method for transmitting
files at high speed over the Internet. There are also e-mail servers
at various BITNET sites which provide e-mail access to FTP archives.
Send the word "HELP" to BITFTP at PUCC.BITNET for details. A sample
session of using FTP to access the BIOSCI archives follows. Keyboard
input is underlined. ### highlights comments about the procedure.

net<1>ftp net.bio.net  ### connect to the BIOSCI computer
Connected to net.bio.net.
220 net.bio.net FTP server (SunOS 4.1) ready.
Name (net.bio.net:kristoff): anonymous  ### login as anonymous
331 Guest login ok, send ident as password.
Password:            ### enter any password; typically your e-mail address
230 Guest login ok, access restrictions apply.
ftp> ls  ### display the directories.  sometimes "dir" is used here
200 PORT command successful.
150 ASCII data connection for /bin/ls (,3225) (0 bytes).
226 ASCII Transfer complete.
72 bytes received in 0.1 seconds (0.7 Kbytes/s)
ftp> cd pub  ### change to the "pub" public directory.  Most FTP
  ------     ### sites place public material in this directory
250 CWD command successful.
ftp> ls  ### list the files again.  BIOSCI archives are in BIOSCI 8-)
  --     ### Be sure to strictly follow upper/lower case in filenames
         ### when accessing FTP sites running UNIX such as net.bio.net
200 PORT command successful.
150 ASCII data connection for /bin/ls (,3227) (0 bytes).
226 ASCII Transfer complete.
42 bytes received in 0.05 seconds (0.82 Kbytes/s)
ftp> cd BIOSCI
250 CWD command successful.
ftp> ls
200 PORT command successful.
150 ASCII data connection for /bin/ls (,3228) (0 bytes).
226 ASCII Transfer complete.
562 bytes received in 0.1 seconds (5.5 Kbytes/s)
ftp> cd PROTEIN-ANALYSIS### We want to look at PROTEIN-ANALYSIS archives
250 CWD command successful.
ftp> ls
200 PORT command successful.
150 ASCII data connection for /bin/ls (,3233) (0 bytes).
226 ASCII Transfer complete.
225 bytes received in 0.12 seconds (1.8 Kbytes/s)
ftp> get 9211  ### Retrieve the file for November 1992.
200 PORT command successful.
150 ASCII data connection for 9211 (,3234) (208763 bytes).
226 ASCII Transfer complete.
local: 9211 remote: 9211
213849 bytes received in 1.4 seconds (1.5e+02 Kbytes/s)
ftp> bye  ### End the FTP session.  Some systems use quit or exit.
221 Goodbye.

Liberal use of the ? key and help at the ftp> prompt will provide
information on other options.


WAIS stands for Wide Area Information Server. WAIS software allows
information to be stored at many sites around the Internet in to a
particular format. Computers running WAIS software can query these
sources remotely using a standard protocol. Free software is available
for many popular hardware platforms, but requires some systems
expertise to install. Now that you know how to use FTP (above), you
can use anonymous ftp to think.com and cd to the "wais" directory for
software and more information. A public WAIS account is accessible to
Internet users by using the command

     telnet quake.think.com

and logging in as "wais" (lowercase).


Gopher is both a user-friendly interface to the FTP program described
above and a network searching tool similar to WAIS (which can also
utilize WAIS information sources). Gopher software is available as
described below for many platforms; TurboGopher on the Macintosh is
especially slick! Don Gilbert (gilbertd at silver.ucs.indiana.edu) at
ftp.bio.indiana.edu runs the excellent IUBIO Gopher Hole with many
services of use to biologists, including search and retrieval of
GenBank entries and BIOSCI/bionet newsgroup postings among many other
information resources. Dan Jacobson (danj at gdb.org) runs an excellent
gopher server at merlot.gdb.org with software, database, news, and
government information archives. In Europe Rob Harper
(harper at finsun.csc.fi) has set up a similar gold mine of information
at gopher.csc.fi. Please see the section on searching the BIOSCI
archives for other useful gopher sites.

The following information is excerpted from the Gopher FAQ. Many
questions have been cut out for brevity.


Common Questions and Answers about the Internet Gopher, a
client/server protocol for making a world wide information service,
with many implementations.  Posted to comp.infosystems.gopher and
news.answers every two weeks.

The most recent version of this FAQ can be gotten through gopher, or
via anonymous ftp:


Those without FTP access should send e-mail to mail-server at rtfm.mit.edu
with "send usenet/news.answers/finding-sources" in the body to find out
how to do FTP by e-mail.
List of questions in the Gopher FAQ:

Q0:  What is Gopher?
Q1:  Where can I get Gopher software?
Q2:  What do I need to access Gopher?
Q3:  Where are there publicly available logins for Gopher?

Q5:  Who Develops Gopher Software?

Q12: What is the relationship between Gopher and (WAIS, WWW, ftp)?
Q13: Are papers or articles describing Gopher available?
Q0:  What is Gopher?

A0:  The Internet Gopher client/server provides a distributed
  information delivery system around which a world/campus-wide
  information system (CWIS) can readily be constructed.   While
  providing a delivery vehicle for local information,  Gopher
  facilitates access to other Gopher and information servers
  throughout the world.

Q1:  Where can I get Gopher software?

A1:  via anonymous ftp to boombox.micro.umn.edu.  Look in the directory

Q2:  What do I need to access Gopher?

A2:  You will need a gopher "client" program that runs on your local PC
  or workstation

  There are clients for the following systems.  The directory
  following the name is the location of the client on the anonymous
  ftp site boombox.micro.umn.edu ( in the directory

   Unix Curses & Emacs   :  /pub/gopher/Unix/gopher1.03.tar.Z
   Xwindows              :  /pub/gopher/Unix/xgopher1.1a.tar.Z
   Macintosh Hypercard   :  /pub/gopher/Mac_client/
   Macintosh Application :  /pub/gopher/Macintosh-TurboGopher
   DOS w/Clarkson Driver :  /pub/gopher/PC_client/
   NeXTstep              :  /pub/gopher/NeXT/
   VM/CMS                :  /pub/gopher/Rice_CMS/ or /pub/gopher/Vienna_CMS/
   VMS                   :  /pub/gopher/VMS/
   OS/2 2.0              :  /pub/gopher/os2/
   MVS/XA                :  /pub/gopher/mvs/

  Many other clients and servers have been developed by others, the
  following is an attempt at a comprehensive list.

   A Macintosh Application, "MacGopher".

   Another Macintosh application, "GopherApp".

   A port of the UNIX curses client for DOS with PC/TCP

   A port of the UNIX curses client for PC-NFS

   A beta version of the PC Gopher client for Novell's LAN Workplace
   for DOS

   A Xwindows/DECwindows client

  Most of the above clients can also be fetched via a gopher client
  itself.  Put the following on a gopher server:

    Name=Gopher Software Distribution.

  Or point your gopher client at boombox.micro.umn.edu, port 70 and
  look in the gopher directory.

  There are also a number of public telnet login sites available.
  The University of Minnesota operates one on the machine
  "consultant.micro.umn.edu" ( See Q3 for more
  information about this.  It is recommended that you run the client
  software instead of logging into the public telnet login sites.  A
  client uses the custom features of the local machine (mouse,
  scroll bars, etc.)  A local client is also faster.

Q3:  Where are there publicly available logins for Gopher?

A3:  Here is a short list, use the site closest to you to minimize
  network lag.

  Non-tn3270 Public Logins:

  Hostname                  IP#              Login   Area
  ------------------------- ---------------  ------  -------------
  consultant.micro.umn.edu     gopher  North America
  gopher.uiuc.edu    gopher  North America
  panda.uiowa.edu    panda   North America
  gopher.sunet.se      gopher  Europe
  info.anu.edu.au     info    Australia
  gopher.chalmers.se    gopher  Sweden
  tolten.puc.cl        gopher  South America
  ecnet.ec             gopher  Ecuador

  tn3270 Public Logins:

  Hostname                  IP#              Login   Area
  ------------------------- ---------------  ------  -------------
  pubinfo.ais.umn.edu    -none-  North America

  It is recommended that you run the client software instead of
  logging into the public login sites.  A client uses the
  custom features of the local machine (mouse, scroll bars, etc.)
  and is local client is also faster.

Q5:  Who Develops Gopher Software?

A5:  Gopher was originally developed in April 1991 by the University
  of Minnesota Microcomputer, Workstation, Networks Center to help
  our campus find answers to their computer questions.

  It has since grown into a full-fledged World Wide Information
  System used by a large number of sites in the world.

  Many people have contributed to the project, too numerous to

  The people behind the much of the gopher software can be reached
  via e-mail at gopher at boombox.micro.umn.edu, or via paper mail:

   Internet Gopher Developers
   100 Union St. SE #190
   Minneapolis, MN 55455  USA

  Or via FAX at:

   +1 (612) 625-6817

Q12: What is the relationship between Gopher and (WAIS, WWW, ftp)?

A12: Gopher is intimately intertwined with these two other systems.
  As shipped the Unix gopher server has the capability to:

    - Search local WAIS indices.
    - Query remote WAIS servers and funnel the results to gopher
    - Query remote ftp sites and funnel the results to gopher
    - Be queried by WWW (World Wide Web) clients (either using
      built in gopher querying or using native http querying.

Q13: Are papers or articles describing Gopher available?

A13: Gopher has a whole chapter devoted to it in :

  _The_Whole_Internet_, Ed Kroll, O'Reilly, 1992 (Editors note:
                          ..Great book, go out and buy a bunch!)

  Other references include:

  _The_Internet_Gopher_, "ConneXions", July 1992, Interop.

  _Exploring_Internet_GopherSpace_ "The Internet Society News", v1n2 1992,

  (You can subscribe to the Internet Society News by sending e-mail to
   isoc at nri.reston.va.us)

  _The_Internet_Gopher_Protocol_, Proceedings of the Twenty-Third
       IETF, CNRI, Section 5.3

  _Internet_Gopher_, Proceedings of Canadian Networking '92

  _The_Internet_Gopher_, INTERNET: Getting Started, SRI
       International, Section 10.5.5

  _Tools_help_Internet_users_discover_on-line_treasures, Computerworld,
       July 20, 1992

  _TCP/IP_Network_Administration_, O'Reilly.

   Balakrishan, B. (Oct 1992)
     "SPIGopher: Making SPIRES databases accessible through the
   Gopher protocol".  SPIRES Fall '92 Workshop, Chapel Hill, North

   Tomer, C.  Information Technology Standards for Libraries,
   _Journal of the American Society for Information Science_,
   43(8):566-570, Sept 1992.



The World-Wide Web (WWW) has become the latest hot network item,
especially since the advent of the Mosaic software from the National
Center for Supercomputing Applications at the University of Illinois.

In a nutshell, Mosaic is a "hypertext browser," i.e., an application
program that lets you read through the thousands of cross-linked
hypertext documents, pictures and sound bites now available on the
Internet. A more detailed explanation will be included in a future
version of this FAQ. For now, we recommend using FTP to
ftp.ncsa.uiuc.edu to pick up a version of Mosaic for your hardware
platform. Note that to get the most out of Mosaic, your machine needs
a direct and fast Internet connection. 9600 baud links or lower will
not be a happy compromise except possibly for browsing plain text
documents in some cases.



If you can not get this information by calling the person in question,
there are several other resources that can be of help. As of May 1993,
BIOSCI at net.bio.net began running a BIOSCI user address directory
which can be accessed through gopher to net.bio.net or via WAIS or
waismail. The WAIS source is called biologists-addresses.src and is
updated daily. See the FAQ section entitled "How do I find back issues
of BIOSCI postings?" for information on WAIS and waismail access.
Instructions for using the address source are included in the waismail
help file which can be retrieved by sending the word "help" to
waismail at net.bio.net (leave the Subject: line of your message blank.)

The second easy route is to post your request to the
BIONAUTS/bionet.users.addresses newsgroup managed by Rob Harper. Odds
are that you will get a response fairly promptly, but, if not, there
are other routes described below.

If the person in question has posted to BIOSCI/bionet or another
Usenet newsgroup, they will be listed in the "usenet-addresses" WAIS
source. If you are on the Internet, telnet to quake.think.com and
login as "wais" (lowercase). After entering your terminal type, select
the usenet-addresses source from the list presented to you (use the
up-arrow key to get there more quickly since it is near the end of a
long list). When the source is highlighted, press the return key and
then enter the person's surname at the Keywords: prompt to begin the
search. Available commands are listed at the bottom of the screen.
When finished, press "s" to return to the source menu and then "q" to

For those who do not have access to the Internet, the usenet-addresses
source can also be accessed by e-mail. Please send mail to
mail-server at rtfm.mit.edu with "help" in the body of the message in
order to receive more information.

Another source of information for finding Internet, but not BITNET,
addresses is netfind. Use the command

     telnet bruno.cs.colorado.edu

and login as "netfind" without a password. The program is menu-driven
and pretty self-explanatory. Unfortunately it is not available to
people on BITNET.

Gopher is also useful in the address search. For example, Dan Jacobson
provides access to several directories of biologists at his gopher
hole on merlot.gdb.org.

None of the above methods is guaranteed to return you an answer, so
you may still have to resort to the telephone or (groan) regular mail
to make contact 8-(.



(answer contributed by Dr. John Garavelli of PIR)

Brookhaven Protein Data Bank bionet.xtallography
PIR or SWISS-PROT            bionet.molbio.proteins
NCBI GenBank DataBank        bionet.molbio.genbank
EMBL Databank                bionet.molbio.embldatabank
Human Genome Database (GDB)  bionet.molbio.gdb
Museums and Herbaria         bionet.plants, or private inquiry
                               to beach at huh.harvard.edu

Since staff members of these databases usually monitor the
corresponding newsgroups fairly closely, a posting about a problem on
the appropriate board will usually get a response from someone on a
database staff fairly quickly. Problems that might not be of general
interest or corrections to particular entries should be directed as

Database   address
--------   -------
Brookhaven pdb at chm.chm.bnl.gov, pdb at bnlchm.bitnet
PIR        postmaster at nbrf.georgetown.edu, postmast at gunbrf.bitnet
SWISS-PROT bairoch at cmu.unige.ch
GenBank    update at ncbi.nlm.nih.gov
EMBL       update at embl-heidelberg.de
GDB        help at welch.jhu.edu
Herbaria   beach at huh.harvard.edu



(answer contributed by Dr. John Garavelli of PIR)

Researchers should submit nucleotide sequence data directly to GenBank
or EMBL for assignment of an accession number prior to publication.
Derived amino acid sequence data may also be included at the same
time. Amino acid sequence data submitted in this way to GenBank, EMBL
or DDBJ is eventually passed on to PIR, and need not be submitted
separately to PIR. This is done so correct cross-references can be
made between nucleotide and protein sequence accession numbers. All
other determined amino acid sequences may be submitted directly to PIR
when the authors permit their public release prior to publication.

Authors are strongly urged to use the sequence submission software
package AUTHORIN to submit their sequence data to the databanks; a
free copy (for either the IBM PC or Macintosh) can be obtained by
sending your request and regular postal mailing address to:

     authorin at ncbi.nlm.nih.gov

Please be sure to specify the IBM or Mac version when sending your

Japanese authors who use the NEC 9801 PC should communicate directly
with DDBJ, as these machines use a version of DOS that is
significantly different enough to render the discs unreadable on
MS-DOS computers here. The staff at DDBJ will forward the data to the
appropriate databank via electronic mail. DDBJ may be contacted at:

     ddbjsubs at flat.nig.ac.jp

The address for GenBank submissions is:

U.S. mail (for submissions on diskette, indicate whether Mac or PC):
             GenBank Submissions
             National Center for Biotechnology Information
             Bldg. 38A, Room 8N-803
             8600 Rockville Pike
             Bethesda, MD 20894

E-mail submission of new sequences:  gb-sub at ncbi.nlm.nih.gov

E-mail submission of updates:        update at ncbi.nlm.nih.gov

The address for EMBL submissions is:

     EMBL Data Submissions
     Postfach 10.2209
     D-6900, Heidelburg
     Federal Republic of Germany
     Telephone (+49) 6221-387-258
     Electronic mail: DATASUBS at EMBL-Heidelberg.DE

The address for DDBJ submissions is:

     DNA Database of Japan
     Center for Genetic Information Research
     National Institute of Genetics
     111 Yata
     Mishima, Shizuoka 411
     Telephone (+81) 559-75-3651
     Electronic mail:  ddbjsubs at flat.nig.ac.jp

The address for PIR submissions is:

     PIR Submissions
     National Biomedical Research Foundation
     3900 Reservoir Road, NW
     Washington, DC  20007
     Telephone: (202) 687-2121
     Electronic mail:  FILESERV at GUNBRF.BITNET, FILESERV at NBRF.Georgetown.EDU

While we would again urge that AUTHORIN be used as the first choice in
data submission tools, the GenBank/EMBL/PIR Data Submission Form can
be obtained by sending a message consisting of the words


to the PIR FILESERV address. This form can be filled in using any text
editor, saved in ASCII (text) format, and mailed electronically or on
disk to the databanks.

Please, do not submit data either by electronic mail or on disk in
files that are formatted for word processing programs. Such files are
almost always unreadable except by systems with the same configuration
of computer, operating system and word-processing program. For files
sent by disk, either DOS or Mac formatted disks can be used but
regular "double density" disks are preferred to "high density" disks.

More information about the Bionews mailing list

Send comments to us at biosci-help [At] net.bio.net