Bionet FAQ (much new, long)

Una Smith smith-una at yale.edu
Fri Nov 20 16:37:04 EST 1992

           Answers to Frequently Asked Questions (FAQs)

This FAQ sheet was last modified on 20 November 1992.

Many Changes:  item 7 expanded, item 14, 18 and 21 added, others edited.

This is a DRAFT version of a monthly posting to the Usenet newsgroups
bionet.announce and news.answers.  Its purpose is to provide basic
information for people who are new to the Bionet domain of Usenet
newsgroups or are just beginning to read these groups via an e-mail
subscription.  It attempts to answer questions that come up frequently.
Increasingly, this FAQ contains information about resources in biology
that are *not* available via Bionet, but of interest to Bionet users.
In addition, this is a FAQ about what Bionet is good for, not how to
use it.  I leave it to the folks who administer the Bionet groups to
explain how things work.

If you are new to Bionet, please read this article.  If you are an old
hand, please take the time occasionally to look at the questions index;
you might learn something new.

The questions below are presented as an index of sorts;  answers
(such as there are) are grouped together in the next section.  Please
contribute others (and PLEASE, if you contribute a question, include
an answer with it!).

============================== Questions ==============================

 1) How can I get a copy of this article?
 2) What are the Bionet newsgroups for?  How may they be used?  
 3) Are there any special "netiquette" rules I should know about?
 4) Special instructions for Usenet readers?
 5) Special instructions for e-mail subscribers?
 6) How can e-mail subscribers get Usenet at their site?
 7) Where can I get other helpful documents?
 8) Does anyone have an e-mail address for Dr. X?
 9) How to find a good graduate program?
10) Where I can get old Bionet articles?
11) Where can I find biology-related job announcements?
12) Where can I get journal contents online? 
13) Suggestions for freeware or commercial software packages? 
14) What to do about problem X with data base Y?
15) Are there other biology newsgroups or e-mail subscription lists?
16) What is anonymous ftp, and how does it work?
17) How can I access ftp archives from Bitnet?
18) What is Archie, and how does it work?
19) What is Gopher, and how does it work?
20) What is a WAIS, and how does it work?
21) What is the Web (or WWW), and how does it work?
22) Why do so many people contribute questions but not the answers?
============================== Answers ==============================

 1) How can I get a copy of this article?

    Save this now, while you're reading it!  This article will be posted
    monthly to bionet.announce and cross-posted to news.answers.  It
    will therefore be archived at any site that archives news.answers, 
    including pit-manager.mit.edu (  To retrieve this
    article from pit-manager.mit.edu via anonymous ftp, look for the
    file bionet-faq in the directory pub/usenet/news.answers.  If
    you do not have anonymous ftp, send an e-mail message to
    mail-server at pit-manager.mit.edu, containing the lines "help" and
    "index";  you will be sent information on how to search the
    archive and receive files by e-mail.

 2) What are the Bionet newsgroups for?  How may they be used?

    A separate FAQ describing important administrative details of the
    Bionet newsgroups is (more or less) available from biosci at net.bio.net.

    Please read/subscribe to bionet.announce, a moderated group where
    important announcements are distributed.

    The Bionet newsgroups are intended as a forum for biologists of all
    flavors who want to exchange technical or other information, and
    to debate or discuss current issues in biology.  These groups are
    especially good for inter-disciplinary exchange, since the readers
    tend to work in many different areas of biology.

    These types of articles are acceptable (and frequently seen):
    * Discussions on topics of general interest.  Above all else, many
      Bionet participants cite the occasional lengthly discussions on
      various issues as the single most rewarding and useful aspect of
      the Bionet newsgroups.  There is a certain element of psychotherapy
      in any discussion group, and the Bionet groups are no exception: 
      try to keep your comments rational, calm, clear, and concise.  

    * Announcements of upcoming conferences or other events, or grant
      deadlines.  If you get the Bionet groups via Usenet, you should
      set an expiration data for such announcments, so that they go
      away once they are no longer relevant, and limit the distribution
      of your announcement to the appropriate geographical area. 

    * Questions on specific topics, techniques, or organisms.  These
      often lead to interesting discussions, and are generally welcome,
      however esoteric they may be.  If your question is an extremely
      easy or boring one, and you get the Bionet groups via Usenet, 
      you may want to consider restricting the distribution of your
      article to an appropriate region:  your university, perhaps, or
      your state or country.

    * Reports or comments on new books, papers, methods or software.
      People often report on interesting scientific news in the media
      or statements issued by various governments, or forward items
      from other groups or subscription lists.

    * Requests for book or article references.  If what you really
      want is for someone to do a bibliographic data base search
      for you, you are probably better off sending private e-mail
      to someone who is likely to be able and willing to help you.
      Otherwise, feel free to ask;  requests are frequently answered
      with full bibliographic references, often in BibTeX format.

    Unacceptable articles include commercial advertisements, political
    lobbying messages, and anything not pertaining directly to bio-
    logical research.

 3) Are there any special "netiquette" rules I should know about?

    Funny you should ask!  Quite a few documents have been written
    about Usenet etiquette;  several are available in news.answers.
    Rather than repeat their advice here, I'll just touch on the
    points most relevant to the Bionet groups.
    A) Include your full name and e-mail address in the text
    Put these at the end of your message, with your usual signature.
    You might want to use a .signature file (standard on most Unix
    systems, also implemented under VM/CMS) to make this automatic.
    This is necessary because strange things can happen to headers
    in e-mail or Usenet articles sent from one network to another,
    and some people use software that strips the header information.
    B) How to write useful summaries   
    Whenever a question or request for information results in many
    replies, it is expected that the person who posted the original
    article will compile and post a summary of the responses.  That
    person is expected to exercise discretion and tact when compiling
    and editing the replies, to ensure a fair and accurate summary.
    Answers to very esoteric questions are often best sent directly
    to the person who asked for help, rather than to the newsgroup;
    the choice of whether to post a (public) reply or send (private)
    e-mail is a personal decision.  If you send a reply by e-mail,
    and would prefer that it be kept private, you should say so in 
    your note, because otherwise the other person may share your
    comments with others.  If the original poster promises to post
    a summary at the outset, then all replies should be sent by 
    e-mail, unless the reply constitutes an important re-direction
    of the original question.
    Care should be invested in writing summaries:
    * A simple concatenation of all the answers is not adequate;
      instead redundancies, irrelevancies, verbosities and errors
      of fact or spelling should be edited out.  It is appropriate
      to use square brackets and dots to indicate editing [...].   
    * The answers should be separated clearly, and nicely formatted.
    * The contributors of each answer (or of a group of answers all
      along the same lines) should be identified, unless they asked
      that their names not be used.
    * The "best" answers should come first.
    C) How to avoid starting "flame wars", a.k.a. nasty arguments
    Biology is very much a compilation of theories and dogmas, and
    thus virtually every discussion eventually uncovers some point of
    basic disagreement among the participants.  It can be difficult
    to keep discussion on any topic from drifting into argument, and
    bitter arguments do no one any good.  So, to keep things cool,
    when an article angers you, save it for a few hours while you go
    off to a meal, or to do something else.  Then come back to the
    message when you are calm and relaxed (and have had a chance to
    think out a good rebuttal ;-).  You may find that, on a second
    reading, the article no longer offends you so much.
    Although English is the language in which the vast majority of
    Bionet articles are written, English is not the first language of
    quite a few participants, nor are all native English-speakers
    equally skilled at expressing themselves.  Try to remember this
    when interpreting the arguments made by others.  More importantly,
    try to appreciate that the Bionet readers represent an enormously
    wide spectrum of specialties, each with its own founding principles,
    theories, literature, philosophy, classic examples, and techniques.
    You can learn a lot here, and you can also teach others a lot, but
    only if great care is taken to avoid excessive jargon.  Although 
    almost all of us are biologists, it is nonetheless necessary for 
    each of us to write as though addressing a general audience of 
    scientists.  And, anyway, the exercise will be good for you.
    If you simply must say something highly critical, consider sending
    it via personal e-mail, rather than posting or mailing to the group.  

 4) Special instructions for Usenet readers? 

    Please keep in mind 

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