Bionet FAQ (new, improved!)

[Una Smith]

           Answers to Frequently Asked Questions (FAQs)


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.

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!).

This FAQ sheet was last modified on 27 October 1992.


============================== 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) Is there a database for X?
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 gopher, and how does it work?
19) What is a WAIS, and how does it work?
20) 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 (18.172.1.27).  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?

    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.

    * Announcements of upcoming conferences or other events, or grant
      deadlines.  If you get the Bionet groups via Usenet, you should
      use an expiration data on such announcments, so that they go
      away once they are no longer relevant.

    * 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, articles, methods or software.
      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.  People often report
      on interesting scientific news in the media, or statements issued
      by various governments, or relate data gathered and posted else-
      where.

    * 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;  nearly all requests are answered
      with full bibliographic references, often in BibTeX format.

    Unacceptable articles are advertisements of any sort, 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 that, unlike many other newsgroups in Usenet,
    the Bionet groups all have parallel mailing lists.  Thus, you should
    avoid cross-posting, since at this time those unfortunate people who
    must use e-mail subscriptions will get multiple copies of cross-posted
    articles.
   
    The Usenet newsgroup news.newusers.questions has several useful FAQs,
    including:
   
   	Answers to Frequently Asked Questions
	How to Get Information about Networks
        Rules for Posting to Usenet
        How to Create a New Newsgroup 

    Bionet has slighly different rules for forming new groups;  to request
    an outline of these rules, send e-mail to biosci at genbank.bio.net.
   
   
 5) Special instructions for e-mail subscribers?

    You are encouraged to get yourself a Usenet distribution feed.
    Usenet is *better* and *easier* than e-mail for following group
    discussions.  For help with Usenet, see the next item.


 6) How can e-mail subscribers get Usenet news at their site?
   
    Way back in the dawn of the information age, people started to
    create discussion groups and subscription lists.  Some of these
    became so active that it was a burden to wade through all the
    electronic mail that came each day.  So an alternative was created:
    Usenet.  Usenet software is free, and behaves somewhat like a familiar
    e-mail reader, but with some significant improvements, such as the
    collection of messages pertaining to a given discussion group being
    grouped together.  

    Many people who get Bionet by e-mail may already have Usenet on their
    machines and just don't know about it.  Some of them probably just
    need a newsreader on their PC or Macintosh to access a campus news
    server that already exists (and possibly need to have the responsible
    person prodded to get the Bionet groups).  Some of them just need to
    be made aware of it.

    If you are an e-mail subscriber, and you're tired of getting so much
    mail, all jumbled together, try typing "news", "rn", "rrn", "vnews",
    or "readnews" at the command prompt.  If your computer does something
    other than complaining about an unknown command, chances are you've
    got news on your system and I would urge you to ask somebody how it
    works at your site, and if your site gets, or can get, the Bionet
    groups.  If your site has some sort of on-line help facility, try
    looking for information about any of the above, and/or "usenet" and
    see if you find anything.  If it turns out you don't have news, but
    you or your site administrator are interested in running it, feel
    free to contact the people at biosci at genbank.bio.net;  they will be
    happy to do whatever they can to help you get it and learn to use it.
    Or ask for help in bionet.general.  But the best thing to do is get
    copies of several documents which are posted in news.newusers.questions.
    True, you can't read them there because you don't have Usenet, but
    you CAN ftp the documents from the archive on pit-manager.mit.edu
    (details in item 1 above).  Some titles and archive file names are:
    
    What is Usenet?				what-is-usenet/part1
    How to become a USENET site			site-setup
    USENET Software:  History and Sources	usenet-software/part1


 7) Where can I get other helpful documents?

    You will learn a great deal about the Internet and what it has
    to offer you if you track down some of the items listed in this
    FAQ.  If you still want to know more, browse around in Usenet. 
    Also, a number of commercial books have been published recently
    which give a very thorough guide to the Internet.  Check at your
    local academic bookstore or university library.  


 8) Does anyone have an e-mail address for Dr. X?

    The quickest, most efficient way to answer this is to call or write
    to Dr. X directly.  If anyone can help you with this, it's Dr. X.
    To date, most biologists don't have e-mail addresses, or if they do,
    they don't read their e-mail, so you really are better off contacting
    the person directly.  If you must try to find this information via
    the computer networks, please start by reading the introductory FAQ
    "How to find people's E-mail addresses", posted in news.answers.  
    If you are on an Internet node, you can telnet to bruno.cs.colorado.edu,
    (login: netfind).  Given a name and university or company name, the
    computer may be able to give you an e-mail address for that person.
    Also, you can ask in the newsgroup bionet.users.addresses (which is
    graciously watched-over by Robert Harper).


 9) How to find a good graduate program?

    Go talk to the undergraduate or graduate advisor in your department,
    if you're a college student.  Start browsing through the scientific
    journals, and the new book stack in the library.  Ask your favorite
    professors for advice.  Sadly, Bionet can not be all things to all
    people, and questions about how to pick graduate programs generally
    don't get satisfactory replies.


10) Where I can get old Bionet articles?

    All the Bionet newsgroups are now stored in an anonymous ftp archive
    at ftp.bio.indiana.edu, in the directory usenet/bionet.

    GenBank/IG also has the entire collection of Bionet messages from
    inception (back in 1987), which are available via the biosci.src
    WAIS source at genbank.bio.net.  Contact biosci at genbank.bio.net
    for further help with this.


11) Where can I find biology-related job announcements?

    The bionet.jobs newsgroup is a good place to start, but you might
    also want to check the LISTSERV subscription list run by the
    Ecological Society of America:  ECOLOG-L at UMDD.UMD.EDU.  Subscrip-
    tions to ECOLOG-L are handled by LISTSERV at UMDD.UMD.EDU, which can
    provide logs of previous months' messages on request.


12) Where can I get journal contents online? 

    Bionet.journals.contents is a newsgroup where a number of publishers
    contribute listings of the tables of contents as each issue is done.
    Recently, there has been some discussion about expanding the role
    of this newsgroup.  Stay tuned!


13) Suggestions for freeware or commercial software packages?

    Bionet.software is a good place to look for discussions on this topic.
    If you read it for a few weeks, you will learn about many other sources
    of information.  Among these are digests, special interest mailing
    lists and Usenet newsgroups, and hundreds of anonymous ftp archives. 


14) Is there a database for X?

    [ How to answer this? ]

   
15) Are there other biology newsgroups or e-mail subscription lists?

    There are many;  too many to list here, in fact.  Send e-mail to
    Una Smith <smith-una at yale.edu> asking for the file "bio-lists".
    

16) What is anonymous ftp?

    "FTP" stands for File Transfer Protocol;  on many systems, it
    is also the name of a user-level program that implements that
    protocol.  This program allows a user to transfer files to and
    from a remote network site, provided that network site is
    reachable via the Internet or a similar facility.  (Ftp is also
    usable on many local-area networks.)

    "Anonymous FTP" indicates that a user may log into the remote
    system as user "anonymous" with an arbitrary password.  A common
    convention is that some sort of identification is supplied as the
    password, e.g. "yourname at yournode".  This is useful for those 
    archive managers who must justify the time spent providing this
    free (but not cheap) service to their bosses, so please cooperate.
    Also note that most sites restrict when transfers can be made, or
    at least suggest that large transfers be made only during off-hours.


17) How can I access ftp archives from Bitnet?

    Bitnet is not capable of supporting telnet or ftp sessions, but
    many Bitnet nodes are also Internet nodes, so your site may have
    telnet and ftp after all.  If not, if your site is a strictly 
    Bitnet node, you can use a service provided by Princeton University;
    BITFTP at PUCC.  By sending your ftp request to BITFTP via e-mail, you
    can search anonymous ftp archives elsewhere, and the results will be
    sent to you by e-mail.  For help, send the message HELP to BITFTP at PUCC.
      

18) What is gopher, and how does it work?

    Gopher is a user-interface program that makes ftp connections for
    you when you select an item in a menu.  It is a user-friendly way
    to get stuff off the Internet without having to know where the
    stuff lives.  Gopher is free, and there are nice versions for most
    types of computers, especially Unix workstations and Macs.  Ask
    your system administrator to find and install gopher for you, since
    this is a tool that everyone will want to use.


19) What is WAIS, and how does it work?

    [I could use some help here, folks!]


20) Why do so many people contribute questions but not the answers?

    The answer to this is a mystery to me.  Contributions are always
    welcome, but those including concise, lucid answers deserve my
    eternal gratitude (and mention in the list of contributors ;-).


============================ Contributors ============================

Good ideas for format, etc. were stolen from the comp.text.tex
FAQ, by Bobby Bodenheimer.  Other contributors include (in no
particular order):

David Kristofferson	<kristoff at genbank.bio.net>
Harvey Chinn		<harvey at ecst.csuchico.edu>
Andy F. Johnston	<bm477 at cleveland.Freenet.Edu>
Josh Hayes		<josh at cqs.washington.edu>
Jim McIntosh		<jim at american.edu>
Jonathan I. Kamens	<jik at athena.mit.edu>
Steve Clark		<clark at salk-sc2.sdsc.edu>
Christophe Wolfhugel	<wolf at grasp1.univ-lyon1.fr>
Ross Smith		<smith at mcclb0.med.nyu.edu>
Roy Smith		<roy at alanine.phri.nyu.edu>

Anyone who wishes to contribute to this FAQ sheet, please e-mail me. 
To save me much time and effort, please use the format used here. 
Thanks in advance!

-- 

      Una Smith      Biology Department       smith-una at yale.edu
                     Yale University
                     New Haven, CT  06511