From: smith-una@yale.edu (Una Smith)
Newsgroups: bionet.plants,bionet.software
Subject: Bionet FAQ (much new, long)
Date: 20 Nov 1992 16:37:04 -0500
Organization: Yale University Science & Engineering UNIX(tm), New Haven, CT 06520-2158
Distribution: world
NNTP-Posting-Host: minerva.cis.yale.edu



           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 (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@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@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 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@net.bio.net.
   
   
 5) Special instructions for e-mail subscribers?

    A separate FAQ describing important administrative details of
    the Bionet newsgroups is available from biosci@net.bio.net.
    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", "nn",
    "trn", "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
    someone at your site how it works, 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@net.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.  

    One particularly useful book is Brendan Kehoe's "Zen and the Art
    of the Internet:  A Beginner's Guide to the Internet".  The first
    edition, January 1992, is available online from many anonymous
    ftp archives around the world, in a directory named something like
    /pub/zen;  read files stored together with the book for help
    turning this file into a printed document.  Use Archie to locate
    the book on an archive near you, or check the archive on Brendan
    Kehoe's home computer, ftp.cs.widener.edu.  For information about using
    Archie, check in news.answers or bionet.users.addresses.  This book
    is also commercially available from the Prentice Hall publishing
    company for about US $25.  The book is about 100 pages long, and
    most of the information in it was culled directly from documents
    available in Usenet in the newsgroup news.answers and elsewhere.
    Another resource is "The Internet Tour" by BBN, a Mac Hypercard
    stack from ftp.bio.indiana.edu in /help.


 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
    do not 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 WAIS and anonymous
    ftp at net.bio.net.  Contact biosci@net.bio.net for further help.


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@UMDD.UMD.EDU.  Subscrip-
    tions to ECOLOG-L are handled by LISTSERV@UMDD.UMD.EDU, which can
    also 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!

    It is becoming increasingly common for American universities to
    have agreements with bibliographic data base services which allow
    their faculty and students to run online searches from any networked
    computer, including the Macs or PCs on their desks.  Ask your local
    librarian if any such plans are underway where you work.


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. 

    Many of these ftp archives are accessible via Gopher.  One that is
    currently only available via ftp is the Brazilian Medical Informatics
    archive on ccsun.unicamp.br, courtesy of Renato Sabatini.


14) What to do about problem X with data base Y?

    For questions about:                 Try asking for help in:
    --------------------                 -----------------------
    PIR (and SWISS-PROT)                 bionet.molbio.proteins
    The Brookhaven Protein Data Bank     bionet.xtallography
    The Los Alamos GenBank               bionet.molbio.genbank
    The EMBL Databank                    bionet.molbio.embldatabank
    Human Genome Database (GDB)          bionet.molbio.gdb
    Museums and Herbaria on Internet     bionet.plants, or send e-mail
                                             to beach@huh.harvard.edu

    Posting about these data bases to the corresponding newsgroups will
    usually get the attention of someone on the appropriate data base
    staff fairly quickly.  In addition, data base corrections can be
    sent as follows:

    Database      address
    --------      -------
    GenBank       update@genome.lanl.gov
    EMBL          update@EMBL-Heidelberg.DE
    PIR           POSTMASTER@NBRF.Georgetown.EDU, POSTMAST@GUNBRF.Bitnet
    SWISS-PROT    bairoch@cmu.unige.ch
    Brookhaven    pdb@chm.chm.bnl.gov, PDB@BNLCHM.Bitnet
    GDB           (uncertain, you might ask at help@welch.jhu.edu)
    Herbaria      beach@huh.harvard.edu

    Questions about submitting data to these data bases should be
    addressed to the appropriate newsgroups above.  Most of this
    information was graciously compiled by John Garavelli at PIR.

   
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
    me, Una Smith <smith-una@yale.edu>, with the string "bio-lists"
    in the subject line of your message.
    

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@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@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@PUCC.
      

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

    Archie is a program that helps you locate software in any of the
    thousands of anonymous ftp archives around the world.  You can
    get a copy of the software via ftp from any Archie server, in the
    /archie/clients directory.  Also, it's on ftp.cs.widener.edu in
    /pub/archie.tar.Z.  There are versions of Archie for all sorts of
    Unix systems, VMS (with some TCP/IP packages) and on PCs running
    PC/TCP, CUTCP, or PC-NFS.  Ask you system administrator for help,
    or ask around in bionet.users.addresses.


19) 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.  Bionet.general,
    bionet.software, and bionet.users.addresses are good places to learn
    more about biology-related Gopher services.

    Rob Harper's Gopher service on gopher.csc.fi in Finland offers easy
    access to many biology-related archives:

                   Bionaut software and data paradise

      1.  Assorted databases from SERC Daresbury UK (FTP ARCHIVE)/
      2.  GDB Human Genome Data USA (FTP ARCHIVE)/
      3.  Gene Server at University of Houston USA (FTP ARCHIVE)/
      4.  INN EMBL software mirror site ISRAEL (FTP ARCHIVE)/
      5.  Indiana University software server USA (FTP ARCHIVE)/
      6.  Intelligenetics USA (FTP ARCHIVE)/
      7.  Macintosh Scientific & Engineering MacSciTech USA (FTP ARCHIVE)/
      8.  Molecular Biology Software FINLAND (FTP ARCHIVE)/
      9.  NCBI Repository USA (FTP ARCHIVE)/
      10. National Center for Supercomputing Apps USA (FTP ARCHIVE)/
      11. PDB structural coordinates (Brookhaven) USA (FTP ARCHIVE)/
      12. Ribosomal Database Project USA (FTP ARCHIVE)/
      13. The Ultimate Bionaut software search (ARCHIE) <TEL>
 

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

    WAIS stands for Wide Area Information Servers.  It is a rather
    visionary and so far embryonic project that started at Thinking
    Machines, Inc. a few years ago (they build supercomputers).  The
    idea is to make Internet information archives accessible by
    indexing their contents and making those indexes searchable with
    software distributed to anyone on the Internet.  The software is
    primitive so far, but the concept is so powerful that it's worth
    playing with a little now, just to get a feel for the future.  The
    vision is:  type in a few key words and WAIS goes out and finds
    every relevant document on the Internet for you and provides a
    list thereof.  Wow.

    Information indexed at WAIS sites can be text files, graphic files,
    sound files, and other formats.  The software simply invites you to
    type in a few key words and specify which sources (i.e., servers or
    archives) you think are most likely to have the information you're
    looking for.  You can locate those servers beforehand by searching
    with a much more general key word.  For example, you might want to
    find the appropriate source servers by doing a search on the word
    "biology", before picking out a few of these servers and doing your
    search on "AIDS".  Plant biologists:  There is an Arabidopsis WAIS
    server (see the bionet.genome.arabidopsis newsgroup).  Many WAIS
    servers can be queried from Gopher and many people prefer to use
    Gopher, so far.

    Two WAIS access applications are available for the Mac:  HyperWAIS
    and WAISstation (which is available on the anonymous ftp archive at
    think.com). 

    Material for this section was contributed by Thomas Jacob.


21) What is the Web (or WWW), and how does it work?

    WWW stands for World-Wide Web, and is yet another tool for gathering
    information from the Internet.  WWW looks like a document which you
    can open and read, but clicking on certain words causes other files
    to be retrieved and opened for your inspection.  One very popular
    feature of WWW is a routine which searches Usenet for users' names,
    and return their (current) e-mail address.  This is a good way to
    locate people who don't work on Unix computers, but who sometimes
    post articles to Usenet.  See news.answers for details.  The Web
    is an even newer and more visionary idea than WAIS, so it is not
    as useful.  But stay tuned!


22) 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: 
Harvey Chinn, Steve Clark, John Garavelli, Josh Hayes, Thomas Jacob,
Andy Johnston, Jonathan Kamens, David Kristofferson, Jim McIntosh,
Ross Smith, Roy Smith, and Christophe Wolfhugel.

The people primarily due credit for years of effort in creating and
providing these Internet services include:
David Kristofferson, Don Gilbert, Jim Beach, Rob Harper, John Garavelli,
Dan Jacobson
and a cast of thousands.

Anyone wishing to contribute to this FAQ sheet, please e-mail me. 
Thanks in advance!

-- 

      Una Smith      Biology Department       smith-una@yale.edu
                     Yale University
                     New Haven, CT  06511
Xref: sparky bionet.plants:642 rec.gardens:8121 soc.culture.british:16108