MICROBIOLOGY FAQ 2.4 (long)

Martin Latterich latteric at mendel.berkeley.edu
Sun Jul 16 20:49:19 EST 1995


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                       The BIONET.MICROBIOLOGY FAQ
                                  V 2.4
                              July 15, 1995
------------------------------------------------------------------------

This is version 2.4 of the BIONET.MICROBIOLOGY FAQ (frequently asked
questions). This FAQ is largely compiled from suggestions and input from
participants in the MICROBIOLOGY news group. There is always more that can
be added, and I do appreciate additions, info, suggestions, criticism of
interest to the microbiology community. Please send all submissions to
latteric at mendel.Berkeley.EDU with the ³Micro FAQ² as subject header. 

The FAQ will be posted once a month to BIONET.MICROBIOLOGY, as close to
the beginning of the month as humanly possible. This issue and future
issues can also be retrieved by anonymous FTP from mendel.Berkeley.EDU in
the /pub/micro directory, using your e-mail address as password.  Starting
with this issue, there will be two versions of the FAQ: One in ascii
format (.txt) and the other in Word Perfect 3.1 format (.wp).

The FAQ is organized as follows:

I.     What is bionet.microbiology
II.    How to access bionet.microbiology
III.   How to retrieve old articles
IV.    How and what to post in bionet.microbiology
V.     Related newsgroups and bulletin boards
VI.    Other internet sources of interest to microbiologists
VII.   Actual frequently asked questions
VIII.  Miscellaneous



I.  WHAT IS BIONET.MICROBIOLOGY
-------------------------------

bionet.microbiology is an internet news group aimed at the discussion and
information exchange of any relevant microbiological topic. The news group
is in the bionet sector and is accessible to subscription via electronic
mail and/or directly from news servers carrying the bionet newsgroups.

The news group, bionet.microbiology, is intended as a forum for scientific
discussions and questions regarding all aspects of the microbiological
sciences. Topics ranging from the microorganisms¹ biochemistry, evolution,
genetics, host-parasite relationships, molecular biology, pathology,
physiology, role in biotechnology, role in pathogenesis, taxonomy to the
teaching of microbiology will be covered.

In addition, the news group will allow announcements of meetings, funding
sources and job opportunities, a collection of practical advice,
methodologies specific to the field of microbiology, a list of frequently
asked questions, including but not limited to common techniques,
experimental approaches to reoccurring problems, the "to-knows" about
microbes and pointers to other information sources.


II.  HOW TO ACCESS BIONET.MICROBIOLOGY
--------------------------------------

The news group is in the bionet sector and is accessible from your local
news server (NNTP server), assuming it carries the bionet newsgroups. You
also can subscribe to bionet.microbiology via electronic mail.


1) Access by NNTP server

The news group is accessible as bionet.microbiology by NNTP servers
carrying bionet newsgroups. If your NNTP server does not have
bionet.microbiology, it is likely that your local news administrator has
overlooked this news group. Please contact your local news administrator
concerning the addition of this news group to your local news server (see
below).


2) Access by e-mail

Everyone in the AMERICAS and the PACIFIC RIM who has no access to a news
server and wishes to subscribe to bionet.microbiology can send an e-mail
to:

        biosci-server at net.bio.net 

with the following text in the body of the message:

        subscribe microbio



If you are located in EUROPE, AFRICA, OR CENTRAL ASIA and wish to
subscribe to bionet.microbiology, send an e-mail to:

        MXT at dl.ac.uk

with the following text in the body of the message:

        SUB bionet-news.bionet.microbiology


3) General BIOSCI/bionet information

If you like to know more about e-mail subscription and other bionet.*
newsgroups and are located in the AMERICAS or the PACIFIC RIM, send an
e-mail from your account to:

       biosci-server at net.bio.net

with 

       info usinfo

in the body of your message. If you like to know more about e-mail
subscription and other bionet.* newsgroups and are located in Europe,
Africa or Asia, send an e-mail from your account to:

       biosci-server at net.bio.net

with 

       info ukinfo

in the body of your message.

You will receive a file with instructions of how to access the bionet.*
newsgroups and furthermore find pointers to other useful information. Dave
Kristofferson, the BIOSCI/bionet Manager, and others have done an
excellent job in compiling a list of helpful information which are ³a
must² to everybody not familiar with the internet and netnews. This
BIOSCI/bionet FAQ will cover all aspects concerning access to newsgroups,
subscription, cancellation of subscription, how to post articles, what to
post and not to post, how to reply to posts. I strongly recommend everyone
not yet familiar with netnews and e mail subscription to take a few
minutes to familiarize themselves with the BIOSCI/bionet FAQ document. The
FAQ can be retrieved by sending an e-mail to:

       biosci-server at net.bio.net

with 

       info faq

in the body of your message.


III.  HOW TO RETRIEVE OLD ARTICLES
----------------------------------

1) Access of bionet.microbiology archives by anonymous FTP and gopher

Archives for bionet.microbiology can be accessed by anonymous FTP at
net.bio.net [134.172.2.69] in the pub/BIOSCI/MICROBIOLOGY directory. Note
that files are ordered by date, and that the filenames are case sensitive.

The same archived files are accessible via Gopher using net.bio.net as
your gopher server. Gopher also allows you to view the individual messages
within each monthly archive file. The files are in the MICROBIOLOGY
directory. Please see the BIOSCI/bionet faq for details (see above).


IV.  HOW AND WHAT TO POST IN BIONET.MICROBIOLOGY
------------------------------------------------

Any message or post concerning microbiology, it¹s sub disciplines, or any
aspect of interest to the microbiology community are welcome in this news
group, provided they are scientific in nature or are of scientific
interest.

Some technical guidelines to posting messages to the bionet newsgroups are
described in the BIOSCI/bionet faq (see above), and anybody not certain of
how and what to post should become familiar with the document. 

If you like to post to the news group with your favorite news reader,
please follow the instructions of your news reader of how to post an
article.

If you like to post to the news group by e-mail, and are located in the
AMERICAS or the PACIFIC RIM, send an e-mail from your account to:

       microbio at net.bio.net

If you like to post to the news group by e-mail, and are located in
Europe, Africa or Asia, send an e-mail from your account to:

       microbio at daresbury.ac.uk


V.  RELATED NEWSGROUPS AND BULLETIN BOARDS
------------------------------------------

1) Newsgroups

A number of other newsgroups exist which have specialized in certain
aspects of microbiology, or because they deal with a microorganism as a
model system.

These newsgroups are:

bionet.announce
bionet.biology.n2-fixation
bionet.cellbiol
bionet.chlamydomonas
bionet.diagnostics
bionet.general
bionet.immunology
bionet.metabolic-reg
bionet.molbio.evolution
bionet.molbio.hiv
bionet.molbio.methds-reagnts
bionet.molbio.proteins
bionet.molbio.yeast
bionet.mycology
bionet.parasitology
bionet.protista
bionet.virology
sci.bio.microbiology
sci.med.pathology

Anybody interested in accessing these news group can do so as described
above, excepting the cited sci.* newsgroups (NNTP server only).


2) Listserver

The following listserver also contains material of interest:

Leishmaniasis listserv:      To subscribe you need to send the following e mail
                  message -
 
                  address:- listserv at bdt.ftpt.br
                  Subject:- (leave blank)
                  Message:- subscribe Leish-L <your full name>

                  Leave the <>brackets out when you type in your name.


3) Microbiology BBS

There has been a public announcement of a Microbiology Bulletin Board
Service (BBS) whose construction is in progress (Sutton, S. (1994). ASM
News, Vol. 60 Iss. 5, pg. 231). Further information of it¹s purpose and
how to access it can be obtained from: sutton at microbiol.org by sending an
e-mail message to the BBS¹s owner.

NOTE: The access number is 817-557-0330

4) MicroBio Online

MicroBio Online is a new BBS dedicated to networking in the quality
control area medical devices, pharmaceuticals and cosmetics. It is based upon
the "Microbiological Update" newsletter.

Call 303-384-3535 (BBS) or 303-279-4643 (Voice).


VI.  OTHER INTERNET SOURCES OF INTEREST TO MICROBIOLOGISTS
----------------------------------------------------------

1) e-mail
--------

dFLASH server     The dFLASH Group has a new electronic mail server that
                  allows GENBANK and PIR similarity searches with the 
                  FLASH algorithm. Further information can be obtained 
                  by sending:

                  send help
                  in the body of the message to 
                  dflash at watson.ibm.com
                  Make sure you have dflash as subject header.

Polio Server      To join the Polio List owned by Robert Mauro, send e-mail
                  to:
                  listserv at sjuvm.stjohns.edu
                  with the BODY containing the message
                  sub Polio yourfirstname lastname


The following section assumes some basic knowledge and experience with FTP
clients and WWW browsers, such as Fetch, Netscape or Mosaic.  If you are
new to computers and the internet, please consult your local computer
expert first.


2) Anonymous FTP
----------------

E. coli Database  Manfred Kroeger's E. coli datasets are available from 
                  the EMBL FTP site ftp.embl-heidelberg.de

Microbiology FAQ  This Microbiology FAQ can be retrieved from:
                  mendel.berkeley.edu
                  The directory is: /pub/micro
                  Given enough time, I *MIGHT* convert this document into
                  hypertext with links to interesting and scientifically
                  stimulating Web pages.

NIH Forms         The ftp site is:  ftp.u.washington.edu
                  The directory is:  /pub/user-supported/templates


3) Gopher/WAIS/WWW
--------------------

ATCC            The name of the host computer at the AMERICAN TYPE
                CULTURE COLLECTION  (ATCC) used to access catalogue 
                information has been changed from atcc.org to 
                culture.atcc.org.
  
                This change of name affects using gopher to access 
                information describing research materials available from 
                the ATCC. You must point your gopher client to 
                culture.atcc.org (gopher culture.atcc.org).

                The change also affects using telnet to connect to the
                ATCC Recombinant Materials Database (clones, vectors, 
                recombinant libraries, transformation hosts, and 
                oligonucleotides) and searching using IRX (telnet 
                culture.atcc.org, username <search>, password <common>).
                Web users use the following URL:  http://www.atcc.org/

Biomedical      The Biomedical Engineering Group at the University
Engineering     of Surrey (UK) now has some pages of information available on
                the web. The URL is:
                http://www.surrey.ac.uk/MechEng/BioMed/homepage.html
                The group offers (amongst other things) an MSc course, and
                postgraduate research opportunities.

Candida         WWW and gopher severs with information about Candida 
                albicans molecular biology. The servers share most of 
                their text data. The WWW server has additional images 
                and diagrams. To access them:
                Point your gopher client to:      alces.med.umn.edu
                There is a directory with the Candida information.

                The URL for the WWW server is:
                http://alces.med.umn.edu/start.html
                There are links to the Candida information and other 
                information on the server on that page.

Case Western    Department of Biochemistry, Case Western Reserve 
                University School of Medicine WWW server with the
                following URL 
                http://biochemistry.bioc.cwru.edu:80/

DNA sequences   Keith Robinson maintains a HTML listing of all available DNA
                sequences 100Kb or longer. It is available at the URL:
                http://golgi.harvard.edu/100kb/

Earth and       The URL for the EESC server is:
Environmental   http://terrassa.pnl.gov:2080/
Sciences Center For more information please contact:  td_scheibe at pnl.gov

E. coli         The E. coli genetic stock center has a Web server:
                http://cgsc.biology.yale.edu/cgsc.html

                Barbara Bachman's E. coli culture collection can be 
                accessed by gopher under:  cgsc.biology.yale.edu
                This resource can be used more fully if you can hack 
                the SYBASE program,  you can telnet directly and do 
                more powerful searches. The CGSC Gopher files are 
                generated periodically from the public 
                portions of the E. coli Genetic Stock Center (CGSC) 
                database. They include information about strains, 
                mutations, genes, and references.  
                We assume that these files will be used primarily for 
                searching for strains with specific mutations or 
                genotype combinations and secondarily for examining 
                stock center information on mutations and genes.
                The linkage map is being revised, and the list of genes 
                and coordinates in the "Map" file represent the 
                coordinates currently in the database. Access to the 
                "external version" of the CGSC relational 
                database itself is provided either as a menu option 
                (#5) on this gopher (See sub menu item "How to 
                Access..." and "CGSC Database") or by direct telnet to 
                cgsc.biology.yale.edu  To gain direct access, you 
                must obtain a password and login as guest. Send e-mail 
                to  mary at cgsc.biology.yale.edu to obtain the current 
                password for guest.

                --Using the CGSC Gopher v. Querying the CGSC Database--
                The subset of information contained in the CGSC-gopher 
                file can be accessed by text searches via IUWais. (See 
                IUWAIS search features on the "2. CGSC Files and 
                Database" menu.) You may also directly query the CGSC 
                relational database.  If your query is not easily 
                formulated as a simple Boolean search or if a Wais 
                search returns far too many instances to examine one by 
                one, going to the form-based interface of the database 
                will allow you to specify the query in a way that will 
                limit the returns to those of most interest to you. The 
                About file of the submenu provides examples of both 
                types of queries. 
                Read the DBAccess file on the submenu to learn how to 
                navigate between data fields and menu bar and between 
                object-forms. For more detailed instructions, contact 
                Mary at address below for users' guide.

                Strains bearing CGSC numbers (the only strains present 
                in the flat file) are available from the stock center. 
                The stock center and the database development are 
                supported by the National Science Foundation.

                For more information about the database or to request 
                strains, contact Mary Berlyn at CGSC:  
                mary at cgsc.biology.yale.edu

Fungal Genetics This information source can be found under the 
                following URL:       
                http://kufacts.cc.ukans.edu/cwis/units/fgsc/gene.html

GenBank         A searchable GenBank database can be
                accessed by addressing your gopher client to 
                ftp.bio.indiana.edu, and 
                looking under Genbank-Sequences/

                GenBank users can use the World Wide Web (WWW) for submitting
                sequences to GenBank.  The new submission tool - BankIt -
                provides a simple forms approach for submitting your sequence
                and descriptive information to GenBank.  You can access BankIt
                through the GenBank home page:  http://www.ncbi.nlm.nih.gov/

GenomeNet       GenomeNet is a Japanese computer network for genome 
                research and related research areas in molecular and 
                cellular biology. It can be accessed by WWW as:
                http://www.genome.ad.jp

Medlab          MEDLAB-L, a discussion list for medical laboratory
                professionals.  Although it contains members (>430 from 23
                countries) from all disciplines of laboratory medicine,
                microbiology people certainly participate in the goings-on. 
                It is run by Patricia Letendre <pletendr at gpu.srv.ualberta.ca>
                in Edmonton.  You can join the list by sending "Subscribe
                MEDLAB-L" to LISTSERV at VM.UCS.UALBERTA.CA.

Medsearch       The URL is:
America         http://www.medsearch.com:9001

Microbial       The location is http://www.bdt.org.br/msdn/msdn.html
Strain Data     This server includes a large variety of databases and has 
Network (MSDN)  links to other for microbiologists relevant sites.

Microbiology    The WWW Virtual Library ³Microbiology (Biosciences)² is
                accessible at: 
                http://golgi.harvard.edu/biopages/micro.html


Muti-dimens.    The address to what is called "Multidimensional Microscopy
Microscopy      WWW" is:  http://128.205.21.24/

Mycobacterial   MycDB is available free of charge through the World Wide Web
Database        at URL http://www.biochem.kth.se/MycDB.html

Protist Images  Protist Image Data provides pictures and short
                descriptions of selected protist genera, especially 
                those genera whose species are frequently used as 
                experimental organisms or are important in studies of 
                organismal evolution. The pre release version 
                of this database can be accessed through the WWW at the 
                following URL:
                http://megasun.bch.umontreal.ca/protists/protists.html 

SGM             The Society of General Microbiology have their own Web page
                providing information on the Society, including subscription,
                and forthcoming conferences. The URL is:
                http://www.mcc.ac.uk/pharmweb/sgm.html

TB/HIV Research Point your web browser to:
                http://www.brown.edu/Research/TB-HIV_Lab/

Tuberculosis    A web site for Tuberculosis Research has the following URL:
Research        /http://molepi.stanford.edu/


4) Other Resources
------------------

ASM             The American Society for Microbiology has much information for
                students who are interested in biological careers.  Send
                address to Office of Education and Training - Careers,
                American Society for Microbiology, 1325 Massachusetts Ave. NW,
                Washington, DC 20005.

                Important e-mail addresses are:

                Subscriptions       Subscriptions at asmusa.org
                Membership          Membership at asmusa.org
                Workshops, etc      TrainingInformation at asmusa.org
                Career info.        CareerInformation at asmusa.org
                Education info.     EducationResources at asmusa.org
                Meetings info.      MeetingsInfo at asmusa.org

Halophile       Directory of Microbiologists Interested in Halophiles and
Directory       Halophilic Environments. This list will be posted
                approximately once every two months as a service 
                to the community of microbiologists.  To be added to the list
                please send Bob an e-mail message.: Bob Simon
                (simon at uno.cc.geneseo.edu).


VII.  ACTUAL FREQUENTLY ASKED QUESTIONS
---------------------------------------

1.) ³bionet.microbiology is not on my NNTP server ?²

Give an updated version of the so called ³checkgroup-message² to your news
system administrator to update your current list of newsgroups.  
The message is posted to bionet.announce on the first of
each month and is available for retrieval at any time from
net.bio.net via FTP, gopher, and Mosaic:

2) ³How to deal with inappropriate and/or offensive posts ?²

BIONET.MICROBIOLOGY is not moderated, meaning that every post made to that
news group will be distributed to all recipients, irrespective of
content.  The advantages are speed and lack of censorship ;-).  The
obvious disadvantage is that anybody can make an inappropriate or in the
worst case even offensive post.  While I as discussion leader will make
any effort to ³educate² in private individuals who posted letters to the
news group that do not belong there, or as it happened recently take
action against individuals that are guilty of gross violations of news
policy (spamming) resulting in the termination of internet access for that
party, readers will still be able to read inappropriate or offensive
posts.  My humble advice is to delete such messages where the header
suggests that they may be offensive and not read it at all because the
message content can be disturbing.  The only alternative is to have
BIONET.MICROBIOLOGY moderated (and even moderated newsgroups are not fool
proof) which involves a lot of work for the moderator, and certainly will
slow the information flow.  
Having said the above, I personally do not think that ³our² news group has
seen to much inappropriateness.  I very much favor the idea to have an
unmoderated news group because in my opinion moderation will bring along
some low level censorship (dependent on the moderator of course) which is
inhibitory to the free and uninhibited information flow in any field.

3) ³What is the policy on Flame-Wars ?²

Flames (a letter meant to insult or provoke) have become somewhat popular
even among scientists.  While the BIONET.MICROBIOLOGY news group
encourages free expression of opinion and even the unconventional opinion,
freedom of expression has it¹s limits when it obviously interferes with
the rights of another individual.  I strongly encourage people to use
their common sense when making a post, and not post anything that others
might find offensive or worse, with the intend to downplay an opponent.

4) ³Do I need permission to post here ?²

No, anyone is free to post here as long as the post is of scientific
interest, and as long as it does not represent a commercial ad or flame.


VIII.  MISCELLANEOUS
--------------------

This FAQ reaches a size which is no longer convenient to post to the news
group in one piece.  Future editions may be split into two parts; the
first half consisting of news group information and the second half of
microbiological sources.  Once I set up a WWW page for the news group, the
source information will no longer be posted to the news group, unless a
significant number of people want to see it here.





ACKNOWLEDGMENTS
----------------

Thanks to Dave Kristofferson and the ³bionetters² for compiling an
excellent and comprehensive BIOSCI/bionet faq, which served as the basis
to the technical subscription information in this MICROBIOLOGY FAQ in
sections II. and III.  Also many thanks to Keith Robinson, Harvard
University, for much information on internet resources and Jim Graham,
Indiana, for contributing Barbara Bachman's E. coli culture collection
information, and last but not least to Meta Kuehn for running the journal
club (yes there is one if people would submit articles of interest ;-) )
and the informal microbiology discussion group.

------------------------------------------------------------------------
More information is always welcome. Please mail your suggestions,
criticism and information to

latteric at mendel.Berkeley.EDU

Martin Latterich, PhD
bionet.microbiology Discussion Leader
University of California, Berkeley



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