MICROBIOLOGY FAQ (long)

Martin Latterich micro at mendel.berkeley.edu
Tue Nov 1 09:06:09 EST 1994


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                       The BIONET.MICROBIOLOGY FAQ
                                  V 1.3
                            November 1, 1994
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This is version 1.3 of the BIONET.MICROBIOLOGY FAQ (frequently asked
questions). This FAQ is largely compiled from suggestions and input
from participants in the MICROBIOLOGY newsgroup. 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 micro at mendel.Berkeley.EDU with the ÒMicro FAQÓ 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.

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 newsgroup aimed at the discussion
and information exchange of any relevant microbiological topic. The
newsgroup is in the bionet sector and is accessible to subscription via
electronic mail and/or directly from newsservers carrying the bionet
newsgroups.

The newsgroup, bionet.microbiology, is intended as a forum for
scientific discussions and questions regarding all aspects of the
microbiological sciences. Topics ranging from the microorganismsÕ
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 newsgroup 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 newsgroup is in the bionet sector and is accessible from your local
newsserver (NNTP server), assuming it carries the bionet newsgroups.
You also can subscribe to bionet.microbiology via electronic mail.


1) Access by NNTP server

The newsgroup 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 newsgroup. Please contact your local news
administrator concerning the addition of this newsgroup to your local
newsserver (see below).


2) Access by e-mail

Everyone in the AMERICAS and the PACIFIC RIM who has no access to a
newsserver 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 Òa
mustÓ 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, itÕs sub disciplines, or
any aspect of interest to the microbiology community are welcome in
this newsgroup, 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 newsgroup with your favorite newsreader,
please follow the instructions of your newsreader of how to post an
article.

If you like to post to the newsgroup 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 newsgroup 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 in the bionet.* sector which have
specialized in certain aspects of microbiology, or because they deal
with a microorganism as a model system.

These newsgroups are:

bionet.prof-society.ascb
bionet.prof-society.faseb
bionet.chlamydomonas
bionet.biology.n2-fixation
bionet.immunology
bionet.molbio.evolution
bionet.molbio.hiv
bionet.molbio.methds-reagnts
bionet.molbio.yeast
bionet.mycology
bionet.parasitology
bionet.protista
bionet.software.www
bionet.virology

Anybody interested in accessing these newsgroup can do so as described
above.


2) Prototype Newsgroups

The prototype newsgroup for diagnostics can be subscribed to by e-mail
by sending

subscribe diagnost

in the body of the message to the address

biosci-server at net.bio.net


3) 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.


4) 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 itÕs purpose and
how to access it can be obtained from:
SSUTTON at Eckert.acadcomp.monroecc.edu by sending an e-mail message to
the BBSÕs owner.

NOTE: I tried to contact the owner of the BBS concerning access
information, but as yet I have not had any reply.



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

Under construction; a few select entries are:

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.



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

E. coli Database  Manfred Kroeger's E. coli datasets are available from

                  the EMBL FTP site ftp.embl-heidelberg.de

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>).

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/

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/


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


Microbiology     The WWW Virtual Library ÒMicrobiology (Biosciences)Ó
is
                 accessible at: 
                 http://golgi.harvard.edu/biopages/micro.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 prerelease version 
                 of this database can be accessed through the WWW at
the 
                 following URL:

                 http://megasun.bch.umontreal.ca/protists/protists.html




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

Under construction; need more questions to do the stats to see if they
are frequent or not ;-).

1.) Òbionet.microbiology is not on my NNTP serverÓ

Give an updated version of the so called Òcheckgroup-messageÓ 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:



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

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

Thanks to Dave Kristofferson and the ÒbionettersÓ 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.

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

micro at mendel.Berkeley.EDU

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





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