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The BIONET.MICROBIOLOGY FAQ
V 1.9 March 21, 1994
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This is version 1.9 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 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.
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 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 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 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
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 it¹s purpose and
how to access it can be obtained from:
SSUTTON at Eckert.acadcomp.monroecc.edu by sending an e-mail message to the
BBS¹s 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
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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
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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
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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/fgsc/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 ³Microbiology (Biosciences)² 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
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Under construction; need more questions to do the stats to see if they are
frequent or not ;-).
1.) ³bionet.microbiology is not on my NNTP server²
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:
VIII. MISCELLANEOUS
--------------------
Please watch out for Version 2.0 of the Microbiology FAQ. This coming
version will be completely overhauled and contain many new internet sites
of interest to the microbiology community.
I was busy conducting a job search and had to cut back on bench time and
especially time on the computer. Now that I am waiting for hopefully good
news I am back in business.
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.
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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
