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The BIONET.MICROBIOLOGY FAQ
V 2.0
April 9, 1995
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This is version 2.0 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
micro at mendel.Berkeley.EDU with the "Micro FAQ" 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 microorganisms' 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 "a must" 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, it's 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
Anybody interested in accessing these news group can do so as described
above, excepting sci.bio.microbiology (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 it's purpose and how to access it
can be obtained from: sutton at microbiol.org by sending an e-mail message to
the BBS's 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
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 "Microbiology (Biosciences)" 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.
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.) "bionet.microbiology is not on my NNTP server ?"
Give an updated version of the so called "checkgroup-message" 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) "How to deal with inappropriate and/or offensive posts ?"
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
"educate" 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 "our" 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) "What is the policy on Flame-Wars ?"
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 it's 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) "Do I need permission to post here ?"
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 "bionetters" 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
micro at mendel.Berkeley.EDU
Martin Latterich, PhD
bionet.microbiology Discussion Leader
University of California, Berkeley
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