MICROBIO FAQ 3.1 (long)

Martin Latterich mlatterich at aim.salk.edu
Tue Sep 3 04:16:39 EST 1996

                       The BIONET.MICROBIOLOGY FAQ
                                  V 3.1
                           September 1, 1996

This is version 3.1 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
mlatterich at aim.salk.edu with Micro FAQ as subject header. 

New versions of this FAQ will be posted once a month to BIONET.MICROBIOLOGY,
as close to the beginning of the month as humanly possible. 

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


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 microorganisms9 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.


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


       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


       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


       info faq

in the body of your message.


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 [] 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).


Any message or post concerning microbiology, it9s 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


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:


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-
                  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 it9s purpose and how to access it can
be obtained from: sutton at microbiol.org by sending an e-mail message to the
BBS9s 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).


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
                  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

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:
                  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 
                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:
                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:
                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 

DNA sequences   Keith Robinson maintains a HTML listing of all available DNA
                sequences 100Kb or longer. It is available at the URL:

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:

                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

E. coli Index   The index contains a new section on Microbiology related
                Conferences and Courses, apart from an excellent section 
                on E. coli.

                The E. coli index URL is: 

Fungal Genetics This information source can be found under the 
                following URL:       

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:

Medlab          MEDLAB-L, a discussion list for medical laboratory
                professionals.  Although it contains members (>591 from 29
                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 ubvm.cc.buffalo.edu.

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: 

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

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:

SGM             The Society of General Microbiology have their own Web page
                providing information on the Society, including subscription,
                and forthcoming conferences. The URL is:

TB/HIV Research Point your web browser to:

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).


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 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 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 it9s 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.


This FAQ reaches a size which is no longer convenient to post to the news
group in one piece. I may set up a WEB page containing links to other
sites of microbiological interest and delete this information in future
editions of the FAQ.


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.  Thanks to Mark Pallen for creating an HTML version of this FAQ. 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

mlatterich at aim.salk.edu

Martin Latterich, PhD
bionet.microbiology Discussion Leader
The Salk Institute

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