Mycology FAQ

Tom Adams TOM at BIO.TAMU.EDU
Mon Dec 5 16:13:36 EST 1994


------------------------------------------------------------------------
                       The BIONET.Mycology FAQ
                                  V 1.1
                            December 5, 1994
------------------------------------------------------------------------

This is version 1.1 of the BIONET.MYCOLOGY FAQ (frequently asked
questions). This FAQ is adapted from one supplied by the MICROBIOLOGY 
newsgroup and also addresses questions and comments raised by the Mycology 
newsgroup users. Additional suggestions for future postings should be sent 
to:
tom at bio.tamu.edu
leland at straylight.tamu.edu
gsmay at bcm.tmc.edu

The FAQ will be posted once a month to BIONET.MYCOLOGY, as close to
the beginning of the month as possible. 
The FAQ is organized as follows:

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



I.  WHAT IS BIONET.MYCOLOGY
-------------------------------

bionet.mycology is an internet newsgroup aimed at the discussion and 
information exchange of any relevant mycologyical topic. The newsgroupis in 
the bionet sector and is accessible to subscription via electronicmail 
and/or directly from newsservers carrying the bionet newsgroups.

The newsgroup, bionet.mycology, is intended as a forum for scientific 
discussions and questions regarding all aspects of the mycological sciences.  
Topics to be discussed include such diverse aspects of fungal biologyt as 
genetics, molecular biology, evolution, biochemistry, host-parasite 
relationships, pathology, physiology, biotechnology, pathogenesis, taxonomy, 
and the teaching of mycology.

The newsgroup also provides a forum for announcing meetings, funding 
sources, job opportunities, and pointers to other information sources such 
as the fungal genetics stock center world wide web page.  In addition, the 
newsgroup encourages posting of abstracts for papers that have been accepted 
for publication in peer reviewed journals.


II.  HOW TO ACCESS BIONET.MYCOLOGY
--------------------------------------

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.mycology by NNTP servers carrying 
bionet newsgroups. If your NNTP server does not have bionet.mycology, 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.mycology can send an e-mail to:

        biosci-server at net.bio.net 

with the following text in the body of the message:

        subscribe mycology

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.mycology

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.mycology 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/MYCOLOGY 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 MYCOLOGY directory. Please 
see the BIOSCI/bionet faq for details (see above).


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

Any message or post concerning mycology, or any
aspect of interest to the mycology 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:

       mycology 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:

       mycology at daresbury.ac.uk

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

1) Newsgroups

A number of other newsgroups exist in the bionet.* sector which may be of 
general interest to mycologists.

These newsgroups are:

bionet.prof-society.ascb
bionet.prof-society.faseb
bionet.immunology
bionet.molbio.evolution
bionet.molbio.methds-reagnts
bionet.molbio.yeast
bionet.mcrobiology
bionet.protista
bionet.software.www

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


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

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/main.html
WWW server at Keck-IBT filamentous fungal databases URL:
                 http://keck.tamu.edu/ibt.html
or             gopher://keck.tamu.edu

Saccharomyces genomic information resource URL:
                 http://genome-www.stanford.edu/

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

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 >=Microbiology (Biosciences)<= is
                 accessible at: 
                 http://golgi.harvard.edu/biopages/micro.html

NCBI       http://www.ncbi.nlm.nih.gov

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.  MISCELLANEOUS
--------------------

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

This FAQ is adapted from a FAQ generated by Martin latterich, University of 
California, Berkeley.  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 MYCOLOGY 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.

------------------------------------------------------------------------
More information is always welcome. Please mail your suggestions,criticism 
and information to one of the following Discussion Leaders for 
bionet.mycology:

tom at bio.tamu.edu
leland at straylight.tamu.edu
gsmay at bcm.tmc.edu

Tom Adams
Texas A&M University

Leland Ellis 
Texas A&M University

Greg May
Baylor College of Medicine

Tom Adams
Department of Biology
Texas A&M University
College Station, TX  77843
409-845-1468
Tom at bio.tamu.edu



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