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CELEGANS/bionet.celegans Frequently Asked Questions (FAQ)

William R. Morgan wmorgan at ACS.WOOSTER.EDU
Wed Jul 12 11:48:38 EST 1995

I sent this out July 1, but it may have gotten lost due to computer
difficulties at BIOSCI/bionet.  My apologies if you received this twice. 

Frequently Asked Questions (FAQ) 

(last revised by William Morgan (wmorgan at acs.wooster.edu) on 1 July 1995)

This document supplements the CELEGANS/bionet.celegans Charter and answers
some common questions of interest to C. elegans researchers. Both documents
are available for anonymous FTP and gopher retrieval (port 70) from
net.bio.net []. 

The FAQ is posted at (ir)regular intervals to the CELEGANS/bionet.celegans

IF YOU WOULD LIKE TO ADD OTHER QUESTIONS (preferably with an answer) OR
MAKE REVISIONS, please e-mail them to wmorgan at acs.wooster.edu.  All
contributions will be gratefully acknowledged by including the author's
name along with the answer provided.


1. Are there any Gopher or World Wide Web (WWW) sites of particular
interest to  
   C. elegans researchers? 

2. Where can I find a list of recent research articles on C. elegans? 

3. Where can I find a list of C. elegans researchers?

4. What ever happened to the Worm Community System (WCS)? 

5. Where can I get help with the Worm Community System (WCS)? 

6. How can I get the latest version of ACEDB? 

7. Where can I find more information about the BIOSCI/bionet newsgroups? 

1. Are there any Gopher or World Wide Web (WWW) sites of particular
interest to C. elegans researchers? 

Leon Avery (leon at eatworms.swmed.edu) has set up a WWW server which C.
elegans researchers will find particularly useful.  The URL is
"http://eatworms.swmed.edu/".  Many Internet servers either specifically about
C. elegans, or of particular interest to C. elegans researchers can be found
in the "Information from C elegans labs" and "Genome data" pages of the
eatworms.swmed.edu server.  

He writes:

I have set up a Caenorhabditis elegans WWW server on
eatworms.swmed.edu.  The URL is "http://eatworms.swmed.edu/".  I would
be very grateful if C elegans researchers (and anyone else) would:

(1) Use it.  Use the "Open URL..." function of your WWW browser.  (In
Mosaic it's in the File menu.)  Once you're there, you can add it to your

(2) Criticize it.  (Use the comments form, or e-mail to
leon at eatworms.swmed.edu.)

(3) Contribute to it.

(a) There is an Announcements page.  Announcements posted to
bionet.celegans will automatically be included.  In addition, I will accept
announcements by e-mail.  You can write these in plain text or, if you want
to take advantage of WWW hypertext capabilities, in HTML.  If I'm feeling
real industrious, I may even type in announcements from the WBG.

(b) I'll give a login on eatworms, a directory in the server tree, and
technical help to any C elegans lab that wants.  Preparing documents for
the WWW is easy and fun (for computer geeks, anyway), you can do it on any
kind of computer, and no special software is necessary.

For Gopher users, the CGC has a Gopher site at elegans.cbs.umn.edu (port
70); that includes apointer (Other Worm Gophers) to additional Gophers of
interest to C.elegans researchers including eatworms.swmed.edu (port 70)
and weeds.mgh.harvard.edu (port 70), as well as this newsgroup's archives
at net.bio.net.  

2. Where can I find a list of recent research articles on C. elegans? 

The Caenorhabditis Genetics Center (CGC) maintains a complete bibliography
of C. elegans research articles, which is available by Gopher at
elegans.cbs.umn.edu (port 70).   

According to Bob Herman, the CGC director,.

we update the CGC bibliography on our gopher about once a month.  A few
months back we started a new entry, called "Additions to CGC Bibliography
Since Last WBG Listing".  This is a small enough file that it doesn't need
to be searched.  It also omits abstracts, which many of the references in
the cumulative bibliography contain.  

You can also do more powerful searches of the CGC Bibliography, the Worm
Breeder's Gazette, and other literature at Leon Avery's Caenorhabditis
elegans WWW server (see #1, above).

3. Where can I find a list of C. elegans researchers?

The best place to look is the Worm Breeder's Gazette Subscriber Directory,
which is available on line from Leon Avery's Caenorhabditis elegans WWW
server and the CGC Gopher (see #1, above).

4. What ever happened to the Worm Community System (WCS)? 

In July 1994, Curt Jamison, Community Systems Laboratory, University of
Illinois, Urbana-Champaign (jamison at csl.ncsa.uiuc.edu) wrote:

WCS is alive and well and living at NCSA, U of I. We have released a new
version, WCSr2 which contains all the functionality of the original, as 
well as some new functions. We are in the midst of fully updating all
the data and should be done by mid-August (We are using version 1.10
data from ACeDB right now. The final version of WCSr2 will contain
version 2.10 data).

WCS still provides access to literature, including abstracts from most
the CGC bibliography, full text from the gazette, and meeting abstracts.
The data includes genomic data from the MRC/WUSTL sequencing project, 
community data from the CGC about people and strains, and the beginnings
of a cellular database including cell lineage. New tools include a
thesaurus to aid in searching, and the ability to generate new links and 
add new data (with any level of security protection) which should aid
long-distance collaborations.

The new release of WCS requires an Internet connection from a Sun
workstation to access the the CSL server. This is because all the data,
search engines, thesaurus, etc reside here at UIUC (saving you lots
of storage at a minor speed cost). We suggest using a SparcStation 5,
SparcStation LX, SparcStation 10 or 20 (in that order). Much slower, but
still possible are SparcStation 2, 1+, or IPX. Whichever machine, you
need at least 32 Mb RAM and SunOS 4.1.x or Solaris 2.3 with the SunOS
4.*.* binary compatability package.

The local (front-end) software requires am X-windows environment and
about six Mb hard drive space (at present). We use both X11R5 and
OpenWindows with much success.

You can run a Macintosh node from the local Sun workstation, providing
you have an Ethernet connection between the workstation and the node.
Your Mac should have a minimum of 8 Mb RAM and should be in the 68040
family in order to run an X emulator. We use MacX for our Mac nodes.
Also, the monitor should have 1024x768 resolution, although the Apple
16" monitor (800x600) has been deemed as tolerable.

Where to get it:
The front-end to run WCS is available by anonymous ftp from
csl.ncsa.uiuc.edu ( Installation instructions and 
configuration info is also available there in the README files. The
user's manual is also available, in Word 5.0 for Mac and Postscript
formats, as well as plain ASCII text.

WCS is a constantly evolving system, and we like to have feedback from
the community. If you have questions, requests, or even complaints, we'd
like to hear them. Send us a note at wcs at csl.ncsa.uiuc.edu

5. Where can I get help with the Worm Community System (WCS)? 

Laura Shoman wrote:

WCS has accompanying documentation -- a users' manual, and some README*
files that describe the system and setup, and address some of the problems
that have been reported to date.  These documents are available from the
anonymous  ftp site, csl.ncsa.uiuc.edu.

In addition, I'm the user support person -- the Help Desk, if you will, for
users.  The system in release 2.0 has been installed at a dozen or more
sites around the country.

If you're having problems running WCSr2, or setting it up, or if you'd
like to gripe about it, send e-mail to wcs at csl.ncsa.uiuc.edu.

6. How can I get the latest version of ACEDB? 

>From the May 1995 announcement of the latest ACEDB release by Richard Durbin
<rdurbin at watson.wustl.edu>:

ACEDB data updates 4-1 to 4-6 for C. elegans

There is a new version of the C. elegans ACEDB database.  This uses   
version 4_0 of the ACEDB code (subversion beta4).  There will be a 
separate email message about the code for those using ACEDB for other 
organisms. To build the C. elegans database you will need to get all 
six update files update.4-1.tar.Z to update.4-6.tar.Z.

The total database size is now approximately 160Mbytes.  As well as a 
large amount of new sequence data, this contains all the genetic mapping
data submitted to the CGC in Cambridge up to April 1995, together with
a draft new map, and the abtracts for the 1995 Worm Meeting with links
to Gene, Rearrangement and Sequence objects.  

This release is fully up to date with respect to the physical map, the
CGC information, and gene/genetic map information prior to that
resulting from the recent call for data (which we are working on now).
We have also added over 200 Medline references and a significant
number of missing Gazette pages.  There is also a lot of new genomic
sequence information.

Macintosh version

There will be a new macace self-extracting archive containing this
data.  It can be obtained by anonymous ftp from genome.lbl.gov/pub/macace. 

Instructions for obtaining updates/the whole thing

All the files are available in the following public access accounts
(anonymous ftp sites) accessible over internet:

  ncbi.nlm.nih.gov ( in the USA, in repository/acedb/celegans
and in a few days from
  sanger.ac.uk in England, in pub/acedb/celegans
  lirmm.lirmm.fr ( in France, in directory genome/acedb/celegans

In each case, log in as user "anonymous" and give a user identifier
as password.  Remember to transfer the files in BINARY mode by
typing the word "binary" at the start of your ftp session.  Many
thanks to NCBI for letting us share in their excellent resource.


ftp ncbi.nlm.nih.gov
login: anonymous
password 'your email address'
cd repository/acedb/ace4
mget *
get README  y/n   answer yes   etc



Get all the update.4-n.tar.Z and read the files README and NOTES before
proceeding further.

Always get a copy of the INSTALL script.  Move it and the .tar.Z files
into the home directory in which you are installing ACEDB.  Type
"source INSTALL".  Start acedb (normally by typing "acedb") and choose
"Add Update File" from the menu (right button), and press "All
updates" with the left mouse button.

If you have a problem making the program work, look at the section
on problems in NOTES, and if that fails to help, let us know.

Please send any comments, especially about anything you think is
wrong to one of us:

Richard Durbin (rd at sanger.ac.uk)
Sylvia Martinelli (sylvia at sanger.ac.uk)

7. Where can I find more information about the BIOSCI/bionet newsgroups? 

Newsgroup users are encouraged to read the BIOSCI Information Sheet for
your region and the BIOSCI Frequently Asked Questions (FAQ) list for
further information.  These are available by ftp and Gopher at net.bio.net
and by e-mail.  To receive the BIOSCI Information Sheet by e-mail, send the
message "info ukinfo" (if in Europe, Africa, or Central Asia ) or "info
usinfo" (if in the Americas or the Pacific Rim), to
biosci-server at net.bio.net.  To receive the BIOSCI FAQ by e-mail, send the
message "info faq" to biosci-server at net.bio.net.

****************************** end of FAQ *******************************
William R. Morgan
Assistant Professor
The College of Wooster
Department of Biology                   Phone:  216-263-2026
931 College St.                         FAX:    216-263-2378
Wooster, OH  44691                      E-mail: wmorgan at acs.wooster.edu

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