bionet.celegans FAQ

William R. Morgan wmorgan at ACS.WOOSTER.EDU
Tue Aug 1 07:18:24 EST 1995


CELEGANS/bionet.celegans
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 [134.172.2.69].

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

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.

CONTENTS:

  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?

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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 hotlist.
(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.
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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).
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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.

Requirements: 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 (141.142.221.11). 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
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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.
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6. How can I get the latest version of ACEDB?



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