CELEGANS/bionet.celegans
Frequently Asked Questions (FAQ)
(last revised by William Morgan (wmorgan at acs.wooster.edu) on 1 December
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]. An HTML version is also available at the
following address: http://eatworms.swmed.edu/celegans.faq.html
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. Where can I get hold of some worms?
5. Where can I find methods for growing C elegans, preparing DNA, etc?
6. What ever happened to the Worm Community System (WCS)?
7. Where can I get help with the Worm Community System (WCS)?
8. How can I get the latest version of ACEDB?
9. 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 UT Southwestern Caenorhabditis elegans 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..." or "Open Location..." function of
your WWW browser. (In Mosaic and Netscape 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.
+ 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.
+ 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 a pointer (Other Worm Gophers) to additional
Gophers of interest to C.elegans researchers including
eatworms.swmed.edu (port 70) and weed s.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 the UTSW 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 the UTSW Caenorhabditis
elegans WWW server and the CGC Gopher (see #1, above).
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4. Where can I get hold of some worms?
The Caenorhabditis Genetics Center (CGC) acquires, maintains and
distributes genetic stocks of Caenorhabditis elegans (and a few other
nematode species) for use by investigators initiating or continuing
research on this nematode. The CGC's collection of more than 2300
strains includes one allele of each mapped gene, all available
chromosome rearrangements, and selected multiply mutant stocks for
genetic mapping. Requests for strains should include a brief statement
of the research or training activity for which the stocks are intended.
Recipients are asked to acknowledge the CGC, which is supported by
NIH's National Center for Research Resources, in publications resulting
from use of the strains and to provide the CGC with reprints of those
publications. Inquiries should be addressed to:
Theresa L. Stiernagle, Curator
Caenorhabditis Genetics Center
250 Biological Sciences Center
1445 Gortner Avenue
University of Minnesota
St. Paul, MN 55108-1095
Telephone: 612-625-2265
email: stier at molbio.cbs.umn.edu
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5. Where can I find methods for growing C. elegans, preparing DNA, etc?
There are three main sources of C. elegans protocols. First, the Cold
Spring Harbor book The Nematode Caenorhabditis elegans, edited by WB
Wood et al, has a brief Methods appendix by John Sulston and Jonathan
Hodgkin. This is a useful place to start, but you will probably need
more detail. Second, there is the Comprehensive Protocol Collection,
maintained by the Ambros Lab. This is probably the best source of
detailed protocols. Finally, there is the recently published
Caenorhabditis elegans:Modern Biological Analysis of an Organism,
edited by HF Epstein and DC Shakes, from Academic Press. This is
probably the best source for explanations of the reasons behind the
methods.
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6. 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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7. 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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8. 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:
o ncbi.nlm.nih.gov (130.14.20.1) in the USA, in
repository/acedb/celegans
and in a few days from
o sanger.ac.uk in England, in pub/acedb/celegans
o lirmm.lirmm.fr (193.49.104.10) 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.
Example:
ftp ncbi.nlm.nih.gov
login: anonymous
password 'your email address'
cd repository/acedb/ace4
binary
mget *
get README y/n answer yes etc
..
..
quit
--------------------------------
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)
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9. Where can I find more information about the BIOSCI/bionet newsgroups?
Newsgroup users are encouraged to read the BIOSCI Information Sheet for
your region (the Americas and the Pacific Rim OR Europe, Middle East
and Africa) 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
