CELEGANS/bionet.celegans Frequently Asked Questions (FAQ)
William Morgan
wmorgan at ACS.WOOSTER.EDU
Sun Jul 14 14:09:45 EST 1996
CELEGANS/bionet.celegans
Frequently Asked Questions (FAQ)
(last revised by William Morgan (wmorgan at acs.wooster.edu) on 14 July =
1996)
An HTML version of this FAQ is available at the following address:
http://eatworms.swmed.edu/celegans.faq.html
This document supplements the CELEGANS/bionet.celegans Charter (avail=
able at
http://net.bio.net/bioarchives/CELEGANS/CHARTER )
and answers some common questions of interest to C. elegans researche=
rs.
The FAQ is posted at (ir)regular intervals to the CELEGANS/bionet.cel=
egans
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 contrib=
utions
will be gratefully acknowledged by including the author's name along =
with
the answer provided.
CONTENTS:
1. Are there any 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. elegan=
s?
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. How can I get the latest version of ACEDB?
8. Where I can find old messages posted to the bionet.celegans news=
group?
9. Where can I find more information about the BIOSCI/bionet newsgr=
oups?
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1. Are there any 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 whi=
ch C.
elegans researchers will find particularly useful. The URL is
"http://eatworms.swmed.edu/". Many Internet servers either speci=
fically
about C. elegans, or of particular interest to C. elegans resear=
chers
can be found in the "Information from C elegans labs" and "Genom=
e 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 w=
ould be
very grateful if C elegans researchers (and anyone else) would:
1. Use it. Use the "Open URL..." or "Open Location..." functio=
n 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 t=
o
bionet.celegans will automatically be included. In add=
ition,
I will accept announcements by e-mail. You can write t=
hese in
plain text or, if you want to take advantage of WWW hy=
pertext
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 serv=
er
tree, and technical help to any C elegans lab that wan=
ts.
Preparing documents for the WWW is easy and fun (for c=
omputer
geeks, anyway), you can do it on any kind of computer,=
and no
special software is necessary.
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2. Where can I find a list of recent research articles on C. elegan=
s?
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 fil=
e that
it doesn't need to be searched. It also omits abstracts, which m=
any 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 Caenorh=
abditis
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 Caenorhabdit=
is
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 continu=
ing
research on this nematode. The CGC's collection of more than 230=
0
strains includes one allele of each mapped gene, all available
chromosome rearrangements, and selected multiply mutant stocks f=
or
genetic mapping. Requests for strains should include a brief sta=
tement
of the research or training activity for which the stocks are in=
tended.
Recipients are asked to acknowledge the CGC, which is supported =
by
NIH's National Center for Research Resources, in publications re=
sulting
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, note Leon =
Avery
and Norio Suzuki :
o First, the Cold Spring Harbor book The Nematode Caenorhabdi=
tis
elegans, edited by WB Wood et al, has a brief Methods appen=
dix by
John Sulston and Jonathan Hodgkin. This is a useful place t=
o
start, but you will probably need more detail.
______________________________________________________=
_____
The Nematode Caenorhabditis elegans
Monograph 17
Edited by William B. Wood
This "Book of the Worm" serves as a reference source f=
or
C. elegans investigators as well as an introductory
monograph for other biologists.
1988, Cold Spring Harbor Press, 667 pp.
ISBN 0-87969-433-5
Paper $45
There are four ways to order books:
+ Send electronic mail to cshpress at cshl.org.
+ Phone 1-800-843-4388 (United States and Canada) o=
r
516-349-1930 (other locations) to place an order.
+ Fax an order form to 516-349-1946.
+ Order Online! (Forms-capable clients only) at
http://www.cshl.org/books/c_elegans.html
______________________________________________________=
____
o Second, there is the Comprehensive Protocol Collection, mai=
ntained
by the Ambros Lab. This is probably the best source of deta=
iled
protocols.
o Finally, there is the recently published Caenorhabditis
elegans:Modern Biological Analysis of an Organism, edited b=
y HF
Epstein and DC Shakes, from Academic Press. This is probabl=
y the
best source for explanations of the reasons behind the meth=
ods.
______________________________________________________=
____
Methods in Cell Biology (Vol 48)
Subtitle: Caenorhabditis elegans:Modern Biological
Analysis of an Organism,
Edited by Henry F. Epstein, and Diane C.Shakes
Description: The first of its kind, this laboratory
handbook emphasizes diverse methods and technologies
needed to investigate C. elegans, both as an integrate=
d
organism and as a model system for research inquiries =
in
cell, devlopmental, and molecular biology, as well as =
in
genetics and pharmacology. Four primary sections -
Genetics and Culture Methods, Neurobiology, Cell and
Molecular Biology, and Genomics and Informatics - cros=
s
disciplines in this Volume's integrated approach to C.
elegans. Illustrated with more than 100 tables and
figures.
1995, Academic Press, Pages: 619
Comb bound: ISBN: 0122405455
UK Price: =3D=A3 44.00
US Price: $59.95
Case bound: ISBN: 0125641494
UK Price: =3D=A3 81.00
US Price: $110.00
There are four ways to order books:
+ Send electronic mail to ap at acad.com (U.S.) or
cservice at hbuk.co.uk (U.K.)
+ Phone 1-800-321-5068 (U.S. and Canada) or 0181 30=
0
3322 (U.K.)
+ Fax an order form to 1-800-336-7377 (U.S. and
Canada) or 0181 309 0807 (U.K.)
+ Order Online! (Forms-capable clients only) at
http://www.hbuk.co.uk/ap/apwelcom.htm
______________________________________________________=
____
[Thanks to Thomas B=8Drglin for supplying the detailed info=
rmation
on both books.]
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6. What ever happened to the Worm Community System (WCS)?
In July 1996, Curt Jamison (cjamison at gig.usda.gov) University of
Maryland, Genome Informatics Group, wrote me:
At this point, I believe that WCS is a dead system. Bruce and I =
pulled
the plug on it about a year ago. I don't know if Bruce is planni=
ng to
attempt a resurrection (I doubt it), but I can't in good conciou=
s
recomend anyone even attempt to use it since the data hasn't bee=
n
updated for over 18 months.
The major portions of WCS which people were using were the on- l=
ine WBG
articles and simplified ACeDB searches. The functionality of the=
se two
components have been reproduced elsewhere, namely in Leon Avery'=
s
webpage and in the WWWace servers at USDA/NAL (the URLs are
http://eatworms.swmed.edu/ and http://probe.nalusda.gov/ respect=
ively).
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7. How can I get the latest version of ACEDB?
On 14 May 1996, Richard Durbin (rd at mrc-lmb.cam.ac.uk) sent the
following message:
New ACEDB software and data
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
Acedb version 4_3 is now available in both binary and source for=
m from
our standard ftp distribution sites (see end of this messsage). =
It
replaces version 4_1 as the current official acedb release.
The new version contains a large number of efficiency and consis=
tency
improvements and some interface changes, e.g. a much improved
bibliography display tool. There are also some critical bug fixe=
s. In
particular, it fixes the bug that prevented the most recent C.el=
egans
data updates being loaded on Solaris machines.
Version 4_3 is compatible with databases produced by 4_1. It als=
o
supports named databases with their own named series of update f=
iles
(see below for C.elegans usage of this).
New C.elegans data releases WS1-8 and WG1-3
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
The last series of updates (4-1 to 4-14) became extremely cumber=
some to
load in, and we decided to start again from scratch. We also rea=
lise
that the database is becoming too large for some users with limi=
ted
disk space or memory. There are therefore now two alternative da=
tabase
versions:
WS1: updates WS1.4-1 to WS-8. This contains all information, as =
up
until now. The current genomic sequence total in WS-8 is 35,483,=
730
bases. The current size of this database is 220 Mb. It will cont=
inue to
grow, probably over 500 Mb.
WG1: update WG1.4-1 to WG1.4-3. This does not contain the genomi=
c
sequence and material directly related to that. It will however =
allow
people with limited resources to access genetic and physical map=
s and
the CGC data, and gives a version of the physical map showing th=
e state
of the sequencing, and EMBL/Genbank accession numbers for sequen=
ced
clones and a map. The size of this database is 46 Mb, and it sho=
uld
stay around 50 Mb in the future.
You should make a decision which version you want, and get updat=
e files
only for that version. If you choose to get WG-1, then in place =
of
getting update files you can get a preloaded database, currently=
in the
file database.WG1.4-3.tar.Z.
***************************** IMPORTANT ************************=
******
To correctly install and load the new updates, either WS1 or WG1=
, you
need to get acedb 4_3, and an up to date copy of the INSTALL scr=
ipt.
****************************************************************=
******
Instructions for obtaining updates/the whole thing
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D
All the files are available in the following public access accou=
nts
(anonymous ftp sites) accessible over internet:
ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb
ftp.sanger.ac.uk in England, in pub/acedb
lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/ac=
edb
In each case, log in as user "anonymous" and give a user identif=
ier as
password. Remember to transfer the files in BINARY mode by typin=
g the
word "binary" at the start of your ftp session. Many thanks to N=
CBI for
letting us share in their excellent resource.
Example:
ftp ncbi.nlm.nih.gov
login: anonymous
password: your user id or email address
cd repository/acedb # change to relevant directoy
binary # IMPORTANT
dir # display files in this directory
get README
get NOTES
get INSTALL
cd ace4 # change to ace4 directory
get bin.sunos.4_3.tar.Z # get program
cd ../celegans # change to worm data directory
mget update.WS1.4-*.tar.Z # get all update files
quit
--------------------------------
Get any update files that you do not have already and read the f=
ile
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"). If y=
ou
have installed database.WG1.4-3 then you should be fine now. If
starting from scratch with update files, when you first start up=
you
are asked to confirm initialising the database; click "Yes". The=
n to
load the updates into the database 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 secti=
on
on problems in NOTES, and if that fails to help, let us know.
****************************************************************=
**
Comments about the data should be sent to the data curator, Sylv=
ia
Martinelli (sylvia at sanger.ac.uk).
Comments about the program, or the installation procedure, shoul=
d be
sent to one of us:
Richard Durbin (rd at sanger.ac.uk)
Jean Thierry-Mieg (mieg at kaa.cnrs-mop.fr)
__________________________________________________________
Macintosh versions of the most recent C.elegans acedb release ar=
e now
available as self-extracting archives from the following two loc=
ations:
ftp://ftp.sanger.ac.uk/pub/acedb/macace
ftp://ncbi.nih.gov/repository/acedb/macace
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8. Where I can find old messages posted to the bionet.celegans news=
group?
All messages posted to the bionet.celegans newsgroup are archive=
d and
may be reviewed at http://www.bio.net:80/hypermail/CELEGANS. At =
this
site, you can search the archives for a keyword or phrase, or yo=
u can
directly access the archives (which are separated into monthly f=
olders
at the bottom of that Web page). You can also post a message to =
the
newsgroup at this site.
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9. Where can I find more information about the BIOSCI/bionet newsgr=
oups?
Newsgroup users are encouraged to read the BIOSCI Information Sh=
eet 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 at
http://www.bio.net/BIOSCI/docs.html and by e-mail. To receive th=
e
BIOSCI Information Sheet by e-mail, send the message "info ukinf=
o" (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 r=
eceive
the BIOSCI FAQ by e-mail, send the message "info faq" to
biosci-server at net.bio.net.
****************************** end of FAQ ***************************=
****
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Last Updated:Wednesday, July 14, 1996; 3:00 pm ET;
William Morgan, wmorgan at acs.wooster.edu
More information about the Celegans
mailing list