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?

     ----------------------------------------------------------------=
-------
  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.
     ----------------------------------------------------------------=
-------
  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).
     ----------------------------------------------------------------=
-------
  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).
     ----------------------------------------------------------------=
-------
  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
     ----------------------------------------------------------------=
-------
  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.]
     ----------------------------------------------------------------=
-------
  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).
     ----------------------------------------------------------------=
-------
  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.
     ----------------------------------------------------------------=
-------
  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 ***************************=
****
---------------------------------------------------------------------=
-------
Last Updated:Wednesday, July 14, 1996; 3:00 pm ET;
William Morgan, wmorgan at acs.wooster.edu




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