CELEGANS/bionet.celegans
Frequently Asked Questions (FAQ)

(last revised by William Morgan (wmorgan@acs.wooster.edu) on 20 July 1998)

An HTML version of this FAQ is available at the following address: http://elegans.swmed .edu/Newsgroup/celegans.faq.html.
Belorussian translation provided by fatcow.

This document supplements the CELEGANS/bionet.celegans Charter (available at http://net.bio.net/bi oarchives/CELEGANS/CHARTER )
and answers some common questions of interest to C. elegans researchers.

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@acs.wooster.edu. All contributions will be gratefully acknowledged by including the author's name along with the answer provided.

CONTENTS:

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

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

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

Where can I get hold of some worms?

Where can I find methods for growing C. elegans, preparing DNA, etc?

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

How can I get the latest version of ACEDB?

Where I can find old messages posted to the bionet.celegans newsgroup?

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


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

    Leon Avery (leon@eatworms.swmed.edu) has set up a WWW server which C. elegans researchers will find particularly useful. The URL is "http://elegans.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 elegans.swmed.edu. The URL is "http://elegans.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@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 elegans, 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.


    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... about once a month. "Additions to CGC Bibliography Since Last WBG Listing"... 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.

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


    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).


    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@molbio.cbs.umn.edu


    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 :


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

    In July 1996, Curt Jamison (cjamison@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 planning to attempt a resurrection (I doubt it), but I can't in good concious recomend anyone even attempt to use it since the data hasn't been updated for over 18 months.

    The major portions of WCS which people were using were the on- line WBG articles and simplified ACeDB searches. The functionality of these two components have been reproduced elsewhere, namely in Leon Avery's webpage and in the WWWace servers at USDA/NAL (the URLs are http://elegans.swmed.edu/ and http://probe.nalusda.gov/ respectively).


    How can I get the latest version of ACEDB?

    According to Richard Durbin <rd@sanger.ac.uk> on 16 Feb 1998:

    New ACEDB data release WG4 and WS4 for C. elegans

    =================================================

    *** A Macace version is available for WG4 (without sequences only just now) ***

     

    With this release we are again starting a new series of database updates from scratch, rather than adding on to WS3. The new series is called WS4 (and correspondingly WG4 for the version without sequences).

    Because both series are new, you must get all the updates from the series you want (WS4 or WG4), and rebuild a new database using them.

    If you have a working acedb version built with the WS3 or a previous series, you must remove your current database/ directory (ideally after backing it up in case of difficulties). As well as removing the database directory, you can also remove any update.WS3...tar.Z or rawdata/update.WS3... files.

    If you do not remove the contents of the database directory, when you start up acedb it will still say "WS3" in the title bar, and will not be able to load the WS4 updates. When you have emptied it properly, it will ask if you want to reinitialise, and put WS4 in title bar.

    You should be using these updates in conjunction with release 4_5 of the acedb software (released in August 1997).

    Reminder: there are now two versions of the C.elegans database. The WS4 update series contains everything, whereas the WG4 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources.

    (N.B. at the end of this file is a list of the contents of each update file).

    The additions since the last release are :

    for both types of update

    - a physical map update with a lot of changes (mid Jan) all but one chromosome is now a single contig

    - accumulated genetic data corrections, inclusion of phenotypes

    from C. elegans II

    - from CGC : bibliography, wbg subscribers and strains

    - from Leon Avery : wbg15.1 contents and abstracts

    - Expression patterns from Julie Ahringer and Ian Hope, many more pictures form Ian Hope

    and for just the complete database including sequences (WS4)

    Data fom St Louis and Sanger Sequence databases taken in mid-December:

    - there are now 2520 (2237 before) cosmids totalling 75458714 (66969575

    before) bases.

    - there are also many new ESTs from Yuji Kohara.

    The total database directory sizes after adding these updates are

    around 870MB for the WS4 database and around 75MB for the WG4. database.

     

    Macace

    ======

    We have made a macace version of WG4, the database without sequence data. This can be obtained as a self-extracting archive from subdirectory macace on the ftp site, file name macace.WG4.sea.bin. We will try to build a macace.WS4, but this will need to be distributed in multiple self-extracting archive files, with instructions on how to put the resulting files back together. This will be the subject of a future message.

     

    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 (130.14.20.1) in the USA, in repository/acedb

    ftp.sanger.ac.uk (193.60.84.11) in England, in pub/acedb

    lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb

    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 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.* # get all WS1 update files

    quit

    --------------------------------

    Get any update files that you do not have already and read the file 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"), click "Yes" to accept initialising the database if starting from scratch, then 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.

    ******************************************************************

    Comments about the data should be sent to the data curator, Sylvia Martinelli (sylvia@sanger.ac.uk).

    Comments about the installation procedure, should be sent to Richard Durbin (rd@sanger.ac.uk)

    ********************************************************************

    According to Steve Jones <sjj@sanger.ac.uk> on 18 Jun 1998:

    The latest ACEDB data release is now available on-line.

    This can be accessed through webace

    see:- http:// www.sanger.ac.uk/Projects/C_elegans/webace_front_end.shtml

    You can also access the database using an graphical ACEDB client which connects to our server.

    see:- http:// www.sanger.ac.uk/Projects/C_elegans/xaceclient_howto.shtml


    Where I can find old messages posted to the bionet.celegans newsgroup?

    All messages posted to the bionet.celegans newsgroup are archived and may be reviewed at http://www.bio.net:80/hyper mail/CELEGANS. At this site, you can search the archives for a keyword or phrase, or you can directly access the archives (which are separated into monthly folders at the bottom of that Web page). You can also post a message to the newsgroup at this site.


    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 at http://www.bio.net/BIOSCI/docs.html 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@net.bio.net. To receive the BIOSCI FAQ by e-mail, send the message "info faq" to biosci-server@net.bio.net.

****************************** end of FAQ *******************************


Last Updated: July 20, 1998

William Morgan, wmorgan@acs.wooster.edu