From owner-celegans@net.bio.net Sat Jul 13 23:00:00 1996 Path: biosci!ACS.WOOSTER.EDU!wmorgan From: wmorgan@ACS.WOOSTER.EDU (William Morgan) Newsgroups: bionet.celegans Subject: CELEGANS/bionet.celegans Frequently Asked Questions (FAQ) Date: 14 Jul 1996 12:09:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 513 Sender: daemon@net.bio.net Distribution: world Message-ID: <31E9541A.2AC6@acs.wooster.edu> NNTP-Posting-Host: net.bio.net CELEGANS/bionet.celegans Frequently Asked Questions (FAQ) (last revised by William Morgan (wmorgan@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@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@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@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@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@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@acad.com (U.S.) or cservice@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@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@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@sanger.ac.uk). Comments about the program, or the installation procedure, shoul= d be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@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 ----------------------------------------------------------------= ------- 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@net.bio.net. To r= eceive the BIOSCI FAQ by e-mail, send the message "info faq" to biosci-server@net.bio.net. ****************************** end of FAQ ***************************= **** ---------------------------------------------------------------------= ------- Last Updated:Wednesday, July 14, 1996; 3:00 pm ET; William Morgan, wmorgan@acs.wooster.edu .