CELEGANS/bionet.celegans Frequently Asked Questions (FAQ)
(last revised by William Morgan (wmorgan at acs.wooster.edu) on 17 November 1994)
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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]. A Hypertext version of the FAQ is also available on
the Newsgroup page of Leon Avery's WWW server; the URL is
"http://eatworms.swmed.edu/" (see below for additional information on this
WWW site).
The FAQ is posted the 15th of each month to the CELEGANS/bionet.celegans
newsgroup.
If you would like to add other questions to this list, please send them to
wmorgan at acs.wooster.edu. I would also appreciate your sending the *answer*
to the question if possible. All contributions will be gratefully
acknowledged by including the author's name along with the answer provided.
CONTENTS:
1. Where can I find a list of recent research articles on C. elegans?
2. What ever happened to the Worm Community System (WCS)?
3. Where can I get help with the Worm Community System (WCS)?
4. How can I get the latest version of ACEDB?
5. Are there any Gopher or World Wide Web (WWW) sites of particular
interest to C. elegans researchers?
6. Where can I find more information about the BIOSCI/bionet newsgroups?
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1. Where can I find a list of recent research articles on C. elegans?
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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.
Expanding on this, Leon Avery <leon at eatworms.swmed.edu> writes...
I've set up an entry on my WWW server that mirrors Bob Herman's "Additions
to CGC Bibliography Since Last WBG Listing". It is identical information;
in fact it works by contacting the CGC gopher server and fetching the file.
But it has a little advantage over the gopher interface in that, if the
abstract of any article is available, you can click on the title to see it.
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2. What ever happened to the Worm Community System (WCS)?
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Laura Shoman <shoman at csl.ncsa.uiuc.edu> writes...
Community Systems Laboratory at the University of Illinois,
Urbana-Champaign, is pleased to announce the availability of the Worm
Community System, Release 2.0. The biological data has been updated to
ACeDB 2.14. The documents include Worm Breeder's Gazette, to vol. 13,
issue 3 (issue 4 is on the way), and much of the CGC bibliography.
Beta version users should pick up the new front end, since it includes new
functionality, performance enhancements, and bug fixes.
The system overview, including contents, system requirements, and retrieval
information are outlined below.
Many thanks to our users for their patience, continued feedback and
support. Thanks to Jean Thierry-Mieg and Richard Durbin for the genome
data from ACeDB and to Theresa Stiernagle and Bob Herman who provide stock
data and edit the Worm Breeder's Gazette (WBG) which CSL then digitally
encodes.
*********************************************************
Where to get WCS Software and Documentation
The front-end needed to run WCS is available via anonymous ftp from
csl.ncsa.uiuc.edu (141.142.221.11). The users' manual is also available via
anonymous ftp from csl.ncsa.uiuc.edu. Formats include Postscript, and plain
ASCII Text. A limited number of printed copies of the manual are
available, upon request.
Please review the Systems Requirements below.
Announcements of WCS data and feature updates will be announced on the
usenet group, bionet.celegans, and on the celegans listserve.
*********************************************************
System Overview
The Worm Community System (WCS) is a digital library that contains
information about Caenorhabditis elegans and a software environment that
enables you to interact with this community library across the
international computer network, the Internet. The functions of the software
environment enable you to (1) search and browse the existing knowledge of
the community and (2) add your own data and literature to the library, for
your own private use, collaboration with colleagues at local or remote
sites, or for wider distribution to the community. The purpose of the
system is to support the display and recording of patterns in the
information space, where the patterns are formed by links between objects
and represent important relationships. The capacity for dynamically
updating the information, both from central archives and from local labs,
should help to better propagate the knowledge across the community.
WCS Contents
The information in the worm community library attempts to span the range of
all that you might find useful, including formal and informal literature
and data. The literature includes abstracts from most of the CGC
bibliography, full text of all articles from the complete Worm Breeder's
Gazette (WBG), and citations from the most recent worm meetings. The data
include genomic data from the MRC/WUSTL mapping and sequencing project
(genes, maps, sequences), community data from the Minnesota stock center
(strains, people), and the beginnings of cellular data (cells, lineage).
As a tool, WCS complements ACeDB. WCSr2 contains version 2.14 data from
ACeDB. Although WCS and ACEDB are both hypermedia-based biological
databases, they differ in a number of ways. WCS is a community system. To
that end, it allows interactive creation and editing of new objects by end
users within the system. It also supports editorial and privacy controls,
allowing users to restrict access to data and to determine how reliable a
particular piece of data is. Finally, while ACEDB distributes its database
with the software, WCS has a client-server architecture with a central
database. This allows all users immediate access to new data, instead of
relying on periodic updates of the database.
What's New in r2.0?
* As mentioned above, the system architecture in this release is different
from that in WCSr1. Release 2 has a client-server architecture with a
central database. This allows for instantaneous updates from both the
central site (CSL), and the remote labs connected to the system.
* There is no gateway to the ACeDB database from the WCSr2 interface.
* You can enter new information of any known type as documents or forms.
* You can restrict access to data you enter to control its propagation to
the community.
* Two types of search windows are available: a quick and dirty Simple
Window, and the Full Search Window that allows several different methods of
searching. You can search all the data, or restrict searching to particular
data types and/or fields. You can also create complex searches using
Boolean operators (AND/OR).
* You can browse different data types, selecting a specific name within a
type to gain direct access to related information.
* You can revise your personal information.
System Requirements
* Network Connections
You will need to have an Internet connection from a Sun workstation (the
local client) in order to access the CSL server. (The data, search engines,
thesaurus server, etc., reside on the Community Systems Laboratory (CSL)
server at UIUC.) If you choose to run a node off the local Sun
workstation, you will need an Ethernet connection between the workstation
and the node.
* Local Client
We suggest the following machines for local clients: SparcStation 5 (a
fast, good machine), SparcStation LX (older, slower, but less expensive),
SparcStation 10 or 20. The system can also be run on slower, less expensive
machines such as the SparcStation 2, 1+, and IPX. The Sun station should
run at least 32 megabytes of RAM (more is better, 64 or more is optimal).
These workstations should run version 4.1.x of Sun's operating system or
Solaris 2.3 or later. We have not tested WCS r2 on earlier version of
Solaris. You must have the SunOS 4.*.* binary compatibility package
installed to use WCSr2 with Solaris.
* X-Windows Environment
The local software (front end) requires an X-windows environment and, in
addition to that environment, will take approximately 10 megabytes on a
hard drive. This disk space requirement may increase over releases, but no
dramatic increase is anticipated. On Sun workstations, we use both X11R5
and OpenWindows (the Sun product) with good results. We run MacX on our
Macintosh nodes. The previous release ran fine on a PC-clone using the NCD
X- windows package.
* Nodes from your Local Client
If you run a Macintosh node, your Mac should have a minimum of 8 megs of
RAM (more is better). The Mac should also be in the 68040 processor family
(faster is better). Higher-end 68030 Macs will run MacX acceptably IF no
other applications are running.
If you run a DOS-based node, your node should have a minimum of 8 megs of
RAM (more is better). The processor should be a 486/66 (faster is better).
The node monitor should have a resolution of 1024 x 768 pixels. Apple's 16"
monitor has a resolution of 800 x 600 pixels and has been called tolerable
by some of our users here. One site is using an NEC MultiSync 5FGe Monitor
on a Mac Quadra 650. NEC has control panel software ("DPI on the fly") that
allows for changing the resolution of the monitor on the fly while the
machine is running (no rebooting): thus, one can change easily between
1024x768 for WCS, and return to 832x624 or 640x480 for word processing.
* Input Devices
The interface requires a keyboard and a mouse (or trackball) input device.
* Output Devices
Printing can be done from a Sun workstation transparently; Printing from a
Macintosh is done through MacX.
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3. Where can I get help with the Worm Community System (WCS)?
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Laura Shoman, User Support Coordinator, Worm Community System, Community
Systems Laboratory, Graduate School of Library & Info Science, University
of Illinois at Urbana-Champaign (shoman at csl.ncsa.uiuc.edu ) writes:
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, please give me a call or drop me e-mail.
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4. How can I get the latest version of ACEDB?
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>From the announcement of the latest ACEDB release by Richard Durbin
<rd at mrc-lmb.cam.ac.uk>:
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/ace2
cele.mrc-lmb.cam.ac.uk (131.11.84.1) in England, in pub/acedb/ace2
lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb/ace2
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/ace2
binary
mget *
get README y/n answer yes etc
..
..
quit
If installing for the first time
--------------------------------
Get all the update tar.Z and read the files README and NOTES before
proceeding further.
If updating an existing system
------------------------------
Just get the last update.tar.Z file, plus INSTALL.
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".
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.
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5. Are there any Gopher or World Wide Web (WWW) sites of particular
interest to C. elegans researchers?
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The CGC Gopher (elegans.cbs.umn.edu (port 70); see #1 above) includes a
pointer (Other Worm Gophers) to additional Gophers of interest to C.
elegans researchers including eatworms.swmed.edu (port 70) and
weeds.mgh.harvard.edu (port 70), as well as this newsgroup's archives at
net.bio.net.
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/". 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
eatworms.swmed.edu 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..." function of your WWW browser. (In
Mosaic 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.
(a) 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.
(b) 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.
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6. Where can I find more information about the BIOSCI/bionet newsgroups?
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Newsgroup users are encouraged to read the BIOSCI Information Sheet for
your region 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.
Posted by:
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
