Worm Breeder's Gazette 12(2): 12 (January 1, 1992)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

Availability of WCS (Worm Community System), Release 1

Bruce Schatz, Terry Friedman, Ed Grossman, Kevin Powell, Andrey Yeatts, Larry Peterson, Scott Hudson, Samuel Ward

Community Systems Laboratory, University of Arizona, Tucson AZ 85721

Release 1 of WCS is now running in more than 10 worm labs. The goal of this system is to make "all" knowledge about C. elegans, both formal and informal, easily available to you in your labs. The intention of this release is to indicate possible functionality and to learn some of the major problems in providing a complete system useful to the community. While this "consciousness-raising" is on-going, we are actively designing Release 2. Starting next summer, our plan is to release and evolve a system of increasing functionality. We also plan to expand our project to provide active user support. Please send us your comments (to wcs@csl.biosci.arizona.edu) so that the system can become more useful to the community. Many thanks go to the people who have already used the early release and provided good feedback.

WCS supports browsing multiple interconnected sources and adding new data. All data distribution is done automatically and electronically, both for the system-added archival sources, such as the WBG, and the user-added informal sources, such as annotations. The current sources include: the complete WBG, the CGC bibliography with abstracts where available (currently about half), abstracts from the last Worm Meeting, the gene list, the physical map, Genbank C. elegans sequences, CGC strains, WBG subscribers, and sample informal data. Thanks to Mark Edgley for help of many sorts.

acedb (Durbin & Thierry-Mieg, WBG v12 , n1 , p13 )is distributed with WCS and runs side-by-side with it. The programs communicate, so that the acedb genetic map can be called from within WCS and a WCS annotation can be made from within acedb.

Our plans for release 2 of WCS are to completely rewrite the current system, improving many inadequacies. Features being considered include: user entry of many types of data, e.g. gene descriptions, with appropriate editorial control; increased literature coverage with faster and more powerful search; portability across many common computer platforms; and a distributed architecture, with a separate front end and back end permitting multiple access. We are also investigating displays for additional worm data, e.g. the cell lineage, the cell anatomy, and the wiring diagram. In this regard, we are actively seeking a biologist to come work with us (see ad elsewhere in this issue).

The current release runs on Sun workstations, although the display can be run on any X-windows terminal. A full setup, such as at Arizona, has a Macintosh in the worm lab running MacX connected via a building Ethernet to a central Sun file server running WCS. Note this requires an Ethernet card for the Mac, and preferably, a 2 page monitor. Most of the current sites have bought Sun workstations to run this software. One typical configuration is a SPARCstation-2 which for about $9000 university price comes with a monochrome monitor, 32 MB RAM, and 400 MB disk. Many sites have added an external 1 GB disk and additional 32 MB RAM for a $13K total cost.

For instructions to obtain WCS, use ftp from a machine connected to the Internet:

$ ftp csl.biosci.arizona.edu (ftp

Name: anonymous

Password: your-login@your-machine

ftp> cd wcs

ftp> get README.FTP

ftp> quit

You can also run WCS remotely across Internet from your workstation running X-windows to our server by telnet csl.biosci.arizona.edu login:wcs password:nematode. Be warned that the response time using the NSFNET is slow at present.

We look forward to receiving your gripes and annotations!