Worm Breeder's Gazette 11(4): 6

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.

The Worm Community System

Bruce Schatz, Samuel Ward, Scott Hudson and Larry Peterson

The Worm Community System project is building an interactive 
computer environment that will enable biologists to easily access 
knowledge about C.  elegans and to record their observations about 
this knowledge.  The goal is to make the personal computer in the 
laboratory of every worm biologist a portal into an information space 
of 'all' the information about the worm and 'all' the annotations on 
this information.  You will be able to rapidly browse the information, 
run analysis programs on selected units, group selected units into new 
information, and share these groupings with the worm community.  This 
project is underway in the Computer and Biological Systems Laboratory 
at the University of Arizona at Tucson, whose mission is to bring 
computer science research to bear on problems of biological science by 
building computer systems which interactively manipulate knowledge 
about biological systems.  The project is funded by a major grant from 
the National Science Foundation sponsored by both the Computer and 
Biological Science Directorates.  There are close collaborations with 
the mapping and sequencing projects at MRC-LMB and Washington 
University and with the CGC.  The worm information space will comprise 
as much of the knowledge of the worm community as is possible to 
capture in electronic form.  Eventually, the data types will include 
text, graphics, and image, spanning the following sources.  
Experimental data will include genomic data (gene list, genetic map, 
physical map, DNA sequences) and anatomical data (cell list, cell 
lineage, wiring diagram).  Literature information will include the 
bibliography, abstracts from Medline, scanned full-text and page 
images, this Gazette, Worm Meeting proceedings, and the Worm Book.  
Informal information will include lab directories, strain lists, and 
protocols, and may include images of micrographs and gels.  Much of 
the informal material, the annotations, and the connections between 
units of information will hopefully be entered by you as members of 
the worm community.  The worm information space will be accessible via 
any personal computer running an X-windows server which is connected 
across the national NSFNET network to machines containing the data and 
the software.  Associative keyword search will be supported, as will 
connection links to related information such as genes referred to in 
literature or map regions containing genes.  Groups of information 
will be selectable to be passed into external programs for analysis or 
transformed into other information units for later access.  The system 
is thus meant to serve a wide variety of the communication needs of 
the worm community, both retrieval and analysis, as well as rapid 
sharing of knowledge with others.  An early prototype of the system is 
running at Arizona.  It contains genomic data and literature abstracts,
and it supports rapid browsing and sharing of information stored 
locally.  It will be placed into the labs of initial users by the end 
of this year.  This version requires a local Unix  workstation to run 
the software, although the display can be run on an Apple Macintosh  
running an X-windows terminal emulator.  Subsequent versions will 
relax this requirement.  The distribution is currently being limited 
to computer sophisticates who are willing to invest time in using and 
improving an incomplete system.  This will permit rapid evolution of 
the system into a form suitable for use by the entire worm community.  
People with interest in serving as initial users are encouraged to 
contact Bruce Schatz via the Internet as 'schatz@cs.arizona.edu'.  
Also requested from anyone are pointers to data already available in 
electronic form and comments on useful software functionality and data 
sources.  Carrying out this project to provide electronic support to 
continue the special cooperation within the worm community will only 
be possible with the active help and support of all of you.