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 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 'firstname.lastname@example.org'. 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.