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Human Genome News Archive Edition

Human Genome News, July-August 1995; 7(2):6

ACEDB Version 4.0 Debuts at Annual Meeting

Since its 1991 introduction for the Caenorhabditis elegans community, ACEDB has served as a data-management model for other research projects and has been adopted by a number of diverse organizations and individuals to maintain and distribute data on more than 40 genomes, including human, bovine, Drosophila, yeast, mycobacteria, Arabidopsis, grains, trees, and fungi. At the May 14-29 ACEDB conference and workshop in Geyserville, California, participants represented 10 countries, 4 continents, 38 organizations, 20 databases, and 19 organisms.

John McCarthy [Lawrence Berkeley National Laboratory (LBNL)] organized this year's meeting. Sponsors included DOE, NIH National Center for Human Genome Research, U.S. Department of Agriculture, National Science Foundation, and European Data Resource for Human Genome Research. Conference hardware and software were provided by LBNL, Digital Equipment, Sun Microsystems, Silicon Graphics, Network Computing Devices, Microsoft, and Stanford University.

The main goal of the 3-day conference, attended by about 70 people, was information exchange via tutorials, oral presentations, posters, online demonstrations, and discussions. Some 45 people stayed on for the 10-day workshop, whose goals were code development and consolidation, database building, documentation writing, interest-group discussions, and long-range planning. Investigators agreed to continue their collaborations after the meetings ended. For the first time, WWW was used extensively before, during, and after the conference and workshop to circulate instructions, document drafts, and meeting summaries.

Selected meeting highlights are described below; details are given in a series of WWW pages (see addresses in ACEDB Application Examples). Workshop Documents are available at http://probe.nalusda.gov:8000/ace95/index.html

Meeting Highlights

  • First public release of ACEDB version 4.0. Several curators converted their data models and databases to take advantage of new features, and programmers modified software modules to conform with version 4. During the workshop a number of bugs were identified and eliminated [report bugs to the ACEDB newsgroup [acedb@net.bio.net]. The current release version is 4.1, available via ftp [ftp site no longer available].
  • Software enhancements to run multiple ACEDB clients for different databases, linked together via Perl scripts and HTTP servers [Doug Bigwood and John Barnett (National Agricultural Library {NAL}), Jeroen Coppieters (European Bioinformatics Institute), Jean Thierry-Mieg (Centre National de la Recherche Scientifique), and Steve Rozen (Massachusetts Institute of Technology)].
  • Module for displaying multiple maps, including different levels (e.g., cytogenetic bands, STS locations, P1 clones, and DNA sequences) of the same region [Arun Aggarwal (LBNL)]. Substantial progress on a prototype protein-sequence display module [Eric Sonnhammer (Sanger Centre)].
  • HTML documentation for map display and sequence-assembly modules [Sam Cartinhour (Texas A&M and NAL), John Morris (Massachusetts General Hospital), and Kate Rice (Sanger Centre)]. The documentation working group recommended using HTML for all future ACEDB documentation.
  • More than 20 different software tools listed for converting data to and from .ace files and various formats such as spreadsheets, Medline, and FASTA [Detlef Wolf (Integrated Genomic Database) and query tools working group].
  • ACEDB conversion begun for Windows-NT by Richard Bruskiewich (University of British Columbia), Richard Durbin (Medical Research Council, U.K.), Thierry-Mieg, and others.

Future Meetings

The 1996 ACEDB conference and workshop will be held near Heidelberg, Germany, and hosted by Otto Ritter's group (Integrated Genomic Database Project). NAL will host the 1997 meeting, for which Bigwood and Dave Matthews (Cornell University) are cochairs.

ACEDB Application Examples

Encyclopaedia of Drosophila 2.0

Of the many groups using ACEDB, the Drosophila Genome Project has made the greatest number of modifications to the program for their specialized needs. ACEDB was originally customized for use with Drosophila by Suzanna Lewis and Cyrus Harmon [Berkeley Drosophila Genome Project (BDGP)] to produce Flydb, the laboratory database of BDGP. MacAce, the Macintosh-compatible version of ACEDB, was written by Frank Eeckman (Lawrence Berkeley National Laboratory), Richard Durbin (Sanger Centre), and Harmon.This Macintosh version was further customized by Harmon and Lewis for the Encyclopaedia of Drosophila (EofD), which is a joint product of BDGP and FlyBase. EofD displays published and unpublished BDGP data as well as data collected by FlyBase from the scientific literature and other genome projects. Since Release 1.0 became available in April, FlyBase and BDGP have distributed more than 1500 copies of the EofD CD-ROM,giving it the largest installed user base of any ACEDB implementation. Release 2.0 is now available on CD-ROM for the Macintosh ($15, including 36-page reference manual) and by ftp for the UNIX version. [Ordering information and computer requirements: eofd-sales@morgan.harvard.edu ]

Sanger Centre 22ace

The first release of the human chromosome 22 physical mapping database 22ace from the Sanger Centre is now available by ftp from ftp.sanger.ac.uk in the directory pub/human/chr22/physical_map. The database is implemented in version 4.1 of ACEDB. Details about ACEDB and the Chromosome 22 mapping group can be found on WWW (http://www.sanger.ac.uk/hum22) (choose Chromosome 22).

Agricultural Server

ACEDB acts as the back-end data server for all databases that are part of the USDA Agricultural Genome Information Server. With release of the ACEDB aceserver, which can output ACEDB objects as Perl code, this programming language is being used to develop sophisticated cross-species database queries and draw data from molecular biology databases throughout the Internet.


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