Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
Human Genome News, July-August 1995; 7(2):6
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
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.
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: firstname.lastname@example.org ]
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).
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.
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v7n2).
The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.
Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.