From owner-acedb@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: feature request: Show All Values Date: 1 Feb 1995 10:52:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502011851.AA05105@greengenes.cit.cornell.edu> When formulating a query, it would sometimes be nice to see all the values of a field that exist in the database. Can this be done? E.g. in the Query Builder there might be an option in the dropdown menu for the third or fourth field to "Show all values". This would be similar to the wonderful "follow" command, as in "find Germplasm; follow Allele". But it would also allow following to values of type ?Text and boolean #types, as in "follow Characteristic" or "follow Type". This would be especially useful for the ?Text's, as there doesn't seem to be any other easy way to get examples of very many possible values, much less all the existing values. (Currently I build a tablemaker table, then pass it through some fancy unixations involving sort | uniq.) hopefully, - Dave From owner-acedb@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!GENOME.STANFORD.EDU!cherry From: cherry@GENOME.STANFORD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: First release from the Saccharomyces Genome Database Date: 2 Feb 1995 14:18:45 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 74 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502022218.OAA06441@stout.Stanford.EDU> NNTP-Posting-Host: net.bio.net First public release from the Saccharomyces Genome Database project The first public release from the Saccharomyces Genome Database (SGD) at Stanford University is now available using the ACEDB software developed by Durbin and Thierry-Mieg. This Ace database is called SacchDB and is available for Macintosh and a variety of UNIX systems, as well as through the Internet. A partial list of the contents of version 2.3 SacchDB: o All Saccharomyces genes contained in the Registry of Gene Names on January 21, 1995. o Results of the seven completed chromosomal sequencing projects have been integrated into the database. This includes chromosomes: I, II, III, V, VIII, IX, and XI. o Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. o For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. o All Saccharomyces DNA sequences contained within GenBank release 86 (December 7, 1994) are incorporated. o Literature references, most including abstracts, for the information contained within the database. o Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. o Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. The SGD project at Stanford is funded by a grant from the National Center for Human Genome Research, National Institutes of Health. The collection and maintenance of the Registry of Gene Names was transferred to the SGD in early 1994 by R. Mortimer, University of California, Berkeley. The collection and maintenance of the hybridization results to the Olson/Riles prime filters was transferred to the SGD in early 1994 by M. Olson, University of Washington, and L. Riles, Washington University in St. Louis. The SacchDB database is available through the Internet using the World Wide Web from the URL "http://genome-www.stanford.edu/" or using Internet Gopher to the host named genome-gopher.stanford.edu (port 70). The complete ACEDB database for use on a Macintosh or UNIX computer is available via Anonymous FTP from genome-ftp.stanford.edu (pub/yeast/SacchDB) or ncbi.nlm.nih.gov (repository/SacchDB). Please retrieve the file README.installation first to decide which files you need for your particular system. Please send any suggestions or corrections on the database or the SGD project to yeast-curator@genome.stanford.edu. Forms are available on the above ftp servers, the forms are simply suggestions of the types of information we wish to receive with the registration of a gene name or for submission of mapping data. In the future electronic Internet forms will be available. The SGD Project Mike Cherry, Cathy Ball, Rita Schmidt, Karen Davis, Selina Dwight, Mark Schroeder and David Botstein. Contacts for the Saccharomyces Genome Database Project (SGD) E-mail: yeast-curator@genome.stanford.edu ftp: genome-ftp.stanford.edu Gopher: genome-gopher.stanford.edu WWW: http://genome-www.stanford.edu/ Telephone: 415-725-8956 FAX: 415-723-7016 From owner-acedb@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: feature request: Show All Values Date: 3 Feb 1995 15:27:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502032326.AA08992@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net In answer to my question, > When formulating a query, it would sometimes be nice to see all the values > of a field that exist in the database. Can this be done? jean replied, > table-maker > hide all columns except what you want > this effectivelly does sort -u om the reamining column > i.e. lists all possible value as of the part of the database you explored This is brilliant. Looks like you have to Switch the column you want into the first column before you hide the other columns. Thanks jean! - Dave From owner-acedb@net.bio.net Sat Feb 04 22:00:00 1995 Path: biosci!rutgers!gatech!swrinde!pipex!uunet!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: josephk1@aol.com (JosephK1) Newsgroups: bionet.software.acedb Subject: Biology SOFTWARE Date: 4 Feb 1995 21:55:57 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 8 Sender: root@newsbf02.news.aol.com Message-ID: <3h1ent$as6@newsbf02.news.aol.com> Reply-To: josephk1@aol.com (JosephK1) NNTP-Posting-Host: newsbf02.mail.aol.com Hello I'm a student with a phyiology major and I'm interestd in any biology related program with an affordable price. Please let me know if you any Thank you Have a good day JosephK1 Future M.D. From owner-acedb@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!galaxy.ucr.edu!library.ucla.edu!agate!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 8 Feb 1995 17:42:22 GMT Organization: Dendrome, A genome database for forest trees Lines: 1158 Approved: news-answers-request@MIT.Edu Message-ID: <3havpu$6a@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.pswfs.gov Summary: Frequently Asked Questions about finding and getting started with the database system ACEDB. ACEDB is used to collect information regarding the molecular biology of the genome. Xref: biosci bionet.software.acedb:533 news.answers:32086 Archive-name: acedb-faq Last-modified: 2/7/95 Version: 1.18 Common Questions, with Answers, about ACEDB. Q0: What is ACEDB? Q1: What is the current version of ACEDB? Q2: What hardware/software do I need to run ACEDB? Q3: Where can I get ACEDB? Q4: What ACEDB databases exist? Q5: What written documentation exists for ACEDB? Q6: Where can I find further information about ACEDB? Q7: How should ACEDB be cited? Q8: Is ACEDB object-oriented? Q9: What's all this about Gopher|WAIS|ftp|WWW|URL ... Q10: How can I get on/off the ACEDB announcements mailing list? Q11: When and where is the next ACEDB Workshop? Q411: Who prepared this document & where is the current version? Questions marked with + are new, those with ! have substantially changed answers. Q0: What is ACEDB? A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [see Q4]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage -missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions ---------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: [This answer refers to the software not the C. elegans data.] Currently there are two threads of the ACEDB kernel: the 2.x series which represents the C. elegans project under the tutelage of Richard Durbin, and the 3.x series from Jean Thierry-Mieg. However, the differences in the code are slight and the two authors committed to a single kernel at the ACEDB workshop in July, 1994. The most recent release is an experimental version 3.3 which is available from the repositories. [Richard Durbin writes that the source code is now fully integrated in an intermediate version available at NCBI as /repository/acedb/test.source.3.6a.tar.gz --bks] A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q10. Return to List of Questions ---------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: Unix and X11: Sun/SunOS 4.x Sun/Solaris DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series PC 386/486 with Linux (free Unix) [note from Jeff Bryer, jbryer@darwin.mbb.sfu.ca] I just installed up Linux yesterday and today spent the many hours to compile in the C. elegans data for ACEDB v2.0 So to save other people the trouble of doing the same the entire package ACEDB for Linux 2-10 is available on trog.mbb.sfu.ca in /pub/acedb as linux.2_10.tar.Z The data was compiled in on a 486DX-33 with 16MBs of RAM running Linux 1.1.18 (Slackware 2.0.0 distribution) and a 32MB swap device (and it chugged away for a couple hours chewing up all 16MBs and half the swap space). File size is about 73MBs uncompressed, 26MBs compressed. This is based on the ACEDB v2.0 port for Linux that Ken Clark (ken@darwin.mbb.sfu.ca) did. There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu MSDOS/Windows/NT: A port to NT is rumored to be in the works. Macintosh: [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a decent color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. To retrieve the software see Q3. For cost savings, a combination of a high-end Intel platform with Linux appears very attractive. [Though the port does not seem robust, yet --bks] Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems SPARCstation II, and users can interact using Macintoshes and PC-clones by using X11 implementations for the personal computers and a LAN. X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions ---------------------------------------------------------------------- Q3: Where can I get ACEDB? A3: All the files are available in the following public access accounts (anonymous ftp sites) accessible via Internet: lirmm.lirmm.fr (193.49.104.10) in pub/acedb cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb. MacAce is available from: genome.lbl.gov (131.243.224.80) in pub/macace cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb/macace Linux; ACEDB version 2.0 for Linux 2-10: trog.mbb.sfu.ca /pub/acedb as linux.2_10.tar.Z A typical session would be: ftp ncbi.nlm.nih.gov login: anonymous password: your email address cd repository/acedb/ace3 binary ls get README_3 get NOTES get INSTALL get bin.sparc.3.0.tar.Z quit Return to List of Questions ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alphabetic order by Database name. Curators, submit changes as new paragraphs.--bks] Database : AaeDB Species : Aedes aegypti Last_update : December 1994 ACEDB_version : 3.0 http://klab.agsci.colostate.edu/index.html PI : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Contact : aaedbmgr@klab.agsci.colostate.edu Database : AAnDB-1.0 Species : Aspergillus nidulans PI : Leland Ellis Last_update : February 1994 ACEDB_version : 3.0 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : AAtDB Species : Arabidopsis thaliana Current version : 3-4 Last_update : November 1994 Curator : John Morris Contact : curator@frodo.mgh.harvard.edu Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x Availability : Macintosh version in /aatdb/MacAAtDB directory URL : gopher://weeds.mgh.harvard.edu/ URL : http://weeds.mgh.harvard.edu:80/index.html URL : http://probe.nalusda.gov:8300/ Database : ABtDB-1.0 Species : Bovine, Bos taurus ACEDB_version : 3.0 extended PI : Leland Ellis Last_update : February 1994 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : AboutDB Curator : Staffan Bergh PI : Staffan Bergh Subject : ACEDB itself (Is this meta-meta-metadata) ACEDB 3.0 Contact : staffan@biochem.kth.se URL http://kiev.physchem.kth.se/AboutDB.html Database : ACeDB Species : Caenorhabditis elegans Current version: 2-10 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@mrc-lmb.cam.ac.uk Contact : mieg@kaa.crbm.cnrs-mop.fr Last_update : May 1994 DataBase : AceMap Species : Homo sapiens (Mus musculus under development) Focus : Physical mapping of human chromsome X and 21 ACEDB_version : 3.0 Curator : Hugues Roest Crollius PI : Hans Lehrach Availability : beta release of the X chr. data/models by anonymous ftp to ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap. Get the README file in the directory above. Contact : hrc@gea.lif.icnet.uk (Hugues Roest Crollius) ICRF, Lincoln's Inn Fields London, UK. Last_update : August 94 Database : AGsDB A Genus species Database Species : Aspergillus nidulans Species : Neurospora crassa Species : cow w/ human anchor loci Species : cotton (demo) Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast PI : Leland Ellis Curator : Leland Ellis Last_update : March 1994 ACeDB_version : 3.0 (beta still), with extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe) yeast); interacting loci via defined Interactions for each locus Models : as of 3.13.94 Data : as of 3.13.94 Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux (ducoux@moulon.inra.fr). URL : http://keck.tamu.edu/ibt.html Contact : leland@straylight.tamu.edu Database : ChlamyDB Species : Chlamydomonas PI : Elizabeth Harris Contact : chlamy@acpub.duke.edu Availability : ChlamyDB 1.0, using ACEDB 3.0, is now on WWW and gopher (probe.nalusda.gov). Complete version using ACECB 3.0 now available by ftp from probe.nalusda.gov in the pub/chlamydirectory. URL : http://probe.nalusda.gov:8300 Last_update : 25 Oct, 1994 Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel USDA-ARS Southern Crops Research Laboratory Route 5, Box 805, College Station, Texas 77845 Curator : Gerard R. Lazo Curator : Sridhar Madhavan Last_update : January, 1995 (version 95.1) ACEDB_version : 3.0 Contact : glazo@tam2000.tamu.edu (Gerard R. Lazo) Contact : rjk0339@zeus.tamu.edu (Russell J. Kohel) URL : http://probe.nalusda.gov:8000/index.html Phone : 409-260-9311 Fax : 409-260-9333 Database : CSNDB Focus : Cell Signalling Molecules and Interactions Contact : Takako Igarashi National Insitute of Health Sciences Division of Chem-Bio Informatics Setagaya-ku, Tokyo, Japan 158 taka@nihs.go.jp Database : EcoDB Species : E. coli PI : Staffan Bergh Contact : staffan@biochem.kth.se Availability : Proposed Last_update : Aug. 1994 Database : 11DB Species : Homo sapiens Focus : Physical mapping of chromosome 11 Availability : under development Curator : Benedict Arnold PI : Peter Little Contact : Benedict Arnold Dept. Biochemistry, Imperial College, London, SW7 2AZ b.arnold@ic.ac.uk Database : The Encyclopaedia of the Drosophila Genome. Acronym : (none) Species : Drosophilidae (primarily D. melanogaster) Availability : MacFly/FlyDB-based distribution by ftp and CD-ROM due early 1995 Developer : Suzanna Lewis Contact : suzi@fly2.berkeley.edu Developer : Cyrus Harmon Contact : sly@fly2.berkeley.edu Developer : Edward Welbourne Contact : eddy@gen.cam.ac.uk Curation : Data is provided by the collaborating organisations: Collaborator : The FlyBase Consortium, flybase@morgan.harvard.edu Collaborator : The Berkeley Drosophila Genome Project URL : gopher://fly.bio.indiana.edu:70+/11/Flybase Database : Flydb Species : Drosophila melanogaster Curator : Suzanna Lewis Contact : suzi@fly2.berkeley.edu Database : GrainGenes Species : Wheat, barley, oats, relatives Availability : Anonymous ftp from probe.nalusda.gov:pub/grains Availability : Gopher greengenes.cit.cornell.edu port 70 Availability : Gopher probe.nalusda.gov port 7002 Curator : David E. Matthews PI : Olin D. Anderson Contact : matthews@greengenes.cit.cornell.edu Contact : oandersn@wheat.usda.gov URL : gopher://greengenes.cit.cornell.edu/1/ Data_version : 1.3 Released : 12 Jan 1994 Based_on : acedb.1-10 Availability : See following WWW URL URL : http://probe.nalusda.gov:8300 Last_update : Feb. 1994 Database : human.c17 Species : Homo sapiens Availability : the database is under development Contact : lsprilus@weizmann.weizmann.ac.il Focus : mapping & sequencing of Human Chromosome 17 Based_on: acedb.3-0 Last_update : Jan. 1994 Database : IGD - the Integrated Genomic Database Species : Homo sapiens (later mouse and other mammalian species) Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter [ o.ritter@dkfz-heidelberg.de ] Curator : tba Description : IGD - the Integrated Genomic Database - aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie_paule Lefranc Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr Database : Maize Species : Zea mays L. ssp. mays Focus : Maize genome Acedb_version : 1.9 FTP : probe.nalusda.gov, pub directory; anonymous ftp Comment : Maize is an acedb front end for the Maize Genome Database, MaizeDB, a SYBASE database. Comment : MaizeDB is updated daily and has WWW connectivity to external databases: GenBank (loci, alleles and probes), SwissProt (gene products) and the E. coli Stock Center (loci). Data : Major data categories: 4522 mapped loci (located to chromosome or better) including 684 mapped genes and 1423 mapped probed sites (gene candidates); 982 probes; 1850 map scores; 1533 gel patterns (Probe/Enzyme/Stock); 4231 stocks; 5105 Variations (alleles, DNA polymorphisms, rearrangements, etc); 465 phenotypes; 223 traits; 547 gene products; 5314 bibliographic references; 1979 persons with addresses. Gopher : host = teosinte.agron.missouri.edu, port = 70 Telnet : telnet teosinte.agron.missouri.edu login as guest, use password 'corncob' HTTP : http://teosinte.agron.missouri/top.html HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant Genome Database Comment : Genera is a software toolkit for creating and extracting data from Sybase databases; used to create MaizeDB and Worldwide Web connectivity. HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu Curator : Pat Byrne byrne@teosinte.agron.missouri.edu Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu Curator : Mary Polacco maryp@teosinte.agron.missouri.edu Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Curator : Christiane Fauron FAURON@GENE1.med.utah.edu Curator : Carolyn Wetzel cmwetzel@iastate.edu Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU Design : Stan Letovsky letovsky-stan@CS.YALE.EDU Design : Mary Berlyn mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 25 April 1994 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. PI : Staffan Bergh PI : Stewart Cole PI : Doug Smith Curator : Staffan Bergh Contact : staffan@biochem.kth.se Last_update : Apr. 1994 WWW : http://kiev.physchem.kth.se/MycDB.html ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb Database : PomBase Curator : Sean Walsh Curator : Marie-Adele Rajendream PI : Bart Barrell Species : Schizosaccharomyces pombe Contact : svw@sanger.ac.uk Contact : barrell@sanger.ac.uk Comment : Not yet available for distribution DataBase : Mousedb Species : Musculus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Michelle Kirby Curator : Rachael Selley PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 For other information contact Michelle Kirby. Contact : kirbym@har-rbu.mrc.ac.uk (or mkirby@hgmp.mrc.ac.uk) rselley@har-rbu.mrc.ac.uk MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD Last_update : October 1994 Database : RiceGenes Species : Rice (O. sativa) Availability : Anonymous ftp from probe.nalusda.gov:pub/rice Availability : Gopher nightshade.cit.cornell.edu port 70 Availability : Gopher probe.nalusda.gov port 7007 Curator : Edie Paul PI : Susah McCouch Contact : epaul@nightshade.cit.cornell.edu Release : ACEDB 1-10 Last_update : May 1994 Database : SacchDB Species : Saccharomyces cerevisiae Focus : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 2.0, MacAce 2.0b4 FTP : genome-ftp.stanford.edu, /pub/SacchDB FTP : ncbi.nlm.nih.gov, /repository/SacchDB Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. Gopher : host = genome-gopher.stanford.edu, port = 70 HTTP : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Rita Schmidt, bleb@genome.stanford.edu Programmer : Karen Davis, karen@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Last_update : 2 February 1995 Database : SolGenes Coverage: Solanaceae - tomato, potato, pepper Availability : Anonymous ftp from probe.nalusda.gov:pub/solgenes Availability : Gopher nightshade.cit.cornell.edu port 71 Availability : Gopher probe.nalusda.gov port 7006 Curator : Edie Paul PI : Steve Tanksley Contact : epaul@nightshade.cit.cornell.edu Release : ACEDB 3.0 Last_update : May 1994 Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz USDA-ARS Dept. of Soil & Crop Sciences Texas A&M University College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 E_mail : schertz@tamvm1.tamu.edu Curator : Najeeb U. Siddiqui Southern Crop Improvement Facility Crop Biotechnology Center Texas A&M University College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 E_mail : nus6389@tamsun.tamu.edu Last_update : July 1994 ACEDB_version : 3.0 Availability : Under Development Database : SoyBase Species : Soybeans Curator : Lisa Lorenzen PI : Randy Shoemaker Contact : lorenzen@mendel.agron.iastate.edu Phone : 515-294-0421 Fax : 515-294-2299 Last_update : Sept. 1993 Database : Sybace Species : Homo sapiens Creator : Detlef Wolf Comment : Custom software --ACEDB front-end to SYBASE data Contact : D.Wolf@dfkz-heidelberg.de See_also : IGD Database : TreeGenes Species : Forest trees Availability : alpha, contact curator ACEDB_version : 1-10 Curator : Bradley K. Sherman PI : David B. Neale Contact : Dendrome@s27w007.pswfs.gov Contact : bks@s27w007.pswfs.gov Contact : dbn@s27w007.pswfs.gov Last_update : March 1994 URL : gopher://s27w007.pswfs.gov/ URL : http://s27w007.pswfs.gov/ URL : ftp://probe.nalusda.gov/pub/trees Database : 21Bdb Species : Homo sapiens Focus : STS content mapping & sequencing of Human Chromosome 21 Availability : by request, via ftp, world-wide-web Based_on : acedb.1-10 plus moulon server URL : ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z URL : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy Contact : DFDavy@lbl.gov Contact : aggarwal@genome.lbl.gov Focus : STS content mapping & sequencing of Human Chromosome 21 PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng Last_update : Apr. 1994 Database : 22ace Species : Homo sapiens Curator : Ian Dunham Focus : Physical mapping of chromosome 22 PI : Ian Dunham Contact : Ian Dunham Sanger Centre Hinxton Hall, Cambs. UK. id1@sanger.ac.uk Database : VoxPop Species : Populus spp. Availability : contact curator Curator : Carl G. Riches PI : Reinhard F. Stettler Contact : cgr@poplar1.cfr.washington.edu Contact : STETTLER@coyote.cfr.washington.edu Last_update : Sept. 1993 Database : Xace Species : Homo sapiens Curator : Gareth Maslen Focus : Physical mapping of chromosome X PI : David Bentley Contact : Gareth Maslen Sanger Centre Hinxton Hall, Cambs. UK. glm@sanger.ac.uk Database : ? Species : Homo sapiens Focus : Physical mapping of human chromosome 6. Curator : Ioannis Ragoussis Availability : Unknown Contact : Guy's hospital Database : ? PI : Scott Chasalow Species : Potato Contact : Scottish Crop Institute, Dundee Last_update : Sept. 1993 Database : ? PI : George Murphy PI : David Flanders Species : Arabidopsis thaliana Contact : John Innes Center, Norwich, England Last_update : Sept. 1993 Database : ? Species : Homo Sapiens Focus : Physical and linkage mapping of chromosome 8 Availability : Curator : Stephen Wood PI : Stephen Wood Contact : Stephen Wood Dept. Medical Genetics University of B. C. Vancouver, B. C. Canada swood@unixg.ubc.cq Return to List of Questions ---------------------------------------------------------------------- Q5: What written documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000. Primary documents from the developers are: acedb -- A C. elegans Database: I. Users' Guide. acedb -- A C. elegans Database: II. Installation Guide. acedb -- A C. elegans Database: III. Configuration Guide. Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z And ftp://weeds.mgh.harvard.edu/acedb_doc The files are in tex and postscript. [I have had some difficulty printing these. Jean Thierry-Mieg suggests latex xxxx.tex, dvi2ps xxxx.dvi > xxxx.ps, lpr xxxx.ps.] You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angisturte.ps and angistute.hqx available by anonymous ftp at ncbi.hih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Return to List of Questions ---------------------------------------------------------------------- Q6: Where can I find further information about ACEDB? A6: There is a Usenet/Biosci conference titled bionet.software.acedb. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. All of the articles are archived on the gopher at net.bio.net. Mike Cherry has set up an ACEDB Developer's archive. For anonymous ftp use the hostname weeds.mgh.harvard.edu and look in the acedb_dev directory. If you wish to contribute you can put files in the incoming directory. Send a message to Mike (cherry@genome.stanford.edu) that you have put something in that directory then Mike will move it out for general access. For gopher you can connect to weeds.mgh.harvard.edu (132.183.190.21) and ... --> N. FTP Archives for Molecular Biology/ then --> M. ACEDB Developer's archive/ [N and M are integers which are subject to change.] The bionet.software. acedb.conference is archived and can be searched using WAIS. Here is a Gopher-style link to the WAIS archive. (This is also courtesy of Mike Cherry.): # Type=7 Name=ACEDB BioSci Electronic Conference Path=7/.index/acedb-biosci Host=genome-gopher.stanford.edu Port=70 The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: http://moulon.inra.fr/acedb/acedb.html for C. elegans data http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html http://moulon.inra.fr/acedb_conf.html (en francais) The Genome Computing Group, Lawrence Berkeley Laboratory has an anonymous ftp service at machine genome.lbl.gov (131.243.224.80) which contains: flydb - LBL's Drosophila Acedb-style database 21bdb - LBL's Human Chromosome 21 Acedb-style database querdb - LBL's query-language extensions to Acedb metadata - LBL's compendium of Acedb database schema variants macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to dataabases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier Jean Thierry-Mieg et al), and the Interated Genome Database project in Heidelburg (Otto Ritter, Detlef Wolf et al). Return to List of Questions ---------------------------------------------------------------------- Q7: How should ACEDB be cited? A7: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit, available by Anonymous FTP from ... Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions ---------------------------------------------------------------------- Q8: Is ACEDB object-oriented? A8: From the ACEDB User's Guide. A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions ---------------------------------------------------------------------- Q9: What's all this about Gopher/WAIS/ftp/WWW ... A9: These terms all refer to Internet protocols. An excellent introduction to the Internet is: _The Whole Internet User's Guide & Catalog_, by Ed Krol, O'Reilly & Associates, 1992. Or ask your system administrator to provide you with a gopher client or mosaic client and begin navigating on your own. URL is a Universal Resource Locator on the World-Wide Web (WWW). There are many free Internet browsers available that allow you to use an Internet connection and a URL to access services. Mosaic may be the most popular and it is available for Mac, PC or Unix via anonymous ftp from ftp.ncsa.uiuc.edu. Return to List of Questions ---------------------------------------------------------------------- Q10: How can I get on/off the ACEDB announcements mailing list? A10: To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb is on the mailing list. Return to List of Questions ---------------------------------------------------------------------- Q11: When and where is the Next ACEDB Workshop? The 1995 ACEDB Conference and Workshop will be held May 14-27, 1995, at the Isis Oasis, a small retreat center in Geyserville, about 80 miles north of SanFrancisco in Sonoma County, California. We will have exclusive use of the entire retreat center, including the theater (for workstations and primary sessions), dining room, lodge, and other residential facilities. For more information send email to ace95@genome.lbl.gov or vist URL http://genome.lbl.gov/ace95.html on the WWW. If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers taken by Mike Cherry with the camera on an SGI workstation, the URL is: http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html. John Morris has provided some more at URL: http://weeds.mgh.harvard.edu/ace94/ace94.image.html. Return to List of Questions ---------------------------------------------------------------------- Q411:Who prepared this document & where is the current version? [Note to international readers: 411 is the phone number for information in the USA. --bks] This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. Answer 3 demonstrates a sample FTP session. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html http://s27w007.pswfs.gov/Homepage/acedbfaq.html Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov Major contributions in getting this FAQ off the ground were made by John McCarthy and Mike Cherry. Other contributors include: Lisa Lorenzen David Matthews Edie Paul Donn Davy Eric De Mund Sam Cartinhour Please cite as: Sherman,B.K., ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993,1994,1995 approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome Research Program. --bks Return to List of Questions ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Tue Feb 14 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!news.kth.se!sibirien.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.general,bionet.microbiology,bionet.software.acedb,sci.med Subject: MycDB - mycobacterial database, release 3-6 Date: 15 Feb 1995 13:45:22 +0100 Organization: Biochemistry, KTH, Stockholm Lines: 126 Sender: staffan@biochem.kth.se Distribution: world Message-ID: <3hst12$j4n@sibirien.physchem.kth.se> NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Keywords: mycobacteria, tuberculosis, acedb Xref: biosci bionet.general:13558 bionet.microbiology:1425 bionet.software.acedb:535 sci.med:67142 Stockholm & Paris February 15, 1995 The sixth release of the Mycobacterium database, MycDB, is now available. MycDB is a database intended to contain information on all aspects of mycobacteria, relevant to the study of the organisms and diseases caused by them. The focus has initially been on the molecular biology of mycobacteria, such that the database contains data on physical and genetic mapping, nucleotide sequences, and data on antigens and antibodies used in the study of the immunology of mycobacteria. MycDB is implemented in ACEDB, a general database manager initially developed for the C. elegans genome project by Richard Durbin (MRC-LMB, UK) and Jean Thierry-Mieg (CNRS, France, but since adapted for other organisms and also for totally unrelated fields. It is 'object-oriented', and easily configured for different purposes. Objects are heavily crosslinked so that a user can call up (e.g) the Sequence corresponding to an Antigen, and from there look up the Antibody recognizing the antigen, and then look at the bibliography for the antibody. Complex queries can be performed with a built-in query language or with the TableMaker, a facility for producing tables suitable for further processing. MycDB is funded by the WHO and the Fondation Raoul Follereau and is maintained jointly by the Unite de Genetique Moleculaire Bacterienne at the Institut Pasteur in Paris, France and the Department of Biochemistry at The Royal Institute of Technology in Stockholm, Sweden. MycDB is available free of charge, via ftp or through the a World Wide Web server at URL: http://www.biochem.kth.se/MycDB.html. New in release 3-6: * 227 new DNA sequences, current up to January 31, 1995 * Close to 500 new references, from Medline up to January 1995. * The M. leprae contigs have been moved to the new Map class. Most info on M.tuberculosis physical mapping (Clones, Clone_Grids) has been removed as we are working on finishing this. * Model changes. Strain is now a model in its own right and crossreferences to Strain has been added to Sequence, Locus, and others. Gene has disappeared, all Genes are now Loci. In the future we plan to provide a filter for loci connected to coding sequences. * The model changes unfortunately means you will have to restart the database from scratch. (If you have used the database for your own data, contact staffan for further info.) * The WorldWideWeb server has a new address, an alias for the old one: URL http://www.biochem.kth.se/MycDB.html. The old address will continue to work for the forseeable future. New in release 1-5/3-5: * Software version. MycDB now uses ACEDB1-10 (use updates 1-1 to 1-5) or ACEDB3-0 (use updates 3-1 to 3-5). Note that we will in the future only make updates available for version 3 of the software. * Model changes. As a consequence of changing software and feedback from users the models have changed. This unfortunately means you will have to restart the database from scratch. (If you have used the database for your own data, contact staffan for further info.) * A WorldWideWeb server has been set up (replacing the gopher), and can be found at the URL http://www.biochem.kth.se/MycDB.html. * The M.tuberculosis physcal map has been removed, as we are currently working on finishing it. We hope to have this ready by next release. * New sequences. Many new sequences from GenBank/EMBL/DDBJ, with added annotations and similarity search results. Also sequences from Doug Smiths sequencing project at Collaborative Research (Thanx Doug). * Bibliography and address list has been updated. Release 1-2 of MycDB contained: * MycDB now uses version 1-9 of the ACEDB software with, among other improvements, improved query facilities. * The cosmid physical map of M.tuberculosis produced at the LGMB. (this is a working version, kindly provided by Wolfgang Philipp and Sylvie Poulet). * A update of the compilation of nucleotide sequences from mycobacteria in GenBank and EMBL. * An extended list of antigens and antibodies, now including the CDC/WHO list of antibodies available to mycobacteriologists. * Addresses of more than 60 researchers. Release 1-1 of MycDB contained: * The cosmid physical map of M.leprae produced at the LGMB. * A compilation of nucleotide sequences from mycobacteria in GenBank and EMBL. * A compilation of antigens and antibodies, based on the article of Young et al. * More than 1200 references downloaded from Medline. The database currently requires a Unix workstation running X-Windows. A variety of precompiled versions of the ACEDB database software are available through anonymous ftp. See the file MycDB.Retrieval for more info. An (experimental) Macintosh version of the ACEDB software is also available. If you wish to obtain the MycDB database please contact us, via e-mail, fax, mail or telephone. If you are impatient and are already familiar with internet/ftp, all relevant information can be found at the WWW server at the Department of Biochemistry, KTH: http://www.biochem.kth.se/MycDB.html the ftp server at the Department of Biochemistry, KTH: ftp.biochem.kth.se (130.237.52.63 in pub/MycDB the ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in pub/MycDB or the mirror site at the Weizmann Institute in Israel (thanks Jaime!): bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb The file MycDB.Retrieval describes in more detail the database system requirements, network retrieval procedures for obtaining the database and methods of obtaining future updates. For more information contact Staffan Bergh or Stewart Cole. Staffan Bergh Biochemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden Email: staffan@biochem.kth.se Fax: (46 8) 24 54 52 Voice: (46 8) 790 8758 Stewart Cole Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris Cedex 15, France Email: stcole@pasteur.fr Fax: (33 1) 45.68.85.93 Voice: (33 1) 45.68.84.46 From owner-acedb@net.bio.net Wed Feb 15 22:00:00 1995 Path: biosci!biosci!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.announce,bionet.general,bionet.microbiology,sci.med,bionet.software.acedb Subject: MycDB - mycobacterial database, release 3-6 Date: 15 Feb 1995 16:28:08 -0800 Organization: Biochemistry, KTH, Stockholm Lines: 129 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <3hsg1f$j0r@sibirien.physchem.kth.se> NNTP-Posting-Host: net.bio.net Keywords: mycobacteria, acedb, tuberculosis, MycDB Xref: biosci bionet.announce:1819 bionet.general:13571 bionet.microbiology:1432 sci.med:67242 bionet.software.acedb:536 Stockholm & Paris February 15, 1995 The sixth release, called 3-6, of the Mycobacterium database, MycDB, is now available. MycDB is a database intended to contain information on all aspects of mycobacteria, relevant to the study of the organisms and diseases caused by them. The focus has initially been on the molecular biology of mycobacteria, such that the database contains data on physical and genetic mapping, nucleotide sequences, and data on antigens and antibodies used in the study of the immunology of mycobacteria. MycDB is implemented in ACEDB, a general database manager initially developed for the C. elegans genome project by Richard Durbin (MRC-LMB, UK) and Jean Thierry-Mieg (CNRS, France), but since adapted for other organisms and also for totally unrelated fields. It is 'object-oriented', and easily configured for different purposes. Objects are heavily crosslinked so that a user can call up (e.g) the Sequence corresponding to an Antigen, and from there look up the Antibody recognizing the antigen, and then look at the bibliography for the antibody. Complex queries can be performed with a built-in query language or with the TableMaker, a facility for producing tables suitable for further processing. MycDB is funded by the WHO and the Fondation Raoul Follereau and is maintained jointly by the Unite de Genetique Moleculaire Bacterienne at the Institut Pasteur in Paris, France and the Department of Biochemistry at The Royal Institute of Technology in Stockholm, Sweden. MycDB is available free of charge through the World Wide Web (at URL http://www.biochem.kth.se/MycDB.html) or through ftp. Retrieval instructions can be found at the end of this message. New in release 3-6: * 227 new DNA sequences, current up to January 31, 1995 * Close to 500 new references, from Medline up to January 1995. * The M. leprae contigs have been moved to the new Map class. Most info on M.tuberculosis physical mapping (Clones, Clone_Grids) has been removed as we are working on finishing this. * Model changes. Strain is now a model in its own right and crossreferences to Strain has been added to Sequence, Locus, and others. Gene has disappeared, all Genes are now Loci. In the future we plan to provide a filter for loci connected to coding sequences. * The model changes unfortunately means you will have to restart the database from scratch. (If you have used the database for your own data, contact staffan for further info.) * The WorldWideWeb server has a new address, an alias for the old one: URL http://www.biochem.kth.se/MycDB.html. The old address will continue to work for the forseeable future. New in release 1-5/3-5: * Software version. MycDB now uses ACEDB1-10 (use updates 1-1 to 1-5) or ACEDB3-0 (use updates 3-1 to 3-5). Note that we will in the future only make updates available for version 3 of the software. * Model changes. As a consequence of changing software and feedback from users the models have changed. This unfortunately means you will have to restart the database from scratch. (If you have used the database for your own data, contact staffan for further info.) * A WorldWideWeb server has been set up (replacing the gopher), and can be found at the URL http://www.biochem.kth.se/MycDB.html. * The M.tuberculosis physical map has been removed, as we are currently working on finishing it. We hope to have this ready by next release. * New sequences. Many new sequences from GenBank/EMBL/DDBJ, with added annotations and similarity search results. Also sequences from Doug Smiths sequencing project at Collaborative Research (Thanx Doug). * Bibliography and address list has been updated. Release 1-2 of MycDB contained: * MycDB now uses version 1-9 of the ACEDB software with, among other improvements, improved query facilities. * The cosmid physical map of M.tuberculosis produced at the LGMB. (this is a working version, kindly provided by Wolfgang Philipp and Sylvie Poulet). * A update of the compilation of nucleotide sequences from mycobacteria in GenBank and EMBL. * An extended list of antigens and antibodies, now including the CDC/WHO list of antibodies available to mycobacteriologists. * Addresses of more than 60 researchers. Release 1-1 of MycDB contained: * The cosmid physical map of M.leprae produced at the LGMB. * A compilation of nucleotide sequences from mycobacteria in GenBank and EMBL. * A compilation of antigens and antibodies, based on the article of Young et al. * More than 1200 references downloaded from Medline. The database currently requires a Unix workstation running X-Windows. A variety of precompiled versions of the ACEDB database software are available through anonymous ftp. See the file MycDB.Retrieval for more info. An (experimental) Macintosh version of the ACEDB software is also available. If you wish to obtain the MycDB database please contact us, via e-mail, fax, mail or telephone. If you are impatient and are already familiar with internet/ftp, all relevant information can be found at the WWW server at the Department of Biochemistry, KTH: http://www.biochem.kth.se/MycDB.html the ftp server at the Department of Biochemistry, KTH: ftp.biochem.kth.se (130.237.52.63) in pub/MycDB the ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in pub/MycDB or the mirror site at the Weizmann Institute in Israel (thanks Jaime!): bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb The file MycDB.Retrieval describes in more detail the database system requirements, network retrieval procedures for obtaining the database and methods of obtaining future updates. For more information contact Staffan Bergh or Stewart Cole. Staffan Bergh Biochemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden Email: staffan@biochem.kth.se Fax: (46 8) 24 54 52 Voice: (46 8) 790 8758 Stewart Cole Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris Cedex 15, France Email: stcole@pasteur.fr Fax: (33 1) 45.68.85.93 Voice: (33 1) 45.68.84.46 From owner-acedb@net.bio.net Sat Feb 18 22:00:00 1995 Newsgroups: bionet.molbio.yeast,bionet.drosophila,bionet.celegans,bionet.genome.arabidopsis,bionet.software.acedb Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!usc!howland.reston.ans.net!news.sprintlink.net!uunet!news.iij.ad.jp!wnoc-tyo-news!nec-tyo!tyo1-nec!newssv1-nec!necscc!tgn.cl.nec!sano@exp.cl.nec.co.jp From: Tohru Sano Subject: Japanese ACEDB Family Document & ACEDB for NEC-EWS Sender: daemon@tgn.cl.nec.co.jp (0000-Admin(0000)) Message-ID: <199502181425.XAA25035@kirara.exp.cl.nec.co.jp> Date: Sat, 18 Feb 1995 14:25:34 GMT Content-Type: text/plain; charset=ISO-2022-JP X-Mailer: WinMail[2.21] Mime-Version: 1.0 Organization: NEC Corp., Tsukuba JP Lines: 30 Xref: biosci bionet.molbio.yeast:2428 bionet.drosophila:885 bionet.celegans:284 bionet.genome.arabidopsis:3001 bionet.software.acedb:537 Tsukuba Japan; February 18, 1995 (1) "Japanese ACEDB Guide Ver.1.2." and (2) "ACEDB ver.2 for NEC engineering workstation EWS4800 series" is now available. (1) This is Guide of ACEDB family written in Japanese. This postscript file is available via anonymous ftp at ftp.nec.co.jp (192.135.93.2) as /pub/packages/acedb/acemanjp.1_2.ps.Z. This is 40 pages guide. I develop html version, and it will be available soon. (2) ACEDB for EWS4800 is available via anonymous ftp at ftp.nec.co.jp (192.135.93.2) in /pub/packages/acedb/ace2. In the near future ACEDB Ver.4 appears, and we port it to NEC-EWS4800 as soon as possible. For more information contact Tohru Sano. Tohru Sano Fundamental Research Laboratories NEC Corporation Tsukuba, 305, JAPAN e-mail: sano@exp.cl.nec.co.jp FAX: +81-298-56-6136 VOICE: +81-298-50-1507 From owner-acedb@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!cs.utexas.edu!uunet!news.nuri.net!news.kreonet.re.kr!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: New pictures of Ace94 Date: 22 Feb 1995 21:57:05 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 15 Distribution: world Message-ID: <3igbvh$t78@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov Well, better late than never. I have put up a few B&W pictures of the ACEDB '94 Workshop as URL: ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html There are links to the other collections from this document. --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project From owner-acedb@net.bio.net Sun Feb 26 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!redstone.interpath.net!hilbert.dnai.com!emf.emf.net!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: aceformat - perl tool for ace file reformatting Date: 27 Feb 1995 22:40:49 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 48 Distribution: world Message-ID: <3itkdh$b3p@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov Mikel J. Bancroft, a student at Berkeley, wrote a nice little perl script for me last fall. It started out as just a way to move data from ace dumps to spreadsheet files (comma separated fields, one line = one spreadsheet row) and has proven to be generally useful in extracting data for a variety of porting problems. I just used it to make up a set of 3000 mailing labels, e.g. It allow the user to set up a template in a configuration file so that as an ace dump is read, any object whose class matches a template in the configuration file is output in a format defined in the template. You can have multiple templates per class, and multiple classes per configuration file. It also allows string-mapping using a subset of typical unix regular expression syntax. The mapping is also specified in the configuration file. The user can change the field delimiters. For example, setting the field delimiter to newline, and using the string mapping feature, new ace files can be produced. But more mundane separators like tab and colon are also supported. The program is pretty much limited to simple tag : value and it cannot "follow" tags or anything fancy like that. If you're interested, it's available now as ftp://s27w007.pswfs.gov/ACEDB/aceformat1_1.tar and is about 25K bytes. The tar file includes the program, a manual page and some short samples. The file will also be in the official ACEDB tool archive at ftp://weeds.mgh.harvard.edu/acedb_dev real soon now. I wouldn't say we're supporting this software, but I'd be happy to catalogue improvements. Feel free to redistribute as long as Mikel's name remains attached. Have fun, --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project From owner-acedb@net.bio.net Tue Feb 28 22:00:00 1995 Path: biosci!CHROM5.HSIS.UCI.EDU!jvu From: jvu@CHROM5.HSIS.UCI.EDU (John Vu) Newsgroups: bionet.software.acedb Subject: Help: ACEDB WWW Gateway Date: 1 Mar 1995 14:24:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199412011000.CAA27756@net.bio.net> NNTP-Posting-Host: net.bio.net Hi acedb users, I am trying to configure the acedb WWW gateway. I followed the instructions from the only two sources I know of for the WWW gateway: http://moulon.inra.fr/acedb_conf_eng.html and http://keck.tamu.edu/cgi/staff/ace-mosaic-howto.html However, when I access the URL from Mosaic, I receive the following message in Mosaic: !! FATAL ERROR 0: !! R 0: Can anyone tell me what I am doing wrong or perhaps give me more detailed instructions on configuring the gateway? We are running ace 3.5 on a Sun IPX with Sun OS 4.1.3. Thanks. Best regards, John D. Vu INTERNET: jdvu@uci.edu National Human Genome Research Center Phone : (714) 824 - 7447 Department of Biological Chemistry UCI College of Medicine, Medical Sciences I, Rm D240 Irvine, CA 92717