From owner-acedb@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!cs.utexas.edu!news.tamu.edu!128.194.15.2!leland From: leland@straylight.tamu.edu (Leland Ellis) Newsgroups: bionet.software.acedb Subject: AGsDB, A Genus species DataBase Date: 06 Mar 1994 03:27:25 GMT Organization: W.M. Keck Center for Genome Informatics, Institute of Biosciences and Technology, Texas A&M University, Houston Lines: 94 Distribution: world Message-ID: NNTP-Posting-Host: straylight.tamu.edu WWW-AGsDB WWW-ACeDB Server for "A Genus species DataBase" available on the WWW Server of the W.M. Keck Center for Genome Informatics at the Institute Biosciences and Technology Texas A&M University Houston URL: http://keck.tamu.edu/ibt.html WWW-AGsDB is a WWW interface to the data contained in AGsDB-1.0, which is implemented in ACeDB-3.0, the latest (and still beta) version of Richard Durbin and Jean Thierry-Mieg's ACeDB. AGsDB is a prototype for a multi-species database, with datatypes useful in the study of species of agricultural and biomedical interest, as well as model organisms. The interface utilizes the ACeDB Server software (nph-acedb3) developed by Guy Decoux (decoux@moulon.inra.fr), and modified versions of the models and tags of the human C21 database of Otto Ritter and co. The modifications provide for queries between interacting Loci, and between species via Homologs. Data from several species can be found in AGsDB: filamentous fungi (Aspergillus nidulans, Neurospora crassa), cows (with the corresponding anchor loci for humans) and cotton (examples as demo). Recently, we have begun to enter data for the Cell Cycle, which brings in Homlogs between Aspergillus and both budding (C. cerevisiae) and fission (S. pombe) yeast. The WWW-AGsDB server should be regarded as an experimental prototype. We do find it useful, but the data models are still being experimented with, and new data is always being added. Finally, the db is nowhere near comprehensive in the data included, but is illustrative of the datatypes that we routinely use in the study of these organisms. Futher development of both of the previously announced WWW-DataBases, WWW-AAnDB (for Aspergillus nidulans) and WWW-ABtDB (for cows), is now being continued in AGsDB (WWW-AAnDB and WWW-ABtDB have been phased out, but the data therein is now in AGsDB). The WWW-AGsDB server is accessible via the WWW Server of Keck-IBT. This URL http://keck.tamu.edu/ibt.html will take you to the Keck-IBT HomePage -- clicking on the Keck-IBT logo takes you to our 1st page of information, which has a link to AGsDB. Any feedback is very welcome at: leland@straylight.tamu.edu or jkirk@keck.tamu.edu AGsDB is the work of Leland Ellis, Jeff Kirk, Chris Floyd and Janis Bender at Keck-IBT, with advice on Aspergillus from Tom Adams (Texas A&M) and Greg May (Baylor College of Medicine), Neurospora from Dan Ebbole (Texas A&M), cows from Jim Womack (Texas A&M), cotton from Russ Kohel (Texas A&M) and the Cell Cycle from Greg May (Baylor College of Medicine). ---------------------------------------------------------------------------- Leland Ellis, Ph.D. Professor of Biochemistry and Biophysics Director, W.M. Keck Center for Genome Informatics Institute of Biosciences and Technology Texas A&M University 2121 Holcombe Houston, Texas 77030 email: leland@straylight.tamu.edu URL: http://keck.tamu.edu/ibt.html ---------------------------------------------------------------------------- -- Leland Ellis, Ph.D. Professor of Biochemistry and Biophysics Director, W.M. Keck Center for Genome Informatics Institute of Biosciences and Technology Texas A&M University 2121 Holcombe Houston, Texas 77030 email: leland@straylight.tamu.edu URL: http://keck.tamu.edu/ibt.html From owner-acedb@net.bio.net Mon Mar 07 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!sol.ctr.columbia.edu!news.kei.com!yeshua.marcam.com!zip.eecs.umich.edu!umn.edu!msus1.msus.edu!vax1.mankato.msus.edu!vengeance Newsgroups: bionet.software.acedb Subject: Omaha Project Message-ID: <1994Mar8.085329.2385@vax1.mankato.msus.edu> From: vengeance@vax1.mankato.msus.edu Date: 8 Mar 94 08:53:29 -0500 Organization: Mankato State University Lines: 9 I am trying to build a list of names and E-Mail addresses of people in the Omaha Nebraska area for a school related project. If you live in Omaha or go to school there or know someone that does and will be around for three months or more, please reply via E-Mail to Vengeance@vax1.mankato.msus.edu. Thank you very much! Ryan Krueger From owner-acedb@net.bio.net Tue Mar 08 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!ihnp4.ucsd.edu!dog.ee.lbl.gov!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: 9 Mar 1994 20:17:37 GMT Organization: Dendrome, A genome database for forest trees Lines: 790 Approved: news-answers-request@MIT.Edu Message-ID: <2llat1$jdr@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. Archive-name: acedb-faq Last-modified: 3/9/94 Version: 1.9 Xref: biosci bionet.software.acedb:177 news.answers:13604 ---------------------------------------------------------------------- Common Questions and Answers about ACEDB. 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 version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net (134.172.2.69) as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu (18.70.0.209) 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/plant/acedbfaq.html [Until I get more familiar with HTML, it may not be totally synchronized with the plain FAQ. --bks] 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 --Bradley K. Sherman ---------------------------------------------------------------------- The List of questions in the ACEDB FAQ. Questions marked with + are new, those with ! have substantially changed answers: 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|Anonymous ftp|WWW|URL ... Q10: How can I get on the ACEDB announcements mailing list? Q11: When and where is the next ACEDB Workshop? Q411:Who contributed to this document? ---------------------------------------------------------------------- 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 European integrated Genome Project. 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. Current display modes are: TREE for text type objects: papers, authors, genes etc. GMAP genetic map PMAP physical map (Sulston contig style) SEQ DNA sequence - symbolic, features, sequence and translation GRID hybridisation patterns for a probe to a clone grid BIBLIO bibliography attached to any object display modules under development: CMAP whole chromosome physical map plot GEL agarose gel simulation derived from sequence ---------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: As of January 1994, ACEDB has undergone a bifurcation. Those involved with C. elegans will want to to track the 2.x series under the stewardship of Richard Durbin and all other groups should probably track the 3.x series of Jean Thierry-Mieg. Thierry-Mieg writes "... 2 and 3 differ only at the level of displays ..." Version 2.0 was released in December, 1993 and version 3.0 was released in January, 1994. To retrieve the software see Q3. To be kept informed of new releases see Q10. [This question refers to the software not the C. elegans data.] ---------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: ACEDB currently runs on the following Unix systems, under X11: Unix: o Any machine running SunOS 4.x o SPARCstation 10 under Solaris [Probably all Solaris, then --bks] o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series o PC 386/486 with Linux (free Unix) o 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. o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu phil@decster.uta.edu MSDOS/Windows/NT: A port to NT is rumored to be in the works. Macintosh: A port to the Macintosh may become available real soon now. Beta versions of this *might* be found at the ACE archives. See Q3. Here is a note from Richard Durbin: There is now a tested Macintosh version. You need a Macintosh with >16Mb of memory and a decent monitor. You also need some way of obtaining the files from an ftp site (e.g. NCSA telnet, Versaterm Pro...) and Stuffit Deluxe, which I am told costs $65 in the USA, and is useful anyway for compressing/decompressing files. It turns out >that Stuffit Deluxe can decompress Unix .tar.Z archive files. Frank Eeckman has now made available a .tar.Z archive of a complete C. elegans ACEDB database, with updates already read in. Ftp to genome.lbl.gov, folder pub/macace, and follow the instructions in README. Thank you Frank. For cost savings, a combination of a high-end Intel platform with Linux appears very attractive. 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. [This section should be expanded to have a more thorough discussion of X11 interactions. --bks] ---------------------------------------------------------------------- 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. 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 ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alphabetic order by Database name --bks] 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 Availability : Curator : John Morris Current version: 1-5 Contact : curator@frodo.mgh.harvard.edu Last_update : Sept. 1993 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 : ACeDB Species : Caenorhabditis elegans Current version: 2-9 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@mrc-lmb.cam.ac.uk Contact : mieg@kaa.crbm.cnrs-mop.fr Last_update : March 1994 Database : AceMap Species : Homo Sapiens (Saccaromyces Pombe, Mus musculus in development) Focus : Physical mapping of human chromosomes X and 21 Curator : Hugues Roest Crollius Contact : hrc@gea.lif.icnet.uk PI : Hans Lehrach PI : Hugues Roest Crollius Last_update : 22 Feb 1994 Database : AGhDB Species : Gossipium hirsutum (cotton) PI : Leland Ellis Curator : Stephanie Crouch Last_update : March 1994 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html 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 Contact : Leland Ellis (leland@straylight.tamu.edu) Based_on : ACeDB-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 3.6.94 Data : as of 3.6.94 Revision : AAnDB for Aspergillus nidulans and ABtDB forBos 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 Database : ASbDB Species : Sorghum bicolor PI : Leland Ellis Curator : Stephanie Crouch Last_update : March 1994 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Database : ChlamyDB Species : Chlamydomonas PI : Elizabeth Harris Contact : chlamy@acpub.duke.edu Availability : Still under construction Last_update : 30 Sept. 1993 Database : EcoDB Species : E. coli PI : Staffan Bergh Contact : staffan@biochem.kth.se Availability : Still under construction Last_update : 11 Oct. 1993 Database : FlyBase Species : Drosophila melanogaster Availability : gopher or gopher+ ftp.bio.indiana.edu Availability : ACeDB-style interface to SyBase server due by end of 1994 Curator : Edward Welbourne Contact : eddy@gen.cam.ac.uk Contact : flybase@morgan.harvard.edu PI : William Gelbart PI : Michael Ashburner PI : Thomas Kaufman PI : Kathy Matthews PI : John Merriam Database : Flydb Species : Drosophila melanogaster Availability : by request only, via ftp Curator : Suzanna E. Lewis Contact : SELewis@lbl.gov Focus : STS content mapping project summary PI : Gerald Rubin PI : Mike Palazzolo PI : Dan Hartl PI : Alan Spradling Last_update : Sept. 1993 Database : GrainGenes Species : Wheat, barley, oats, relatives Availability : Gopher greengenes.cit.cornell.edu port 70 Availability : ACEDB version by ftp, on request from the curators 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:8000/acedbs/acedbs/graingenes/index.html 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 : Mace Species : Zea mays L. ssp. mays Focus : Maize genome Comment : Mace is the front end for maizedb, a relational (SYBASE) database. It is updated from maizedb by software written by Stan Letovsky. Maizedb is updated daily and will soon be accessible by public login. Curator : Ed Coe Curator : Pat Byrne Curator : Georgia Davis Curator : Mary Polacco Off-Site Curator : Marty Sachs Off-Site Curator : Christiane Fauron Off-Site Curator : Carolyn Wetzel Off-Site Curator : Steve Rodermel Off-Site Curator/Designer : Stan Letovsky Off-Site Curator/Designer : Mary Berlyn Systems Manager : Denis Hancock PI : Ed Coe Contact : maizedb@teosinte.agron.missouri.edu Last_update: 5 October 1993 Database : MycDB Species : Mycobacterium PI : Staffan Bergh PI : Thierry Garnier Contact : staffan@pasteur.fr Last_update : Sept. 1993 Database : RiceGenes Species : Rice (O. sative) Availability : under development, login at own risk Curator : Edie Paul Contact : epaul@nightshade.cit.cornell.edu Last_update : Sept. 1993 Database : SolGenes Coverage: Solanaceae - tomato, potato, pepper (eventually) Availability : Beta ACEDB via login or tar file Curator : Edie Paul Contact : epaul@nightshade.cit.cornell.edu Last_update : Sept. 1993 Database : SoyBase Species : Soybeans Curator : Lisa Lorenzen PI : Randy Shoemaker Contact : lorenzen@mendel.agron.iastate.edu Last_update : Sept. 1993 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 Availability : by request, via ftp, gopher Curator : Donn F. Davy Contact : DFDavy@lbl.gov Contact : aggarwal@genome.lbl.gov Focus : STS content mapping & sequencing of Human Chromosome 21 PI : Jasper Rine PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng Last_update : Sept. 1993 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 : ? Species : Sorghum PI : Leland Ellis Last_update : Sept. 1993 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 mapping of human chromosomes 22 and X Curator : Ian Dunham Contact : idunham@crc.ac.uk id1@sanger.ac.uk PI : Ian Dunham PI : David Bentley Last_update : 28 Sep 1993 [Curators: Please submit an entire paragraph in this format for inclusion or update. --bks] ---------------------------------------------------------------------- Q5: What written documentation exists for ACEDB? A5: The primary documents are included in the Software distribution in the wdoc subdirectory: 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-) You will find other interesting documents in the wdoc subdirectory. By anonymous ftp from ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb: doc.1_9.tar.Z 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. (1993) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press (in press). [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. (1993) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. (Academic Press) (review, in press). [text is available through ftp or gopher from weeds.mgh.harvard.edu] ---------------------------------------------------------------------- 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) 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. 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. 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://moulon.inra.fr/acedb/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. 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). ---------------------------------------------------------------------- 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. ---------------------------------------------------------------------- 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. ---------------------------------------------------------------------- Q9: What's all this about Gopher/WAIS/Anonymous 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. ---------------------------------------------------------------------- Q10: How can I get on 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. ---------------------------------------------------------------------- Q11: When and where is the Next ACEDB Workshop? Q11: From Jean Thierry-Mieg: DATES: The acedb '94 workshop will be held july 2 to 16, in Saint Matthieu de Treviers, a small village, 20 km north of Montpellier, at the foot of the Pic Saint Loup. HOUSING: We have booked a place meant for family vacations which includes ample space, a nice conference room and ten studios meant for 5 people (bathroom, shower, kitchenette, terrace, all nice and clean) that we plan to share among 3 to 4 participants. Meals will be taken at a local restaurant. The place is ideal for work and informal discussions and will be well equiped with computers. The situation is nice for hiking and allows volley-ball, ping-pong, tennis and petanque. We can provide lists of possible hotels for those who would prefer more privacy or find ways of accomodating families if you let us know very soon (school ends early july in France). Cost for 2 weeks is 1000 FF (about 200 US dollars) for housing on site plus 2500 FF for full meals. We may get enough funding to reduce this cost, but cannot pay for travel. PROGRAM: Formal presentations and general discussions will take place in the mornings and the evenings, alternating network aspects, data handling, displays and genome data analaysis. The afternoons will be dedicated to data manipulation, programming and writing documentation. The idea is to actually implement during the meeting many of the ideas that will come up, to fuse and coallesce the now numerous acedb-based applications into a working modular package, and to import and consolidate large sets of additional data. Towards this goal, we will broadcast the following announcement ACEDB'94 Genome Database Workshop. Montpellier, July 2-16, 1994 This meeting will cover the use and development of the ACEDB database manager central to several major genome projects, including C.elegans, A.thaliana, human, and a number of other plant and animal species. We wish to encourage people with large sets of data on other organisms to attend this workshop. They will be helped to build, during the meeting, a friendly graphic presentation of their own data, in return for discussing their own experience. ******************************************************************* FORMAT: This meeting will be much longer than the 2 previous acedb workshops (Cambridge 92 and Boston 93), in the hope of initiating new collaborations and allowing concrete results. This format is usual in physics summer schools and often very productive. The workshop may be coupled to a 2 days presentation of acedb, open to the general audience, and yet to be organised. We anticipate at least the participation of people from: Berkeley, Boston, Cambridge, Heidelberg and Montpellier, including Richard Durbin (LMB and Sanger Centre, Cambridge), John McCarthy (LBL, Berkeley), Otto Ritter (DKFZ, Heidelberg), Danielle and Jean Thierry-Mieg (CNRS, Montpellier). Please confirm your participation and forward this announcement to your colleagues. Danielle and Jean Thierry-Mieg CNRS-CRBM BP 5051, 34033 Montpellier, France. email mieg@kaa.crbm.cnrs-mop.fr (if this address fails, fall back on mieg@ncbi.nlm.nih.gov) Tel: (33) 67 61 33 24 Fax: (33) 67 52 15 59 ---------------------------------------------------------------------- Q411:Who contributed to this document? [Note to international readers: 411 is the phone number for information in the USA. --bks] A411: 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 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 Office of the Plant Genome, USDA ARS. ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Sun Mar 20 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!lfevold From: lfevold@iastate.edu (Linda J Fevold) Newsgroups: bionet.software.acedb Subject: Any information about Acedb Date: 21 Mar 1994 18:56:14 GMT Organization: Iowa State University, Ames, IA Lines: 3 Distribution: usa Message-ID: <2mkqke$p5v@news.iastate.edu> NNTP-Posting-Host: bus1.iastate.edu -- Linda Fevold lfevold@iastate.edu From owner-acedb@net.bio.net Sun Mar 20 22:00:00 1994 Path: biosci!MIRANDA.UMDS.AC.UK!fsymons From: fsymons@MIRANDA.UMDS.AC.UK (Fernley Symons) Newsgroups: bionet.software.acedb Subject: (none) Date: 21 Mar 1994 11:52:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <1842.9403211940@miranda.umds.ac.uk> NNTP-Posting-Host: net.bio.net unsubscribe From owner-acedb@net.bio.net Mon Mar 21 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!EU.net!howland.reston.ans.net!agate!dog.ee.lbl.gov!overload.lbl.gov!slavsing.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Proposed Extensions for ACEDB Query Builder Followup-To: bionet.software.acedb Date: 22 Mar 1994 19:22:37 GMT Organization: Lawrence Berkeley Laboratory Lines: 210 Message-ID: NNTP-Posting-Host: slavsing.lbl.gov Proposed Extensions for ACEDB Query Builder We'd like your suggestions on proposed Query Builder extensions to make it clearer and permit certain types of queries it currently does not do: I. "Follow" to another class via a tag in the current class; and II. "Next" where there are multiple data fields with a single tag. REVIEW OF CURRENT QUERY BUILDER INTERFACE The current query builder has boxes to fill in as shown below. Here pipes and underscores are used to simulate boxes, % to indicate an editable area selectable by mouse, and @ to represent downward pointing triangles which can be clicked to bring up a list window for permissible values that can be mouse selected for entry in that particular box. (you must display this in a monospace font to line up things correctly in their respective boxes). Query Builder:(Click right mouse button on the shaded boxes for choices) +---------------+ Find and select |%%%%%%%%%%%%% @| items +---------------+ +----------------+ +----------+ +--------+ +-----------+ where |%%%%%%%%%%%%%% @| |%%%%%%%% @| |%%%%%% @| |%%%%%%%%% @| +----------------+ +----------+ +--------+ +-----------+ The first box is used to specify class, while the four on the next line are used to specify tag, operator, value and conjunction, respectively. Values displayed in the list for are determined by the CLASS selected on the first line. If a conjunction other than the default "END" is specified, Query Builder automatically creates another "where" line to be filled in. There can be as many additional where lines as the user wishes. PROPOSED REVISIONS We propose to revise the current Query Builder as follows: A. change wording of first line to indicate triangles for choices; B. delete "and select" before first box and add "class" after it; C. add type of information below each box to help user understanding; D. in conjunctions list, substitute default "to get keyset." for END; E. add "and next field" to the conjunctions list; F. add "and follow" at the end of the conjunctions list; G. use different wording under tag box for "next" and "follow". The net result would look something like as follows: Query Builder: (click triangle in any box for choices) +-------------------------+ Find |%%%%%%%%%%%%%%%%%%%%%%% @| class items +-------------------------+ +----------------+ +----------+ +--------+ +-----------+ where |%%%%%%%%%%%%%% @| |%%%%%%%% @| |%%%%%% @| |%%%%%%%%% @| +----------------+ +----------+ +--------+ +-----------+ (A) proposes to drop pop-up menus as an alternate mechanism for getting lists of allowable values. There is a limitation of the widget currently being used for popup menus that prevents scrolling beyond the top or bottom of the window; so users cannot get at the bottom of very long lists. Until this shortcoming is overcome, it seems best to have a single mechanism -- namely the triangles that bring up separately scrollable windows (which must be dismissed before proceeding). (B) is a relatively minor change in wording to clarify what is being done. [Suggestions for improvement welcome!] The first (default) item on the class list would be changed to "ANY". (C) is intended to help clarify what goes in what box, and to differentiate what happens in lines after "and next field" or "and follow class" (see below). (D,E,F) The expanded list of conjunctions is proposed as follows: to get keyset. and or exclusive or and next field and follow class 1. The first list change is the simple default that terminates a query. The proposal is to change it from "END" to " "to get keyset." Although "END" is shorter, it is less intuitive. 2. The second change is to add a choice "and next field," the result of which would be to bring up an additional "where" line in which the user could specify some constraint on the second data field following the tag (and which would get translated into a "next" ACEDB query phrase). In this case, the label under the first box would change to " and the choices available for that box would be limited to the data fields following the first one in the model (indicated by putting the data type following the tag in that box -- e.g., "Float"). 3. The third conjunction list change is to add "and follow class." If a user chooses "and follow class", the Query Builder will automatically create another "where" line to be filled in, as it does for other conjunctions like "and" or "or." In this case, however, the label under the first box would change to ". The list that appears if the user clicks the triangle in that TAG box is a subset of those tags in the current class whose values are names of other ?Classes. The default operator would remain "exists" (as in the original line). Users can further restrict such "Follow" queries by filling in other operators and values to restrict the values of connected class objects thus chosen, or by choosing another conjunction and going on to another line in which they can specify restrictions on any tag in the connected class specified by the tag in the line following "and follow class." They can also go on to a third connected class by specifying another "and follow class" in the conjunction box. EXAMPLES A simple query might look like this (CAPS FOR VALUES FILLED IN): Find PAPER class items where YEAR > 1990 to get keyset. A query on a tag that had multiple fields might look like this: Find Locus class items where gMap exists and next field where FLOAT > 12 and where FLOAT < 20 to get keyset NOTE: evaluation remains on same data field if "and" is conjunction. An indirect (Follow) query might look as follows: Find GENE items where ITEM NAME CONTAINS ADH and follow class where CLONE ?Clone EXISTS and follow class where SEQUENCE ?Sequence EXISTS and where DNA CONTAINS AATTGG to get keyset I hope this example is more understandable (and legal) than my last one. The idea here is that we (1) find genes that contain the string ADH; (2) proceed to find any clones (a different class) connected to those genes where the clones have sequence information; and (3) get a keyset of clones from those where the DNA sequence contains the substring AATTGG. [Jean: is this ok?] Note that follow can occur after multiple specification of constraints and could even lead back through a class that was used for other purposes earlier in a prior line of the query. "SMART" DEFAULTS David Matthews has suggested that we consider inserting other default values in the initial Query Builder boxes, depending on context. Currently, QB can only be invoked from the main window, and it comes up with "ANY CLASS" in the class box, "ANY TAG" in the tag box, and "contains" in the operator box. One alternative would be to put the name of the class of the currently selected class (top left default) in the first box. If we knew other information (from another window? e.g., tree text display), we could put the currently selected tag in the box after "where" on the next line and could even fill in the other boxes with "equals", and "" if a data field is selected. I'm not sure how easy it is to get such information from a window other than the currently active (main) window. Another alternative might be to make the Query Builder invokable from the Tree Display, but that would add to the length of that already long menu. DISCUSSION The logic of our basic proposal seems OK, and the ACEDB query language already supports it. The problem is that the wording may not be sufficiently clear to help new users understand what is happening. Adding explanatory text below the boxes does add clutter and uses up more vertical real estate, but my hope is that it may help clarify what is going on -- especially for "and next field" and "and follow class." I would very much appreciate any advice about how we might better clarify things via further changes in wording, layout, or whatever. We would also appreciate comments & suggestions about "Smart Defaults." -- +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Mon Mar 21 22:00:00 1994 Path: biosci!UX5.LBL.GOV!suzi From: suzi@UX5.LBL.GOV (Suzanna Lewis) Newsgroups: bionet.software.acedb Subject: Re: ACEDB mailing lists Date: 22 Mar 1994 13:23:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403222124.AA10931@ux5.lbl.gov> NNTP-Posting-Host: net.bio.net ----- Begin Included Message ----- What's the symptom? Is this why when I doubleclick too fast the window system locks up (ignores all mouse and keyboard input, though the clock and perfmeter keep running) and I have to kill xace, and about half the time have to kill the window system too? I never tried "Mouse pointer to focus". - Dave ----- End Included Message ----- Yes thats exactly what we were seeing. The non-fix "fix" is to go to the openlook Properties window for the Miscellaneous category and there you'll find an option for "Set Input Area". The default is "Click SELECT". What works for acedb is "Move Pointer". Just apply this change and a lot of the ace lockups will dissapear. Suzanna From owner-acedb@net.bio.net Mon Mar 21 22:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: ACEDB mailing lists Date: 22 Mar 1994 12:45:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403222049.AA03267@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > From suzi@ux5.lbl.gov Tue Mar 22 15:27:47 1994 > To: acedev@genome.lbl.gov, cherry@genome.stanford.edu > Subject: Re: ACEDB mailing lists > ... > > By the way, another one of those little pesky bugs. I may again > be the last to know, but here goes. If you are using openlook > make sure to change the default focusing scheme. "Click to focus" > doesn't work, it must be "Mouse pointer to focus". Otherwise ace > can get confused about which window has the focus and think that > none of the windows do. > > Suzanna What's the symptom? Is this why when I doubleclick too fast the window system locks up (ignores all mouse and keyboard input, though the clock and perfmeter keep running) and I have to kill xace, and about half the time have to kill the window system too? I never tried "Mouse pointer to focus". - Dave From owner-acedb@net.bio.net Mon Mar 21 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Lockup bug under Olwm. Date: 22 Mar 1994 21:37:03 GMT Organization: University of California, Berkeley Lines: 16 Message-ID: References: <9403222049.AA03267@greengenes.cit.cornell.edu> NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: matthews@GREENGENES.CIT.CORNELL.EDU's message of 22 Mar 1994 12:45:50 -0800 Yes, click to focus under Olwm will get Xace and the WM to not talk to each other anymore. The funny part about all of this is that the Programmers had all changed to "focus follows mouse" while the Biologists had never even heard of this. So they always got bit by the bug and it never bothered us. I've been tasked with fixing up the X widgets, handling WM_PROTOCOL and etc., but I first need a complete style guide for Ace widgets. With that in hand I'll be able to test to make sure that each does exactly what is intended. -- Henry J. Cobb hcobb@fly2.berkeley.edu, SFB Tyrant-for-life "yes, I also suspect that RMS is a MITI agent too." -- Piercarlo Grandi From owner-acedb@net.bio.net Tue Mar 22 22:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: a test - please ignore Date: 23 Mar 1994 06:21:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199403231421.AA02777@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net Detlef From owner-acedb@net.bio.net Tue Mar 22 22:00:00 1994 Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: extending Date: 23 Mar 1994 09:31:14 -0000 Lines: 1 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2mp292$p1i@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk i agree to post here rather than to acedev From owner-acedb@net.bio.net Tue Mar 22 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!trane.uninett.no!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: Lockup bug under Olwm. Date: 23 Mar 1994 09:03:35 -0000 Lines: 8 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2mp0l7$nqt@mserv1.dl.ac.uk> Original-To: hcobb@fly2.berkeley.edu the complete guide style for ace widget is that the user should not be bothered by silly bugs, this point/click to focus should not create a hang it is obviously part of the platform dependant code so should be fixed in xtsubs i guess, anyway totally outside of the mainstream ace code. From owner-acedb@net.bio.net Tue Mar 22 22:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: Proposed Extensions for ACEDB Query Builder Date: 22 Mar 1994 23:43:47 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 25 Message-ID: <2mnvrj$2o6@overload.lbl.gov> References: NNTP-Posting-Host: s27w007.pswfs.gov In article jlmccarthy@lbl.gov (John L. McCarthy) writes: >Proposed Extensions for ACEDB Query Builder So as not to appear ignorant, I thought that I would find the latest documentation on using the query language & the query builder. After about an hour I located a tar file in france that contains some PostScript files that expect A4 paper and some .tex files. I tried using the LaTex and dvips that I have access to, but the programs complained loudly and I gave up. So, I will run the risk of appearing ignorant: Where is the latest documentation on using the Query Language? Where is the latest documentation on using the Query Builder? Are there lots of nice examples? How do I print them here in the states? --bks p.s. Will add this to FAQ. -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Tue Mar 22 22:00:00 1994 Path: biosci!VECTOR.NALUSDA.GOV!scartinh From: scartinh@VECTOR.NALUSDA.GOV (Sam Cartinhour) Newsgroups: bionet.software.acedb Subject: ACEDB documentation Date: 23 Mar 1994 05:46:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403231344.AA17830@vector.nalusda.gov> NNTP-Posting-Host: net.bio.net Hi, Brad Sherman recently asked > Where is the latest documentation on using the Query Language? > Where is the latest documentation on using the Query Builder? > Are there lots of nice examples? > How do I print them here in the states? I am working on an ACEDB documentation server for www and am hoping it may help with these questions. It is intended to be a repository for the most recent ace documentation available. I would like to present ace information of all sorts, contributed by developers and curators, and solicit new as well as existing documentation. Topics will range from user manuals, manuals on how to configure acedb, code documentation for developers, descriptions of specific features, etc etc. I will of course need help!! I am not quite ready to open the server up for public inspection; it still needs some grooming. I think in a week or so perhaps.... sam From owner-acedb@net.bio.net Tue Mar 22 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: xv/ACEDB display on PC's Date: 23 Mar 1994 21:31:59 -0000 Lines: 49 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2mqcgf$4e@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk This message I just received looks relevant to the newsgroup: Date: Wed, 23 Mar 94 12:57:21 EST From: Russell Malmberg Message-Id: <9403231757.AA13867@dogwood.botany.uga.edu> To: rd@mrc-lmb.cam.ac.uk Subject: Acedb, xv, 256 colors Status: R This is something that I ran across, and I thought it might interest you since Acedb uses xv as an image viewer. Recently I've started using an Xwindows package to connect from my DOS-MS-Windows PC to the UNIX server on which the database is installed, (aatdb in this case). I had problems viewing color images on my pc using the xv program, either directly or through Acdb-aatdb. I discussed this with the company that made my Xwin package (MicroXwin from starnet, demo version on internet as "xwindemo") They maintain that there is a problem with xv and more than 256 colors over this kind of linkage. They sent me a FAQ that indicated it was something about depth 24 and 32 bits per pixel - I didn't understand it. So, I can get nice images this way if I configure my video driver and monitor to 256 colors, instead of my standard 65,000 colors. This might happen more in the future since: -- there are more people with PC-Xwindows pacages. -- currently available Windows-DOS systems come standard with powerful video drivers that are built for 65,000 or 16.7 million colors. These are easily re-configurable to 256 colors, by clicking a button and re-starting windows. So: If someone writes you and indicates more or less that they are getting a blank window for an image, or one with weird fuzzy lines -- and they are using an Xwindows to PC program -- you might advise them to switch to 256 colors. I'm not an expert on any of this. Its just what's happened to me so far in trying to use this snazzy linkage to f run Acedb -- aatdb. Russell Malmberg russell@dogwood.botany.uga.edu From owner-acedb@net.bio.net Tue Mar 22 22:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: xv 2.21 for Solaris? Date: 23 Mar 1994 09:15:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403231719.AA04344@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Does anybody have a copy of xv 2.21 that runs on Solaris 2.X? Thanks, - Dave From owner-acedb@net.bio.net Tue Mar 22 22:00:00 1994 Path: biosci!mii.lu.lv!mahinovs From: mahinovs@mii.lu.lv (Jurijs Mahinovs) Newsgroups: bionet.software.acedb Subject: help Date: 23 Mar 1994 08:32:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199403231627.AA03208@circenis.mii.lu.lv> NNTP-Posting-Host: net.bio.net help From owner-acedb@net.bio.net Wed Mar 23 22:00:00 1994 Path: biosci!GENOME.STANFORD.EDU!cherry From: cherry@GENOME.STANFORD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: Proposed Extensions for ACEDB Query Builder Date: 24 Mar 1994 10:17:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199403241818.KAA20661@aeffle.Stanford.EDU> References: <2msjav$m90@overload.lbl.gov> NNTP-Posting-Host: net.bio.net > > ... There is a file called doc.tar.Z > >which exists on all four servers: > > lirmm.lirmm.fr (193.49.104.10) in pub/acedb/ace2 > > cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb/ace2 > > ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb/ace2 > > bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/ace2 > > > In this there are 4 PostScript files: > configuration_guide.ps > installation_guide.ps > syntax.ps > users_guide.ps > which are very helpful. I was unable to print these --at first-- > as they are formatted for A4 paper and my HP LaserJet 4M printer > demanded that I put some in. So I told it that I had put some > in (a lie) and it seems to be printing them okay. > > I will add a note about this to the FAQ. (If anyone wants to > convert the .tex files to 8.5" x 11" format PostScript and > make these available via anonymous ftp, I'll add a pointer.) > > --bks The TeX and PostScript versions of these files are also on the ACEDB Developer's Archive, anonymous ftp to weeds.mgh.harvard.edu look in acedb_doc. The PostScript version print fine on normal US size paper. With the appropriate TeX software you can produce a copy of these papers for most any printer. Also note that in the directory acedb_dev there are many file that might be of interest to folks configuring ACEDB and utilities to convert files into Ace format. Mike From owner-acedb@net.bio.net Wed Mar 23 22:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: Proposed Extensions for ACEDB Query Builder Date: 24 Mar 1994 18:13:57 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 16 Message-ID: <2msl95$mih@overload.lbl.gov> References: <2mnvrj$2o6@overload.lbl.gov> <2mqk0e$cfj@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov In article jlmccarthy@lbl.gov (John L. McCarthy) writes: >As Sam Cartinhour has written in another message, the National Agricultural >Library will very shortly have an experimental WWW server for ACEDB >documentation, including the Syntax document. Excellent! By the way, there is an HTML version of the ACEDB-FAQ available. --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Wed Mar 23 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!dog.ee.lbl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: Proposed Extensions for ACEDB Query Builder Date: 24 Mar 1994 17:40:47 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 32 Message-ID: <2msjav$m90@overload.lbl.gov> References: <2mnvrj$2o6@overload.lbl.gov> <2mqk0e$cfj@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov Okay. I was ignorant. Here's a summary: > ... There is a file called doc.tar.Z >which exists on all four servers: > lirmm.lirmm.fr (193.49.104.10) in pub/acedb/ace2 > cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb/ace2 > ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb/ace2 > bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/ace2 In this there are 4 PostScript files: configuration_guide.ps installation_guide.ps syntax.ps users_guide.ps which are very helpful. I was unable to print these --at first-- as they are formatted for A4 paper and my HP LaserJet 4M printer demanded that I put some in. So I told it that I had put some in (a lie) and it seems to be printing them okay. I will add a note about this to the FAQ. (If anyone wants to convert the .tex files to 8.5" x 11" format PostScript and make these available via anonymous ftp, I'll add a pointer.) --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Wed Mar 23 22:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!slavsing.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Re: Proposed Extensions for ACEDB Query Builder Followup-To: bionet.software.acedb Date: 24 Mar 1994 16:08:43 GMT Organization: Lawrence Berkeley Laboratory Lines: 24 Message-ID: References: <2mnvrj$2o6@overload.lbl.gov> <2mqk0e$cfj@overload.lbl.gov> NNTP-Posting-Host: slavsing.lbl.gov In article <2mqk0e$cfj@overload.lbl.gov>, bks@s27w007.pswfs.gov (Bradley K. Sherman) wrote that he is unable to print syntax.ps or syntax.tex and asked "Is there any documentation for the query builder?" As Sam Cartinhour has written in another message, the National Agricultural Library will very shortly have an experimental WWW server for ACEDB documentation, including the Syntax document. Documentation for the Query Builder is included as part of ACEDB's Help. If you are in the Query Builder, simply click on the "Help" button. This documentation is included as part of the ascii help.wrm file. This on-line help will be revised when the proposed Query Builder extensions are implemented. -- +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Wed Mar 23 22:00:00 1994 Path: biosci!biosci!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb,bionet.announce Subject: MycDB release 1-5/3-5 Date: 23 Mar 1994 20:56:26 -0800 Organization: Biochemistry, KTH, Stockholm Lines: 133 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <2mp4a4$imq@kiev.physchem.kth.se> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software.acedb:194 bionet.announce:1025 MycDB 1-5/3-5 Stockholm & Paris March 18, 1994 The third release of the Mycobacterium database, MycDB, is now available. 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 Departement of Biochemistry at The Royal Institute of Technology in Stockholm, Sweden. MycDB is available free of charge via Internet network transfer. A complete description of the procedure to retrieve the software and database is available (see MycDB.Retrieval). If you are impatient, see the end of this message. Since last release of data, the database manager software has undergone some changes. Partly due to this fact and partly for administrative reasons this release comes in two versions called 1-5 and 3-5, where version 1-5 is configured for ace1 and 3-5 for ace3. Note that the two versions are NOT compatible with each other. There are also some changes to the models, requiring a complete reload of the database. In the future we will only support the ace3 version, so if you already have MycDB set up, consider changing to ace3 and if you do not have the software installed, do install ace3. Addresses and instructions are in the file MycDB.Retrieval. MycDB uses the excellent database software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg (CNRS, France). The ACEDB software allows the user to browse information by simply pointing and clicking with the workstation mouse. A variety of powerful query methods are also available. However, our experience is that most users choose the mouse interface to find the information they are interested in. As far as possible all information is connected to other information in the database. The database software presents the information in separate windows that allow many parts of the database to be viewed at one time. There are also many paths to any piece of information, allowing the user to easily navigate the connections between the various types of information. 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://kiev.physchem.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 Departement of Biochemistry, KTH: http://kiev.physchem.kth.se/MycDB.html The ftp server at the Departement of Biochemistry, KTH: kiev.physchem.kth.se (130.237.52.64) in pub/MycDB The ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in pub/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 Mar 23 22:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: Proposed Extensions for ACEDB Query Builder Date: 23 Mar 1994 23:39:58 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 42 Message-ID: <2mqk0e$cfj@overload.lbl.gov> References: <2mnvrj$2o6@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov In article <2mnvrj$2o6@overload.lbl.gov> bks@s27w007.pswfs.gov (Bradley K. Sherman) writes: > >So as not to appear ignorant, I thought that I would find the latest >documentation on using the query language & the query builder. After >about an hour I located a tar file in france that contains some >PostScript files that expect A4 paper and some .tex files. I tried >using the LaTex and dvips that I have access to, but the programs >complained loudly and I gave up. Let me be clearer about this. There is a file called doc.tar.Z which exists on all four servers: lirmm.lirmm.fr (193.49.104.10) in pub/acedb/ace2 cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb/ace2 ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb/ace2 bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/ace2 This file when uncompressed and untar'ed has a variety of documentation. The files syntax.ps and syntax.tex document the query languate. But I cannot print them! My HP laserjet 4M printer which seems happy with most standard PostScript files complains and will not print the .ps files --though it does print the Postscript output of ACEDB. I am not a TeX maven, but I tried to convert the .tex file to PostScript using LaTex and dvips but could not as both programs gave error messages. So, how do I print these files? Is there any documentation for the query builder? --bks p.s. I do have hardcopy of the 10 Dec 92 document "Syntactic Definitions for the ACEDB Data Base Manager" but I have a feeling that this was given to me as hardcopy. -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Wed Mar 23 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: homology map Date: 24 Mar 1994 00:22:08 -0000 Lines: 65 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2mqmfg$ki8@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk Dear non-worm breeders I just finised writing for the next ace release (ace.3-1 due soon) 2 modif in the map and multimap display I want to explain here what i did to get feedback if that is not waht is needed. 1) maps I added in the Map model a line Symbol Text UNIQUE Text // class tag so that if present, in that map, object from class class will show with the name of their tag this can be obtained also if for the class in the option file you say -Symbol tag 2) Multimap the following ace file: **************************** MultiMap Test Map I.droso Map II.fly Anchor Locus In_Group Group_Member Locus d1 In_Group p1 Map I.droso Position 1.0 Locus d2 In_Group p2 Map I.droso Position 2.0 Locus d3 In_Group p3 Map I.droso Position 3.0 Locus f1 In_Group p1 Map II.fly Position 1.0 Locus f2 In_Group p2 Map II.fly Position 2.20 Locus f3 In_Group p3 Map II.fly Position 2.9 *************************** will make the mutimap test when clicked to come with joints between d1-f1, d2-f2, d3-f3 the magic tag is the tag Anchor the other names: Locus In_Group Group_Member are to the choice of the model designer On request i can send a prerelease. From owner-acedb@net.bio.net Wed Mar 23 22:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: homology map Date: 24 Mar 1994 10:50:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403241854.AA06267@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Hi Jean, your new Symbol and Anchor features look great as far as I understand them. I think the only thing I don't understand is: > MultiMap Test > Map I.droso > Map II.fly > Anchor Locus In_Group Group_Member > > Locus d1 > In_Group p1 > Map I.droso Position 1.0 > > ... > the magic tag is the tag Anchor > the other names: Locus In_Group Group_Member are to the choice of the > model designer I see how "In_Group" gets used in the Locus record. What does "Group_Member" do, and how do we use it? Also, "Locus" is magic too, right, to specify that "In_Group" is the tag used to anchor Locus objects? - Dave From owner-acedb@net.bio.net Thu Mar 24 22:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: user selection of Symbol and Anchor Date: 25 Mar 1994 11:57:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403251918.AA07701@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net 1. It would be nice if there were some way to allow the user to switch back and forth between two sets of Symbols (object labels used on the Map and Multimap displays). E.g. between the gene names used by researchers in each plant's own research community and the kingdom-wide names assigned by the Commission on Plant Gene Nomenclature. More generally, it would be empowering to let the user pick _any_ tag of the Locus (or other Map object) to use as source of the label. Wouldn't that be neat? Who knows what new information people might be able to spot just by looking at the values of all the tags arrayed against map position. 2. Also there should be some way for the user to select what tag to use as the Anchor. There's no way I'm going to be able to construct all the interesting multimaps in advance and load them as Multimap data, so the users are going to have to be able to make these by creating Tablemaker tables or editing existing ones. - Dave From owner-acedb@net.bio.net Thu Mar 24 22:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: homology map Date: 25 Mar 1994 10:38:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403251842.AA07631@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > ?Map Contains BAC ?BAC XREF Map > > ?BAC Map ?Map XREF BAC #map_location > Bac_Class ?BAC XREF Bac_Bunch > Bac_Bunch ?BAC XREF Bac_Class > > ## with ace file: > > Multimap bacMultiMap > Anchor "BAC" "Bac_Class" "Bac_Bunch" Okay, I understand what the first two parameters do. "BAC_Class" is the tag, of class "BAC", whose value is used to decide which BAC's in adjacent maps should be linked together on the multimap "bacMultiMap". What does "Bac_Bunch" do? - Dave From owner-acedb@net.bio.net Thu Mar 24 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: homology map Date: 25 Mar 1994 12:59:27 -0000 Lines: 36 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2mun7f$1si@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk Mored etail following a question by Matthews: I see how "In_Group" gets used in the Locus record. What does "Group_Member" do, and how do we use it? Also, "Locus" is magic too, right, to specify that "In_Group" is the tag used to anchor Locus objects? ### answer: Locus is the name of the class which uses the In_Group Group_Member tags but it is not magic i could invent now a new sort of clone, the butterfly aerodynamic chromosome or BAC the i will say ?Map Contains BAC ?BAC XREF Map ?BAC Map ?Map XREF BAC #map_location Bac_Class ?BAC XREF Bac_Bunch Bac_Bunch ?BAC XREF Bac_Class ## with ace file: Multimap bacMultiMap Anchor "BAC" "Bac_Class" "Bac_Bunch" this will work the Bac will be dispalyed in the vertical map and react as desired in the homology map although the compiled code has never heard as yet of butterflies. From owner-acedb@net.bio.net Tue Mar 29 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!concert!hearst.acc.Virginia.EDU!portal.gmu.edu!csi.gmu.edu!mark From: mark@csi.gmu.edu (Mark) Newsgroups: bionet.software.acedb Subject: Russian Biological Database Workshop Date: 29 Mar 1994 23:31:31 GMT Organization: George Mason University, Fairfax, Virginia, USA Lines: 152 Message-ID: <2nadoj$1oa@portal.gmu.edu> NNTP-Posting-Host: csi.gmu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: TIN [version 1.2 PL2] An Informal Workshop Biological Database Integration June 8 - June 10, 1994 Pushchino, Russia We invite friends and colleagues interested in the integration of biological databases to join us for an informal workshop in Pushchino, Russia, in late spring. There are substantial benefits be gained by successfully integrating existing biological databases. There are numerous Russian databases that need cross referencing with Western counter parts. Toward this end, we wish to foster an environment in which researchers exchange insights, data, and tools. This particular meeting will focus on topics relating to metabolism, since the new availability of DBEMP --- with its extensive encoding of the literature relating to metabolism --- will offer numerous categories of data that have not been available before. In addition, we will invite a number of representatives from the Russian scientific community to discuss their biological databases. It is, perhaps, worth noting that the Russian scientific community developed a major computational infrastructure similar to that which has developed in Europe, America and Japan. They created substantial collections of data ranging from small efforts done by single experts curating a limited class of data to huge collections on topics like metabolism, medicinal properties of compounds, 3D structural data, sequence data, culture collections, and genetic markers. We intend to provide a framework where the contents of these databases can be discussed examined, and compared with what is currently available in Europe and America. The meeting will be hosted by Evgenii Selkov, the leader of the team that has developed DBEMP over the past decade (the team now includes 24 individuals). The registration fee ($550 US), will cover housing and meals, as well as transportation to and from the Moscow airport (Pushchino is about 100 kilometers or so south of Moscow). In addition, each participant will be given a coupon worth $400 towards a purchase of DBEMP (normally sold at $400 for individuals and $4000 for commercial users). The database includes a detailed encoding of all of the quantitative data in over 10,000 articles on metabolism and enzymes. Graphical representations of the pathways described in DBEMP will also be available. A Prolog version of the pathways will also be made available, and we should be able to recast it to any other desired format on machines that will be available at the workshop. This meeting will not feature scheduled talks; rather, instead we envision organizing impromptu discussions on topics of common interest relating to the goal of integrating Russian biological databases with other international databases. We anticipate a fair amount of discussion relating to metabolism and enzymes, but other topics such as availability and exchange of data relating to phylogeny, alignments, compounds, motifs, and maps will certainly come up. We expect to spend about half of the time discussing the contents, use and how to curate the DBEMP, with its encoding of 10,000 articles on metabolism and enzymes. Informal presentations on the contents of this database, on how it can be connected to existing databases, and how it can be used to address specific computational problems will be discussed. We plan on offering tables that interrelate records in the DBEMP with specific enzyme numbers, specific organisms, and specific metabolic pathways. The remainder of the meeting will include poster sessions and informal demos by representatives of other database efforts within the FSU. We hope to include a number of the larger efforts, including databases relating to sequence analysis, the study of proteins, human genetics, medicine, and pharmacology. If you are actively involved in either the generation or use of integrated biological data, we urge you to consider joining us. Workshop supporters: Chris Beecher Anthony Bonner Terry Gaasterland Pat Gillevet Nat Goodman Niels Larsen Natalia Maltsev George Michaels Harold Morowitz Ross Overbeek Evgenii Selkov Rick Stevens Alexander Zamyatnin Registration Information The workshop is limited to 125 participants. To register for this workshop, complete the registration form and mail with your check made payable to George Mason University, or credit card authorization to: Center for Professional Development Business Office, Mail Stop 3G3 George Mason University Fairfax, VA 22030-4444 To register by FAX, fill out the form below and send it via FAX to 703/993-2112. Follow up by mailing the original enrollment form with your payment. Registration fees must be received by May 30, 1994. For further registration information, please call the Center for Professional Development at (703)993-2090. Center for Professional Development Mail Stop 3G3 Fairfax, Virginia 22030-4444 Workshop Questions can be directed to either Ross Overbeek (overbeek@mcs.anl.gov) George Michaels (gmichael@mason1.gmu.edu) *********************************************************************** NOTE: If you would like to use Mosaic to register for this conference, the URL is: "http://csi.gmu.edu/gsm/ConferenceForm.html" *********************************************************************** Russian Metabolic Database Conference Registration first_name = last_name = e-mail = title = organization = address = city = state = zip = phone = fax = payment_method = CHECK, MASTERCARD, VISA payment_amount = $550 Credit Card Authorization Credit Card Number: Expiration Date: Cardholder Name: Date: Authorizing Signature: From owner-acedb@net.bio.net Wed Mar 30 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: dateType Date: 31 Mar 1994 09:35:21 +0100 Lines: 15 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2ne209$er0@mserv1.dl.ac.uk> Original-To: net@nsfnet-relay.ac.uk I hope it is useful To insure better compatibility with OPM and to the request of Dertlef i introduced a new basic numeric type in acedb _DateType, to be used like _Int and _Float in models the whole code nows a bout it. It is internally a time_t and arithmetics can be preformed on it in particular the query can find the max min average off a set of dates, I am not sure if average works well by the way on dates. The input format is the "%c: unix format described in man ctime sois a string of char but it is internally converted to a time_t number This is part of the soon to be released ace.3-1 From owner-acedb@net.bio.net Thu Mar 31 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!slavsing.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Re: dateType Followup-To: bionet.software.acedb Date: 1 Apr 1994 00:10:54 GMT Organization: Lawrence Berkeley Laboratory Lines: 39 Distribution: bionet Message-ID: References: <2ne209$er0@mserv1.dl.ac.uk> NNTP-Posting-Host: slavsing.lbl.gov In article <2ne209$er0@mserv1.dl.ac.uk>, mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) wrote: > > I hope it is useful > To insure better compatibility with OPM and to the request of Dertlef > i introduced a new basic numeric type in acedb > _DateType, to be used like _Int and _Float in models > the whole code nows a bout it. > > It is internally a time_t and arithmetics can be > preformed on it in particular the query can find the max min average > off a set of dates, I am not sure if average works well by the way on > dates. > The input format is the "%c: unix format described in man ctime > sois a string of char but it is internally converted to a time_t number > > This is part of the soon to be released ace.3-1 I think this will be very useful. As I read man ctime, it says that %c is date and time as %x %X, where %x is date, using locale's date format; and %X is time, using locale's time format e.g, "Thu, 31 Mar 94 02:05:57 PST" If the format's are locale-dependent, could this cause problems if we are passing data among different locations in .ace files, and one location uses different date and time formats from another? If so, perhaps the default should be a locale-independent representation. -- +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Thu Mar 31 23:00:00 1994 Path: biosci!LBL.GOV!eademund From: eademund@LBL.GOV (Eric De Mund) Newsgroups: bionet.software.acedb Subject: Re: dateType Date: 31 Mar 1994 17:48:46 -0800 Organization: Lawrence Berkeley Laboratory, Genome Computing Group Lines: 51 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404010149.AA06082@csr.lbl.gov> Reply-To: Eric De Mund NNTP-Posting-Host: net.bio.net ACEDBers, Jean Thierry-Mieg : ] It is internally a time_t and arithmetics can be ] preformed on it in particular the query can find the max min average ] off a set of dates, I am not sure if average works well by the way on ] dates. ] The input format is the "%c: unix format described in man ctime ] sois a string of char but it is internally converted to a time_t number ] ] This is part of the soon to be released ace.3-1 John McCarthy : ] I think this will be very useful. ] ] As I read man ctime, it says that %c is date and time as %x %X, where ] %x is date, using locale's date format; and ] %X is time, using locale's time format ] ] e.g, "Thu, 31 Mar 94 02:05:57 PST" ] ] If the format's are locale-dependent, could this cause problems if we ] are passing data among different locations in .ace files, and one location ] uses different date and time formats from another? If so, perhaps the ] default should be a locale-independent representation. The internal representation, time_t, _is_ locale independent. It is the number of seconds since the epoch, which is defined to be Jan. 1, 1970, 00:00, Greenwich Mean Time. When producing an ASCII string: ctime(3V) integer seconds since ====================> ASCII string the epoch ctime(3V) takes into account the local timezone. The reverse direction: (pack a struct tm, then call) timelocal(3V) ASCII string ====================> integer seconds since the epoch takes as input a timezone (or the local timezone if none is specified) and produces the (locale-independent) number of seconds since the epoch. Hence it doesn't matter that the displayed representation of the time is not locale independent. Eric De Mund From owner-acedb@net.bio.net Thu Mar 31 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: kristoff (David Kristofferson) Newsgroups: bionet.software.acedb Subject: IMPORTANT BIOSCI INFORMATION Date: 1 Apr 1994 02:00:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 244 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199404011000.CAA21649@net.bio.net> NNTP-Posting-Host: net.bio.net Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending e-mail to biosci-help@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. 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For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: