From owner-acedb@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: tace can Read models Message-ID: <9310081748.AA06255@greengenes.cit.cornell.edu> Date: 8 Oct 93 17:48:25 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 8 Jean has just added "Read models" to the tace command set. I think now we should be able to do any administrative things we need to do to a remote ACEDB installation via scripts, without requiring the X11 interaction. I suppose this will be incorporated in the next release. If you want it sooner you can write me for the Sparc executable or the modified source file. - Dave From owner-acedb@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!agate!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb Subject: ACEDB Genome Database Software FAQ 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. Message-ID: <294oje$rde@overload.lbl.gov> Date: 8 Oct 93 22:11:58 GMT Reply-To: acedbfaq@s27w007.pswfs.gov Followup-To: bionet.software.acedb Organization: Dendrome, A genome database for forest trees Lines: 449 NNTP-Posting-Host: s27w007.pswfs.gov Archive-name: acedb-faq Last-modifed: 10/6/93 Version: 1.2 ---------------------------------------------------------------------- Common Questions and Answers about ACEDB. This document will be posted monthly to the Usenet newsgroup bionet.software.acedb. It is intended to be used as an index to ACEDB databases and to information about the database software. Errors of commission or omission are unintentional. Please send comments and corrections to acedbfaq@s27w007.pswfs.gov. Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. This FAQ has been submitted for approval for Usenet archival storage. It has also been submitted to the Bionet curator. --Bradley K. Sherman ---------------------------------------------------------------------- List of questions in the ACEDB FAQ: 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? 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 data about diverse species [see Q4]. ACEDB allows for automatic cross-referencing of items when loaded and allows for hypertextual navigation of the links using a mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the efforts 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: 1-10. It was released Summer 1993. The next release will be 2.0. (This refers to the software package.) ---------------------------------------------------------------------- Q2: What {hardware | software} do I need to run ACEDB? A2: ACEDB currently runs on the following Unix sytems, under X11: Any machine running SunOS 4.x. Sun SPARCstation 1, 1+, 2, IPC, IPX: SPARCstation 10 running Solaris: DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series PC 386/486 with Linux (public domain Unix) Other Unix: There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, NeXT, Convex. You may have to contact the developer responsible for the port to make these real. Macintosh: A port to the Macintosh may become available by the end of 1993. ---------------------------------------------------------------------- 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) genome/acedb cele.mrc-lmb.cam.ac.uk (131.11.84.1) pub/acedb ncbi.nlm.nih.gov (130.14.20.1) repository/acedb ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alpha order by Database name --bks] Database : AAnDB Species : Aspergillus nidulans PI : Leland Ellis Last_update : Sept. 1993 Database : AAtDB Species : Arabidopsis thaliana Availability : Curator : John Morris Current version: 1-5 Contact : curator@frodo.mgh.harvard.edu Last_update : Sept. 1993 Database : ACeDB Species : Caenorhabditis elegans Availability : Current version: 1-21 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@cele.mrc-lmb.cam.ac.uk Contact : mieg@kaa.cnrs-mop.fr Last_update : Sept. 1993 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 Last_update : Sept. 1993 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 Last_update : Sept. 1993 Database : Mace Species : Zea mays L. ssp. mays Focus : Maize genome Comment : Mace is the frontend for maizedb, a relational\ (SYBASE) database. It isupdated from maizedb by\ Stan Letovsky. Maizedb is updated daily and\ will soon beaccessible by guest 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, Pinus taeda Availability : contact curator 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 : Sept. 1993 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 : Bovine PI : Leland Ellis 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-) By anonymous ftp: doc.1_9.tar.Z --ncbi.nlm.nih.gov (130.14.20.1) repository/acedb You will find other interesting documents in the wdoc subdirectory. "An Introduction to ACeDB: For MycDB a Mycobacterium DataBase" is available. Try anonymous ftp at ftp.pasteur.fr (157.99.64.2) in pub/MycDB. [I could not find this document at first glance, so it may be part of the distribution itself which is in the same directory. Clarification from the curator would be helpful --bks.] ---------------------------------------------------------------------- Q6: Where can I find further information about ACEDB? A6: There is a Usenet Biosci conference titled bionet.software.acedb. 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: # Type=7 Name=ACEDB BioSci Electronic Conference Path=7/.index/acedb-biosci Host=genome-gopher.stanford.edu Port=70 (This is also courtesy of Mike Cherry.) If you do not have access to the Usenet you may receive the conference messages by e-mail. To subscribe to this service send email to biosci@net.bio.net requesting inclusion in the acedb-soft list and explicitly stating the e-mail address at which you wish to receive the mail. ---------------------------------------------------------------------- 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. ---------------------------------------------------------------------- Q411:Who contributed to this document? A411: Bradley K. Sherman (bks@s27w007.pswfs.gov) is currently managing this FAQ. Major contributions in getting it 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 ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Sat Oct 09 23:00:00 1993 Path: biosci!STOUT.STANFORD.EDU!cherry From: cherry@STOUT.STANFORD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: ACEDB FAQ Message-ID: <199310101747.AA04225@stout.Stanford.EDU> Date: 10 Oct 93 17:47:19 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 5 I wish to thank Brad for getting the ACEDB FAQ going. Its great! Thank you very much! Mike From owner-acedb@net.bio.net Sat Oct 09 23:00:00 1993 Path: biosci!STOUT.STANFORD.EDU!cherry From: cherry@STOUT.STANFORD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: models archive Message-ID: <199310101752.AA04240@stout.Stanford.EDU> Date: 10 Oct 93 17:52:39 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 38 Time for some subtle prodding. At the ACEDB Workshop in Boston it was agreed that everyone would donate copies of their models files to the developers archive. To date only three sets of models have been provided: ACeDB, MycDB and AAtDB. These are generally just a compressed tar file of the entire wspec directory. People also expressed an interest in having an archive of utilities available. So far we have scripts and C code provided by Donn Davy, Staffan Bergh and myself. (Thanks Donn and Staffan.) The documentation archive now has text of two papers and the notes of the Workshop by John McCarthy. The papers are: 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). 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). The names and addresses of all those attending the workshop in Boston are also available in the workshop directory. At the original ACEDB workshop everyone also agreed that an active archive would be very useful. However nothing was ever submitted. I hope this same situation is not going to occur again. If there is a desire for the archive to be useful please take action yourself. You can ftp into weeds.mgh.harvard.edu and put files in the acedb_dev/incoming directory. Please also include at least a short readme file. If you like you can just tell me where information can be obtained and I'll put it in the archive for you. Mike From owner-acedb@net.bio.net Sat Oct 09 23:00:00 1993 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: new utilities in the ACEDB Developers Archive Message-ID: <9310102112.AA07382@greengenes.cit.cornell.edu> Date: 10 Oct 93 21:12:07 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 17 In response to 'some gentle prodding', I put a couple of short scripts I've been using into weeds.mgh.harvard.edu:~ftp/acedb_dev/utilities. "gopherize" is for automatically dumping selected classes from an ACeDB database and waisindexing the resulting .ace-format files. Optionally (subcommand "new") it creates a menu link for your Gopher server. "mapm2ace" converts output from the Mapmaker 'map' or 'print chromosomes' command to .ace ?Locus records. Somewhere I read that the Archive's utilities directory was supposed to contain programs for converting data into .ace format. I hope people will also continue to add utilities that, like gopherize, ace2nal and sortpmap, do useful exports as well. HTML generators? Email servers? - Dave Matthews From owner-acedb@net.bio.net Sun Oct 10 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!agate!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb Subject: ACEDB Genome Database Software FAQ 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. Message-ID: <294oje$rde@overload.lbl.gov> Date: 8 Oct 93 22:11:58 GMT Reply-To: acedbfaq@s27w007.pswfs.gov Followup-To: bionet.software.acedb Organization: Dendrome, A genome database for forest trees Lines: 449 NNTP-Posting-Host: s27w007.pswfs.gov Archive-name: acedb-faq Last-modifed: 10/6/93 Version: 1.2 ---------------------------------------------------------------------- Common Questions and Answers about ACEDB. This document will be posted monthly to the Usenet newsgroup bionet.software.acedb. It is intended to be used as an index to ACEDB databases and to information about the database software. Errors of commission or omission are unintentional. Please send comments and corrections to acedbfaq@s27w007.pswfs.gov. Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. This FAQ has been submitted for approval for Usenet archival storage. It has also been submitted to the Bionet curator. --Bradley K. Sherman ---------------------------------------------------------------------- List of questions in the ACEDB FAQ: 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? 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 data about diverse species [see Q4]. ACEDB allows for automatic cross-referencing of items when loaded and allows for hypertextual navigation of the links using a mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the efforts 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: 1-10. It was released Summer 1993. The next release will be 2.0. (This refers to the software package.) ---------------------------------------------------------------------- Q2: What {hardware | software} do I need to run ACEDB? A2: ACEDB currently runs on the following Unix sytems, under X11: Any machine running SunOS 4.x. Sun SPARCstation 1, 1+, 2, IPC, IPX: SPARCstation 10 running Solaris: DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series PC 386/486 with Linux (public domain Unix) Other Unix: There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, NeXT, Convex. You may have to contact the developer responsible for the port to make these real. Macintosh: A port to the Macintosh may become available by the end of 1993. ---------------------------------------------------------------------- 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) genome/acedb cele.mrc-lmb.cam.ac.uk (131.11.84.1) pub/acedb ncbi.nlm.nih.gov (130.14.20.1) repository/acedb ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alpha order by Database name --bks] Database : AAnDB Species : Aspergillus nidulans PI : Leland Ellis Last_update : Sept. 1993 Database : AAtDB Species : Arabidopsis thaliana Availability : Curator : John Morris Current version: 1-5 Contact : curator@frodo.mgh.harvard.edu Last_update : Sept. 1993 Database : ACeDB Species : Caenorhabditis elegans Availability : Current version: 1-21 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@cele.mrc-lmb.cam.ac.uk Contact : mieg@kaa.cnrs-mop.fr Last_update : Sept. 1993 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 Last_update : Sept. 1993 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 Last_update : Sept. 1993 Database : Mace Species : Zea mays L. ssp. mays Focus : Maize genome Comment : Mace is the frontend for maizedb, a relational\ (SYBASE) database. It isupdated from maizedb by\ Stan Letovsky. Maizedb is updated daily and\ will soon beaccessible by guest 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, Pinus taeda Availability : contact curator 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 : Sept. 1993 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 : Bovine PI : Leland Ellis 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-) By anonymous ftp: doc.1_9.tar.Z --ncbi.nlm.nih.gov (130.14.20.1) repository/acedb You will find other interesting documents in the wdoc subdirectory. "An Introduction to ACeDB: For MycDB a Mycobacterium DataBase" is available. Try anonymous ftp at ftp.pasteur.fr (157.99.64.2) in pub/MycDB. [I could not find this document at first glance, so it may be part of the distribution itself which is in the same directory. Clarification from the curator would be helpful --bks.] ---------------------------------------------------------------------- Q6: Where can I find further information about ACEDB? A6: There is a Usenet Biosci conference titled bionet.software.acedb. 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: # Type=7 Name=ACEDB BioSci Electronic Conference Path=7/.index/acedb-biosci Host=genome-gopher.stanford.edu Port=70 (This is also courtesy of Mike Cherry.) If you do not have access to the Usenet you may receive the conference messages by e-mail. To subscribe to this service send email to biosci@net.bio.net requesting inclusion in the acedb-soft list and explicitly stating the e-mail address at which you wish to receive the mail. ---------------------------------------------------------------------- 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. ---------------------------------------------------------------------- Q411:Who contributed to this document? A411: Bradley K. Sherman (bks@s27w007.pswfs.gov) is currently managing this FAQ. Major contributions in getting it 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 ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Fri Oct 15 23:00:00 1993 Path: biosci!S27W007.PSWFS.GOV!bks From: bks@S27W007.PSWFS.GOV (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Test of gateway to bionet.software.acedb Message-ID: <9310162215.AA07694@s27w007.pswfs.gov> Date: 16 Oct 93 22:15:31 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 7 I don't think that postings to acedb@net.bio.net are making it through to bionet.software.acedb. This is a test. [Mailed 10/16/93 15:20 PST] --bks From owner-acedb@net.bio.net Wed Oct 20 23:00:00 1993 Path: biosci!S27W007.PSWFS.GOV!bks From: bks@S27W007.PSWFS.GOV (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Test 2 of gateway Message-ID: <9310201702.AA01028@s27w007.pswfs.gov> Date: 20 Oct 93 17:02:05 GMT Sender: shibumi@net.bio.net Distribution: biosci Lines: 13 This is being mailed to acedb@net.bio.net. It should appear in the Biosci conference bionet.software.acedb. The gateway was *not* working, but should be now, according to the Biosci folk. [Oct. 20, 1993 10AM PST] --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 Tue Oct 26 22:00:00 1993 Path: biosci!GENOME1.BIO.BNL.GOV!willy From: willy@GENOME1.BIO.BNL.GOV (Willy Crockett) Newsgroups: bionet.software.acedb Subject: help Message-ID: <9310271347.AA15331@genome1.bio.bnl.gov.genome1> Date: 27 Oct 93 13:47:09 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 8 Does anyone know of any programs or script files that can process genbank files into an ACeDB database running on a SUN UNIX system? -Willy Crockett Email address willy@genome1.bio.bnl.gov From owner-acedb@net.bio.net Tue Oct 26 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!s850.mwc.edu!s850.mwc.edu!not-for-mail From: sgough@s850.mwc.edu (stephen gough) Newsgroups: bionet.software.acedb Subject: MCAT Prep. Software Avail.? Message-ID: <2am87kINNcu@s850.mwc.edu> Date: 27 Oct 93 16:39:16 GMT Organization: Mary Washington College, CPSC Dept. Lines: 12 NNTP-Posting-Host: s850.mwc.edu X-Newsreader: TIN [version 1.1 PL9] One of my students is looking for software for the Mac that will help her prepare for the MCAT. If anyone knows of vendors/products that apply, please let me know. Also, if you are familiar w/ a particular product your assessment of its value would be helpful. Thanks. Steve Gough Biol. Sciences Mary Washington College Fredericksburg, VA sgough@s850.mwc.edu From owner-acedb@net.bio.net Tue Oct 26 22:00:00 1993 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: help Message-ID: <9310271759.AA22688@greengenes.cit.cornell.edu> Date: 27 Oct 93 17:59:01 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 11 > Does anyone know of any programs or script files that can > process genbank files into an ACeDB database running on a > SUN UNIX system? > > -Willy Crockett > Email address willy@genome1.bio.bnl.gov There are a couple in the ACEDB Developer's Archive, weeds.mgh.harvard.edu: acedb_dev/utilities. - Dave Matthews