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Path: senator-bedfellow.mit.edu!bloom-beacon.mit.edu!nic.hookup.net!swrinde!cs.utexas.edu!howland.reston.ans.net!agate!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: 14 Dec 1993 21:30:18 GMT Organization: Dendrome, A genome database for forest trees Lines: 652 Approved: news-answers-request@MIT.Edu Message-ID: <2elb9a$8mk@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-modifed: 12/14/93 Version: 1.6 Xref: senator-bedfellow.mit.edu bionet.software.acedb:96 news.answers:15809 ---------------------------------------------------------------------- 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. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web (WWW). The Universal Resource locator (URL) for it is: http://probe.nalusda.gov:8000/plant/acedbfaq.html [Until I get more familiar with HTML, it may not be as current as the plain ASCII FAQ. --bks] The latest version of the ACEDB FAQ should be available via anonymous ftp at net.bio.net as: /pub/BIOSCI/ACEDB/ACEDB.FAQ and at rtfm.mit.edu as: /pub/usenet/news.answers/bionet.software.acedb/ bionet.software.acedb.FAQ and via electronic mail from mail-server@rtfm.mit.edu. 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 ... 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: 1-10. It was released Summer 1993. There is apparently an upcoming bifurcation in the code. Durbin will be releasing a 2-x version concentrating on the Nematode project. Thierry-Mieg will be releasing a 3-x version with other features. 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: Any machine running SunOS 4.x e.g. Sun SPARCstation 1, 1+, 2, IPC, IPX. SPARCstation 10 under Solaris [Probably all Solaris, then --bks] DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series PC 386/486 with Linux (free 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. MSDOS/Windows/NT: A port to NT is rumored to be in the works. Macintosh: A port to the Macintosh may become available by the end of 1993. For cost savings, a combination of a high-end Intel platform with Linux appears very attractive. [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) genome/acedb cele.mrc-lmb.cam.ac.uk (131.11.84.1) pub/acedb ncbi.nlm.nih.gov (130.14.20.1) repository/acedb A typical session would be: ftp ncbi.nlm.nih.gov login: anonymous password: your email address cd repository/acedb binary ls get README get NOTES get INSTALL get bin.sparc.1_4.tar.Z quit ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alphabetic 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@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 Contact : staffan@biochem.kth.se Availability : Still under construction Last_update : 11 Oct. 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 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, 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-) 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: From Jean Thierry-Mieg: I am proposing to organize the 1994 acedb workshop Monday, June 6, to Saturday, June 18, in Cargese, Corsica. This place is equipped and used for summer school from may to october every year, this is the only slot yet available. The cost is around 3000F per person including lunch & lodging. Dinner is taken at the local village restaurant, or you can cook for yourself. It is possible to camp on site for free. The place is beautiful, nested on a private beach, with many trees around. And there is plenty of work space. I can find some funding to cover part of the local costs but certainly not pay for travels. The return ticket to Paris is around 1500 FF so 3000 + 1500 = 4500 FF around 900 US $. This can work if at least 40 people would come ideal is between 50 to 80. This may be too large for us. Could you please let me know ASAP if you are interested. I do not need a full commitment, but I have to evaluate the number of participants roughly. I hope 2 weeks would: a) let us enjoy a very pleasant place b) give us time for actual programming to take place on many problems There would be, I hope, plenty of cpu around. --Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr 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 using an WWW server (really http) with the Universal Resource Locator (URL) http://locus.nalusda.gov. 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. [This section will be expanded in the next version. We hope to make this document available as hypertext on the NAL server --bks] 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 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. ---------------------------------------------------------------------- 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.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: I am proposing to organize the 1994 acedb workshop Monday, June 6, to Saturday, June 18, in Cargese, Corsica. This place is equipped and used for summer school from may to october every year, this is the only slot yet available. The cost is around 3000F per person including lunch & lodging. Dinner is taken at the local village restaurant, or you can cook for yourself. It is possible to camp on site for free. The place is beautiful, nested on a private beach, with many trees around. And there is plenty of work space. I can find some funding to cover part of the local costs but certainly not pay for travels. The return ticket to Paris is around 1500 FF so 3000 + 1500 = 4500 FF around 900 US $. This can work if at least 40 people would come ideal is between 50 to 80. This may be too large for us. Could you please let me know ASAP if you are interested. I do not need a full commitment, but I have to evaluate the number of participants roughly. I hope 2 weeks would: a) let us enjoy a very pleasant place b) give us time for actual programming to take place on many problems There would be, I hope, plenty of cpu around. --Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr ---------------------------------------------------------------------- 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 USDA-ARS Plant Genome Database Project. ---------------------End of file acedb-faq----------------------------