From owner-acedb@net.bio.net Mon Jan 10 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!emory!usenet From: bcresas@bimcore.emory.edu (Scott Sammons) Newsgroups: bionet.software.acedb Subject: Problems executing xace Date: 11 Jan 1994 16:32:06 GMT Organization: Biomolecular Computing Resource, Emory University Lines: 28 Distribution: world Message-ID: <2guka6INNls0@emory.mathcs.emory.edu> Reply-To: bcresas@bimcore.emory.edu NNTP-Posting-Host: bimcore.cc.emory.edu I'm having a problem getting acedb to run properly. When I type acedb, I get the following error message: ld.so.1: xace: fatal: libXaw.so.5: can't open file: errno=2 Killed libXaw.so.5 is found in /usr/openwin/lib which is The strange thing is that I can get it to work if I am the owner of the executable xace. Is something wrong with my setuid? The setuid looks like: # ls -l xace -rwsr-xr-x 1 gcgadmin staff 1032732 Dec 23 10:06 xace I don't think that it's my LD_LIBRARY_PATH since when I log in as gcgadmin, my LD_LIBRARY_PATH is the same as other userids that fail to work. Thanks, Scott Sammons ============================================================================== | Scott A. Sammons (404) 727-2780 | | Emory University FAX: (404) 727-3659 | | Biomolecular Computing Resource Internet: sammons@bimcore.emory.edu | | 3025 Rollins Research Center | | Atlanta, GA 30322 | ============================================================================== From owner-acedb@net.bio.net Mon Jan 10 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Dave Matthews" Newsgroups: bionet.software.acedb Subject: syntax for -A aliasing? Date: 11 Jan 1994 20:45:38 -0000 Lines: 9 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gv35i$p4i@mserv1.dl.ac.uk> Original-To: acedb@net.bio.net Is the Alias command -A in .ace files supposed to be working? If so, what is the syntax? I can do Rename with -R Colleague : "Old Name" "New Name" , but -A gives error message "Unrecognized Class -A". (This is using xace version 1-10). - Dave Matthews From owner-acedb@net.bio.net Wed Jan 12 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Dave Matthews" Newsgroups: bionet.software.acedb Subject: REPLIES: syntax for -A aliasing? Date: 13 Jan 1994 21:42:20 -0000 Lines: 26 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2h4f7s$gbl@mserv1.dl.ac.uk> Original-To: acedb@net.bio.net > To: acedb@net.bio.net > From: "Dave Matthews" > Subject: syntax for -A aliasing? > Date: 11 Jan 1994 20:45:38 -0000 > > Is the Alias command -A in .ace files supposed to be working? If so, what > is the syntax? I can do Rename with > > -R Colleague : "Old Name" "New Name" > > , but -A gives error message "Unrecognized Class -A". (This is using xace > version 1-10). Jean replied that it didn't work, so he fixed it: : if you need it badly i can send a fixed ace2/3 source code Richard pointed out some problems with using the Alias feature, either via ..ace files or the menu: : I don't know if it works or not. We don't use it because it doesn't dump : out in ace format, so is not preserved properly in updates etc. It works : internally, but I think is a potential source of confusion and errors, until : we can automatically keep track for the aliased-to object of all its alias : names. From owner-acedb@net.bio.net Thu Jan 13 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "" Newsgroups: bionet.software.acedb Subject: Release 1.0 of an image analysis package for fingerprint gels Date: 14 Jan 1994 12:29:58 -0000 Lines: 27 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2h6386$n2d@mserv1.dl.ac.uk> Original-To: rmott@gea.icnet.uk, mieg@ppsw.cam.ac.uk, ung@ash.tree.caltech.edu, spark@ic.ac.uk, acedb@net.bio.net Release 1.0 of Image, an image analysis package for fingerprint gels -------------------------------------------------------------------- We have written an integrated program for image analysis of physical mapping fingerprint gels for use at the Sanger Centre. This runs on Unix workstations using X11 for display. It incorporates the VAX film scanning software of Sulston et al. (CABIOS 5, 101-106, 1989) and uses the ACEDB graphics package. It analyses scanned fingerprint gels, finding lanes, extracting bands from lanes, and correcting for gel distortion by aligning known standard marker lanes. At each stage there are hand editing tools for correcting errors. The output format can be read by the Contig9 fingerprint assembly routines being integrated into ACEDB. The package is available by anonymous ftp from rona.sanger.ac.uk (193.60.84.39), in directory /pub/image. Read the files README in /pub/image and TUTORIAL in the untarred archive for further information. Friedemann Wobus (fw@sanger.ac.uk) Richard Durbin (rd@sanger.ac.uk) From owner-acedb@net.bio.net Mon Jan 17 22:00:00 1994 Path: biosci!s.u-tokyo!kuis-news!wnoc-kyo-news!oskgate0.mei!chorus.mei!panasonic.com!newsserver.jvnc.net!darwin.sura.net!gatech!howland.reston.ans.net!agate!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 17 Jan 1994 19:34:48 GMT Organization: Dendrome, A genome database for forest trees Lines: 640 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <2hep8o$f47@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: 1/17/94 Version: 1.7 Xref: biosci bionet.software.acedb:138 news.answers:11497 ---------------------------------------------------------------------- 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: 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 real soon now. 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 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 : 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 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: 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://mouIon.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. ---------------------------------------------------------------------- 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 $. This can work if at least 40 people would come ideal is between 50 to 80. This may be too large for us. Could you please let me know ASAP if you are interested. I do not need a full commitment, but I have to evaluate the number of participants roughly. I hope 2 weeks would: a) let us enjoy a very pleasant place b) give us time for actual programming to take place on many problems There would be, I hope, plenty of cpu around. --Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr ---------------------------------------------------------------------- Q411:Who contributed to this document? [Note to international readers: 411 is the phone number for information in the USA. --bks] A411: Major contributions in getting this FAQ off the ground were made by John McCarthy and Mike Cherry. Other contributors include: Lisa Lorenzen David Matthews Edie Paul Donn Davy Eric De Mund Sam Cartinhour To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA-ARS Plant Genome Database Project. ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Wed Jan 19 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Acedb 94 worshop Date: 20 Jan 1994 15:18:35 -0000 Lines: 95 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2hm7cb$hkq@mserv1.dl.ac.uk> Original-To: acedb_distrib@lirmm.lirmm.fr acedb '94 ******************************************************************* 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.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 ******************************************************************* ******************************************************************* From owner-acedb@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Dave Matthews" Newsgroups: bionet.software.acedb Subject: new Multimap feature requested Date: 25 Jan 1994 18:53:08 -0000 Lines: 51 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i3pqk$p4p@mserv1.dl.ac.uk> Original-To: mieg@kaa.cnrs-mop.fr Hello Jean, greetings from Plant Genome II! We have a request for a modification of the Multimap function for you, based on discussions with the various groups here (all of whom are showing immense enthusiasm for ACEDB, by the way.) Much of the scientific excitement in plant genomic mapping over the last year has been about the surprisingly high degree of synteny exhibited by relatively distantly related species, and now people want to put together inter-species databases in ACEDB. A problem that arises in doing this with regard to the multimap is that frequently the 'same' (homoeologous) gene or locus is called by different names in different species. The multimap currently only connects common loci by keying on the fact that they are literally the same locus, i.e. they have the same name. John McCarthy and I are thinking that the ideal solution would be if some other tag within the ?Locus object could be used to determine which loci are tied together in the Multimap. Perhaps this tag could be chosen using an option in options.wrm, analogous to the -Title option. E.g. -Title Tag : If present in some object of that class, the text following will be used preferentially when referring to that object. -Multimap Tag : If present, the text following will be used as the key for Multimap comparisons. Then if we set the option '-Multimap Homoeologue_name' for example, the following loci would be tied together when displayed on the multimap: Locus : "cab 22L" Homoeologue_name "Lhcb1" gMap Petunia-6 121 Locus : "Cab-1C" Homoeologue_name "Lhcb1" gMap Pepper-2 143 Locus : "Lhcb1" Homoeologue_name "Lhcb1" gMap Tomato-2 156 Further it would be nice if the names shown on the multimap could be the actual locus names rather than the homoeologue names. I.e. to allow the user to select which map's nomenclature to display, or to show all nomenclatures beside their respective maps. What do you think? best regards, - Dave Matthews, John McCarthy, Lisa Lorenzen, Sam Cartinhour From owner-acedb@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: multimap idea Date: 25 Jan 1994 20:31:08 -0000 Lines: 4 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i3vic$dm@mserv1.dl.ac.uk> Original-To: mieg@ppsw.cam.ac.uk I like the idea from Matthews et al. I also wanted to say I like the 21 database with its multimaps very much. From owner-acedb@net.bio.net Tue Jan 25 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!xlink.net!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!think.com!mbcrr!shih From: shih@mbcrr.dfci.harvard.edu (Deborah Shih) Newsgroups: bionet.software.acedb Subject: ignore test Date: 26 Jan 1994 07:36:10 GMT Organization: Dana-Farber Cancer Institute Lines: 7 Distribution: bionet Message-ID: <2i56haINN1mp@early-bird.think.com> NNTP-Posting-Host: mbcrr.harvard.edu Sorry, just a test posted 02:30 EST Jan 26, 1994 From owner-acedb@net.bio.net Tue Jan 25 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: kirbym@har-rbu.mrc.ac.uk Newsgroups: bionet.software.acedb Subject: homologous genes Date: 26 Jan 1994 15:42:51 -0000 Lines: 59 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i631r$ipm@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk In a recent message posted to this bulletin board by Mathews et al, they say: > Much of the scientific excitement in plant genomic mapping over the last year > has been about the surprisingly high degree of synteny exhibited by > relatively distantly related species, and now people want to put together > inter-species databases in ACEDB. A problem that arises in doing this with > regard to the multimap is that frequently the 'same' (homoeologous) gene or > locus is called by different names in different species. The multimap > currently only connects common loci by keying on the fact that they are > literally the same locus, i.e. they have the same name. and suggest that a tag within the ?Locus object be used to determine which loci are tied together in the Multimap. It's a good idea. However, we have other dificulties with regard to homologous data. There are some species which have homologous genes but the symbols are exactly the same. For example, the human, cow and sheep nomenclature. As you can imagine, trying to store information with the same key causes quite a few problems. To get around this, Jo Dicks and myself decided to use a species prefix for all homologous data and keep the actual symbol as a Text tag. Eg Locus : "HsABL" Symbol : "ABL" Locus : "BvABL" Symbol : "ABL" In fact, if this is done, all data items within the database need to have a species prefix. But when it comes to displaying the data (whether on the maps or in the keySet) we only want the symbol for that individual species, not the symbol with the species prefix. I tried to modify the genetic map code to do this but there are problems. Could someone help me fix my code or if enough people want this facility, could Jean and the acedb team offically implement this please. The data structure for handling data objects to be displayed on the genetic map is the SEG. It usually consists of the object's key, a few flags and the object's position. Instead of using the key to display the object's name (ie gene symbol) I have tried using a character pointer from within the SEG structure. In the gMapConvert routine, this is set to point to the text defined by the Symbol Tag definition in the ?Locus object. (ie is a Text tag, not ?Text tag.) If this is done and later on you try and retrieve the Symbol text, the data is corrupted and appears scrambled. This is a pity because the only alternative which I have found that works is: for each data object on the genetic map, retrieve its data (ie create an OBJ for it) and then find the relevant data within the object for display. It slows the map display down considerably and I am sure there is a better way. How is one expected to get help with acedb problems? Do you use this bulletin board, or do you email Jean directly? Michelle Kirby (email kirbym@uk.ac.mrc.har-rbu) Jo Dicks (email jld@uk.ac.ox.bioch) From owner-acedb@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: multimap idea Date: 27 Jan 1994 22:22:43 -0000 Lines: 13 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i9erj$99c@mserv1.dl.ac.uk> Original-To: acedb@net.bio.net I like the idea of Matthews and Kirby i can implement that as suggested by Mathhews, it will also solve Kirby's problem and I think Danielle's requirement of easier access to homologies. The reason the Text does not work is that a Text is only on disk and its char* is only transient You can only store in seg a KEY then display name(seg->key_of_homology) The notion of -Multipmap like -Title in options is excellent i think more on that in a few days, i ll try to implement that very soon. From owner-acedb@net.bio.net Fri Jan 28 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: multimap idea Date: 25 Jan 1994 20:31:08 -0000 Lines: 4 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i3vic$dm@mserv1.dl.ac.uk> Original-To: mieg@ppsw.cam.ac.uk I like the idea from Matthews et al. I also wanted to say I like the 21 database with its multimaps very much. From owner-acedb@net.bio.net Fri Jan 28 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: "Dave Matthews" Newsgroups: bionet.software.acedb Subject: new Multimap feature requested Date: 25 Jan 1994 18:53:08 -0000 Lines: 51 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i3pqk$p4p@mserv1.dl.ac.uk> Original-To: mieg@kaa.cnrs-mop.fr Hello Jean, greetings from Plant Genome II! We have a request for a modification of the Multimap function for you, based on discussions with the various groups here (all of whom are showing immense enthusiasm for ACEDB, by the way.) Much of the scientific excitement in plant genomic mapping over the last year has been about the surprisingly high degree of synteny exhibited by relatively distantly related species, and now people want to put together inter-species databases in ACEDB. A problem that arises in doing this with regard to the multimap is that frequently the 'same' (homoeologous) gene or locus is called by different names in different species. The multimap currently only connects common loci by keying on the fact that they are literally the same locus, i.e. they have the same name. John McCarthy and I are thinking that the ideal solution would be if some other tag within the ?Locus object could be used to determine which loci are tied together in the Multimap. Perhaps this tag could be chosen using an option in options.wrm, analogous to the -Title option. E.g. -Title Tag : If present in some object of that class, the text following will be used preferentially when referring to that object. -Multimap Tag : If present, the text following will be used as the key for Multimap comparisons. Then if we set the option '-Multimap Homoeologue_name' for example, the following loci would be tied together when displayed on the multimap: Locus : "cab 22L" Homoeologue_name "Lhcb1" gMap Petunia-6 121 Locus : "Cab-1C" Homoeologue_name "Lhcb1" gMap Pepper-2 143 Locus : "Lhcb1" Homoeologue_name "Lhcb1" gMap Tomato-2 156 Further it would be nice if the names shown on the multimap could be the actual locus names rather than the homoeologue names. I.e. to allow the user to select which map's nomenclature to display, or to show all nomenclatures beside their respective maps. What do you think? best regards, - Dave Matthews, John McCarthy, Lisa Lorenzen, Sam Cartinhour From owner-acedb@net.bio.net Fri Jan 28 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: kirbym@har-rbu.mrc.ac.uk Newsgroups: bionet.software.acedb Subject: homologous genes Date: 26 Jan 1994 15:42:51 -0000 Lines: 59 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i631r$ipm@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk In a recent message posted to this bulletin board by Mathews et al, they say: > Much of the scientific excitement in plant genomic mapping over the last year > has been about the surprisingly high degree of synteny exhibited by > relatively distantly related species, and now people want to put together > inter-species databases in ACEDB. A problem that arises in doing this with > regard to the multimap is that frequently the 'same' (homoeologous) gene or > locus is called by different names in different species. The multimap > currently only connects common loci by keying on the fact that they are > literally the same locus, i.e. they have the same name. and suggest that a tag within the ?Locus object be used to determine which loci are tied together in the Multimap. It's a good idea. However, we have other dificulties with regard to homologous data. There are some species which have homologous genes but the symbols are exactly the same. For example, the human, cow and sheep nomenclature. As you can imagine, trying to store information with the same key causes quite a few problems. To get around this, Jo Dicks and myself decided to use a species prefix for all homologous data and keep the actual symbol as a Text tag. Eg Locus : "HsABL" Symbol : "ABL" Locus : "BvABL" Symbol : "ABL" In fact, if this is done, all data items within the database need to have a species prefix. But when it comes to displaying the data (whether on the maps or in the keySet) we only want the symbol for that individual species, not the symbol with the species prefix. I tried to modify the genetic map code to do this but there are problems. Could someone help me fix my code or if enough people want this facility, could Jean and the acedb team offically implement this please. The data structure for handling data objects to be displayed on the genetic map is the SEG. It usually consists of the object's key, a few flags and the object's position. Instead of using the key to display the object's name (ie gene symbol) I have tried using a character pointer from within the SEG structure. In the gMapConvert routine, this is set to point to the text defined by the Symbol Tag definition in the ?Locus object. (ie is a Text tag, not ?Text tag.) If this is done and later on you try and retrieve the Symbol text, the data is corrupted and appears scrambled. This is a pity because the only alternative which I have found that works is: for each data object on the genetic map, retrieve its data (ie create an OBJ for it) and then find the relevant data within the object for display. It slows the map display down considerably and I am sure there is a better way. How is one expected to get help with acedb problems? Do you use this bulletin board, or do you email Jean directly? Michelle Kirby (email kirbym@uk.ac.mrc.har-rbu) Jo Dicks (email jld@uk.ac.ox.bioch) From owner-acedb@net.bio.net Fri Jan 28 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!think.com!mbcrr!shih From: shih@mbcrr.dfci.harvard.edu (Deborah Shih) Newsgroups: bionet.software.acedb Subject: ignore test Date: 26 Jan 1994 07:36:10 GMT Organization: Dana-Farber Cancer Institute Lines: 7 Distribution: bionet Message-ID: <2i56haINN1mp@early-bird.think.com> NNTP-Posting-Host: mbcrr.harvard.edu Sorry, just a test posted 02:30 EST Jan 26, 1994 From owner-acedb@net.bio.net Fri Jan 28 22:00:00 1994 Path: biosci!rutgers!usc!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: kirbym@har-rbu.mrc.ac.uk Newsgroups: bionet.software.acedb Subject: homologous genes Message-ID: <2i631r$ipm@mserv1.dl.ac.uk> Date: 26 Jan 94 15:42:51 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 59 Original-To: acedb@dl.ac.uk In a recent message posted to this bulletin board by Mathews et al, they say: > Much of the scientific excitement in plant genomic mapping over the last year > has been about the surprisingly high degree of synteny exhibited by > relatively distantly related species, and now people want to put together > inter-species databases in ACEDB. A problem that arises in doing this with > regard to the multimap is that frequently the 'same' (homoeologous) gene or > locus is called by different names in different species. The multimap > currently only connects common loci by keying on the fact that they are > literally the same locus, i.e. they have the same name. and suggest that a tag within the ?Locus object be used to determine which loci are tied together in the Multimap. It's a good idea. However, we have other dificulties with regard to homologous data. There are some species which have homologous genes but the symbols are exactly the same. For example, the human, cow and sheep nomenclature. As you can imagine, trying to store information with the same key causes quite a few problems. To get around this, Jo Dicks and myself decided to use a species prefix for all homologous data and keep the actual symbol as a Text tag. Eg Locus : "HsABL" Symbol : "ABL" Locus : "BvABL" Symbol : "ABL" In fact, if this is done, all data items within the database need to have a species prefix. But when it comes to displaying the data (whether on the maps or in the keySet) we only want the symbol for that individual species, not the symbol with the species prefix. I tried to modify the genetic map code to do this but there are problems. Could someone help me fix my code or if enough people want this facility, could Jean and the acedb team offically implement this please. The data structure for handling data objects to be displayed on the genetic map is the SEG. It usually consists of the object's key, a few flags and the object's position. Instead of using the key to display the object's name (ie gene symbol) I have tried using a character pointer from within the SEG structure. In the gMapConvert routine, this is set to point to the text defined by the Symbol Tag definition in the ?Locus object. (ie is a Text tag, not ?Text tag.) If this is done and later on you try and retrieve the Symbol text, the data is corrupted and appears scrambled. This is a pity because the only alternative which I have found that works is: for each data object on the genetic map, retrieve its data (ie create an OBJ for it) and then find the relevant data within the object for display. It slows the map display down considerably and I am sure there is a better way. How is one expected to get help with acedb problems? Do you use this bulletin board, or do you email Jean directly? Michelle Kirby (email kirbym@uk.ac.mrc.har-rbu) Jo Dicks (email jld@uk.ac.ox.bioch) From owner-acedb@net.bio.net Fri Jan 28 22:00:00 1994 Path: biosci!rutgers!sgigate.sgi.com!sgiblab!sdd.hp.com!think.com!mbcrr!shih From: shih@mbcrr.dfci.harvard.edu (Deborah Shih) Newsgroups: bionet.software.acedb Subject: ignore test Message-ID: <2i56haINN1mp@early-bird.think.com> Date: 26 Jan 94 07:36:10 GMT Distribution: bionet Organization: Dana-Farber Cancer Institute Lines: 3 NNTP-Posting-Host: mbcrr.harvard.edu Sorry, just a test posted 02:30 EST Jan 26, 1994 From owner-acedb@net.bio.net Fri Jan 28 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: multimap idea Date: 27 Jan 1994 22:22:43 -0000 Lines: 13 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i9erj$99c@mserv1.dl.ac.uk> Original-To: acedb@net.bio.net I like the idea of Matthews and Kirby i can implement that as suggested by Mathhews, it will also solve Kirby's problem and I think Danielle's requirement of easier access to homologies. The reason the Text does not work is that a Text is only on disk and its char* is only transient You can only store in seg a KEY then display name(seg->key_of_homology) The notion of -Multipmap like -Title in options is excellent i think more on that in a few days, i ll try to implement that very soon. From owner-acedb@net.bio.net Sat Jan 29 22:00:00 1994 Path: biosci!rutgers!usc!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: multimap idea Message-ID: <2i9erj$99c@mserv1.dl.ac.uk> Date: 27 Jan 94 22:22:43 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 13 Original-To: acedb@net.bio.net I like the idea of Matthews and Kirby i can implement that as suggested by Mathhews, it will also solve Kirby's problem and I think Danielle's requirement of easier access to homologies. The reason the Text does not work is that a Text is only on disk and its char* is only transient You can only store in seg a KEY then display name(seg->key_of_homology) The notion of -Multipmap like -Title in options is excellent i think more on that in a few days, i ll try to implement that very soon. From owner-acedb@net.bio.net Mon Jan 31 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software.acedb Subject: IMPORTANT BIOSCI INFORMATION Date: 1 Feb 1994 10:02:39 -0000 Lines: 244 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2il9bv$h7t@mserv1.dl.ac.uk> Original-To: acedb@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 kristoff@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/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending e-mail to biosci@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. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. 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: