From owner-acedb@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: can't get Write Access in ACEDB Date: 3 Mar 1995 02:50:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503031047.AA17945@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net I've never really had trouble getting "Write Access" to show up on the main menu before (since the first ACEDB I installed), but this time I'm stumped. I'm installing a copy of GrainGenes (ACEDB version 3.0) on an SGI in Denmark. I changed passwd.wrm to contain my login name here, which is also the name of the owner of all the directories and files. That name is listed directly in /etc/passwd. The default shell for it is ksh instead of csh, could that make a difference? (I'm running ace from a csh subshell.) I did setenv ACEDB_SU. The database directory and blocks.wrm exist, and are writeable by the owner. Uncommenting "getLoginFailed" in passwd.wrm has no effect. Some other folks have complained of this problem before. Did you fix it, or give up on ACEDB? - Dave Matthews From owner-acedb@net.bio.net Thu Mar 02 22:00:00 1995 Newsgroups: bionet.software.acedb Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!Norway.EU.net!EU.net!howland.reston.ans.net!news.sprintlink.net!alfa02.medio.net!netnews.nwnet.net!ns1.nodak.edu!beangenes.cws.ndsu.nodak.edu!mcclean From: mcclean@PROBLEM_WITH_INEWS_DOMAIN_FILE (Phil McClean) Subject: ANNOUNCEMENT: BeanGenes Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Fri, 3 Mar 1995 22:36:37 GMT Nntp-Posting-Host: beangenes.cws.ndsu.nodak.edu Organization: I need to put my ORGANIZATION here. X-Newsreader: TIN [version 1.2 PL2] Lines: 106 BeanGenes --- A Phaseolus/Vigna sp. Database Phillip E. McClean Department of Plant Sciences North Dakota State University Fargo, ND 58105 mcclean@beangenes.cws.ndsu.nodak.edu Plant Genome Databases Plant genome databases have been designed for a number of important crop species. The goal of these databases is to provide "one-stop shopping" for information that is relevant to a species or group of species. Examples of these databases include GrainGenes (for cereal groups), SolGenes (for Solanaceous species), and SoyBase (for Glycine species). Information that is contained in these databases include molecular mapping data, germplasm information, trait studies, identified quantitative trait loci, pathogen descriptions, relevant publication citations, images pertaining to all aspects of the crop, and colleague addresses. These efforts are each funded by the USDA Plant Genome project. BeanGenes BeanGenes is a plant genome data base which currently contains information relevant to Phaseolus and Vigna species. The BeanGenes project was funded by the USDA/ARS Plant Genome project through the SoyBase project administered by Dr. Randy Shoemaker (USDA/ARS, Ames, Iowa). The hardware component of BeanGenes is a computer containing a Pentium P90 processor, 64 mByte RAM, 2 GByte hard drive, and 8 GByte tape backup drive. The machine is running under the Linux operating system. Linux is a Unix-based operating system designed to run on machines using the Intel X86 series of processors. Internet domain name of the machine is beangenes.cws.ndsu.nodak.edu. The IP address of the machine is 134.129.117.50. Currently, all of the BeanGenes information is stored in the ACeDB software application. This is the most frequently used plant genome database application. Richard Durbin (MRC, England) and Jean Thierry-Mieg (CNRS, France) initially developed ACeDB (an acronym for A C. elegans database) to archive information about Caenorhabditis elegans (Durbin and Thierry-Mieg, 1995). The database runs under the X-Windows environment on machines utilizing some flavor of a UNIX operating system. To access the database as an X-window application, the user must login on the server. Alternatively, a user can obtain a copy of the database and install it on a local X-Windows server. Remote users will need to access the database from a computer running a form of X-Windows. The database can be accessed from any personal computer or MacIntosh computer which has X-Windows emulation software. BeanGenes contains several classes of information. All of the published molecular maps of P. vulgaris are represented in the database. These include the restriction fragment length polymorphism (RFLP) map developed by Dr. Eduardo Vallejos at the University of Florida (Vallejos et al., 1992) and the RFLP map developed by Dr. Paul Gepts at the University of California, Davis (Gepts et al., 1993). The combined RFLP and randomly amplified polymorphic DNA (RAPD) developed by Dr. Michel Dron at University of Paris, Sud can also be accessed. Dr. Nevin Young of the University of Minnesota has provided RFLP maps of mung bean (Vigna radiata) and cowpea (V. unguiculata). Associated with each molecular map are loci and probe information. The loci information describes the probes or RAPDs used to define the locus, and the probe data provides specific information about a given probe. BeanGenes also contains all of the gene information that was complied by Dr. Mark Bassett, University of Florida. This is identical to the recent published list (Bassett, 1993) All published references to the genes are also included. Accessing BeanGenes The BeanGenes database can be accessed in three manners. For those users with X-Windows capability, a login on the BeanGenes server can be established. If you would like to have an account on the BeanGenes machine contact Phil McClean at mcclean@beangenes.cws.ndsu.nodak.edu and an account will be established. Two methods of accessing the database are available that do not require X-Windows capability. The ACeDB form of BeanGenes can be searched on the Agricultural Genome World Wide Web Server at URL http://probe.nalusda.gov:8300/. This WWW site can be accessed by such client software as Mosaic and Netscape. Once the site is reached, find the BeanGenes entry and the database can be navigated using standard point-and-click techniques. The database is also accessible using the Gopher application. The gopher address is probe.nalusda.gov. When the database is accessed via Gopher, the user will able to search for information using the WAIS (Wide Area Information Search) application. Use the following menu steps to find the searchable version of BeanGenes. 2. Plant Genome Informaton 2. Access to Genome Databases 19. Search BeanGenes (Phaseolus sp.) References Bassett, M.J. 1993. List of genes - Phaseolus vulgaris L. Ann. Report of Bean Imp. Coop. 36:vi-xxiii. Durbin, R. and J. Thierry Mieg. 1995. 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. Gepts, P., R. Nodari, S.M. Tsai, E.M.K. Kinage, V. Llaca, R. Gilbertson, and P. Guzmán. 1993. Linkage mapping in common bean. Ann. Report of Bean Imp. Coop. 36:xxiv-xxxviii. Vallejos, C.E., N.S. Sakiyama, C.D. Chase. 1992. A molecular-marker-based linkage Map of Phaseolus vulgaris L. Genetics 131:733-740. From owner-acedb@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: can't get Write Access in ACEDB Date: 3 Mar 1995 07:29:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503031522.AA18191@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > Date: Fri, 3 Mar 1995 14:49:17 GMT > From: jld@bioch.ox.ac.uk (Joanne Dicks) > To: matthews@greengenes.cit.cornell.edu > Subject: Re: can't get Write Access in ACEDB > > Your problem sounds quite similar to one I had some months ago. > In my case, there wasn't a problem with ACEDB itself but with > the computer system. We had recently upgraded our operating > system to Solaris and somehow my machine thought I was the > person who had logged on before me. Typing "whoami" and > "who am i" gave different results. I then added that person's > username to passwd.wrm and everything was fine. I kept it like > this until the system faults had been removed. It wasn't ideal > but at least it worked. > > I hope this is something like your problem, or will give you > an idea of what might be wrong. > > Jo Dicks > Genetics Lab, > Dept. of Biochemistry, > Oxford. Thanks Jo, that may be an excellent lead. It is a newly set-up machine here. I'll check it out as soon as the problem comes back. (As soon as I sent off that message, it started sometimes working, sometimes not. For a while I had two xterm windows on the screen, one of which started up no- Write-Access xaces every time and the other of which started up correctly functioning ones every time. Looks like I finally killed off the bad one so I can't check the who am i result.) regards, - Dave From owner-acedb@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!bcm!convex!news.duke.edu!news.mathworks.com!news.alpha.net!uwm.edu!fnnews.fnal.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: 7 Mar 1995 19:49:44 GMT Organization: Dendrome, A genome database for forest trees Lines: 1001 Approved: news-answers-request@MIT.Edu Message-ID: <3jidco$dv1@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.pswfs.gov Summary: Frequently Asked Questions about finding and getting started with the database system ACEDB. ACEDB is used to collect information regarding the molecular biology of the genome. Xref: biosci bionet.software.acedb:544 news.answers:33933 Archive-name: acedb-faq Last-modified: 3/7/95 Version: 1.19 Common Questions, with Answers, about ACEDB ******************************************* o Q0: What is ACEDB? o +++++++++++++++++++ o !Q1: What is the current version of ACEDB? o +++++++++++++++++++++++++++++++++++++++++++ o Q2: What hardware/software do I need to run ACEDB? o +++++++++++++++++++++++++++++++++++++++++++++++++++ o Q3: Where can I get ACEDB? o +++++++++++++++++++++++++++ o Q4: What ACEDB databases exist? o ++++++++++++++++++++++++++++++++ o Q5: What written documentation exists for ACEDB? o +++++++++++++++++++++++++++++++++++++++++++++++++ o Q6: Where can I find further information about ACEDB? o ++++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q7: How should ACEDB be cited? o +++++++++++++++++++++++++++++++ o Q8: Is ACEDB object-oriented? o ++++++++++++++++++++++++++++++ o Q9: What's all this about Gopher, WAIS, FTP, WWW, URL, ... o +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q10: How can I get on/off the ACEDB announcements mailing list? o ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q11: When and where is the next ACEDB Workshop? o ++++++++++++++++++++++++++++++++++++++++++++++++ o Q411: Who prepared this document & where is the current version? o +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Questions marked with '+' are new, those with '!' have substantially changed answers. Q0: What is ACEDB? ================== A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [Q4 gives contact information]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage -missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions Q1: What is the current version of ACEDB? ========================================= A1: (This answer refers to the software not the C. elegans data.) Most production sites are using 3.0 (or 2.0) binaries. The most recent beta source code distribution (1/95) is test.source.3.6a.tar.gz. A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q10. Return to List of Questions Q2: What hardware/software do I need to run ACEDB? ================================================== A2: The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. o Unix and X11: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series o PC 386/486 with Linux (free Unix) [note from Jeff Bryer, jbryer@darwin.mbb.sfu.ca] I just installed up Linux yesterday and today spent the many hours to compile in the C. elegans data for ACEDB v2.0 So to save other people the trouble of doing the same the entire package ACEDB for Linux 2-10 is available on trog.mbb.sfu.ca in /pub/acedb as linux.2_10.tar.Z The data was compiled in on a 486DX-33 with 16MBs of RAM running Linux 1.1.18 (Slackware 2.0.0 distribution) and a 32MB swap device (and it chugged away for a couple hours chewing up all 16MBs and half the swap space). File size is about 73MBs uncompressed, 26MBs compressed. This is based on the ACEDB v2.0 port for Linux that Ken Clark (ken@darwin.mbb.sfu.ca) did. o There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o MSDOS/Windows/NT: o A port to NT is rumored to be in the works. o Macintosh: o [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a decent color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. o ACEDB for The NEC EWS4800 is available via anonymous ftp at ftp.nec.co.jp (192.135.93.2) in /pub/packages/acedb/ace2. Contact Tohru Sano Fundamental Research Laboratories NEC Corporation Tsukuba, 305, JAPAN, e-mail: sano@exp.cl.nec.co.jp, FAX: +81-298-56-6136, VOICE: +81-298-50-1507 (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. --bks) X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions Q3: Where can I get ACEDB? ========================== A3: The standard ACEDB source and binaries are available in the following public access accounts (anonymous ftp sites) accessible via Internet: o lirmm.lirmm.fr in pub/acedb o cele.mrc-lmb.cam.ac.uk in pub/acedb o ncbi.nlm.nih.gov in repository/acedb o bioinformatics.weizmann.ac.il in pub/databases/acedb. MacAce is available from: o genome.lbl.gov in pub/macace o cele.mrc-lmb.cam.ac.uk in pub/acedb/macace Linux; ACEDB version 2.0 for Linux 2-10: o trog.mbb.sfu.ca /pub/acedb as linux.2_10.tar.Z ACEDB for The NEC EWS4800: o ftp.nec.co.jp in /pub/packages/acedb/ace2. Return to List of Questions Q4: What ACEDB databases exist? =============================== A4: In alphabetic order by Database name ------------------------------------ [Curators, please submit changes as new paragraphs] o Database : AaeDB o Species : Aedes aegypti o Last_update : December 1994 o ACEDB_version : 3.0 o WWW : http://klab.agsci.colostate.edu/index.html o PI : Dennis Knudson, dknudson@lamar.colostate.edu o Curator : Martin Ferguson, martinf@lamar.colostate.edu o Curator : Dave Severson, dave@aedes.vetsci.wisc.edu o Contact : aaedbmgr@klab.agsci.colostate.edu o Database : AAnDB-1.0 o Species : Aspergillus nidulans o PI : Leland Ellis o Last_update : February 1994 o ACEDB_version : 3.0 o Contact : leland@stralight.tamu.edu o URL: http://keck.tamu.edu/ibt.html o Comment : defunct, See AGsDB o Database : AAtDB o Species : Arabidopsis thaliana o Current version : 3-4 o Last_update : November 1994 o Curator : John Morris o Contact : curator@frodo.mgh.harvard.edu o Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x o Availability : Macintosh version in /aatdb/MacAAtDB directory o URL : gopher://weeds.mgh.harvard.edu/ o URL : http://weeds.mgh.harvard.edu:80/index.html o URL : http://probe.nalusda.gov:8300/ o Database : ABtDB-1.0 o Species : Bovine, Bos taurus o ACEDB_version : 3.0 extended o PI : Leland Ellis o Last_update : February 1994 o Contact : leland@stralight.tamu.edu o URL : http://keck.tamu.edu/ibt.html o Comment : defunct, See AGsDB o Database : AboutDB o Curator : Staffan Bergh o PI : Staffan Bergh o Subject : ACEDB itself (Is this meta-meta-metadata) o ACEDB 3.0 o Contact : staffan@biochem.kth.se o URL : http://kiev.physchem.kth.se/AboutDB.html o Database : ACeDB o Species : Caenorhabditis elegans o Current version: 2-10 o Curator : Jean Thierry-Mieg o Curator : Richard Durbin o Contact : rd@mrc-lmb.cam.ac.uk o Contact : mieg@kaa.crbm.cnrs-mop.fr o Last_update : May 1994 o DataBase : AceMap o Species : Homo sapiens (Mus musculus under development) o Focus : Physical mapping of human chromsome X and 21 o ACEDB_version : 3.0 o Curator : Hugues Roest Crollius o PI : Hans Lehrach o Availability : beta release of the X chr. data/models by anonymous ftp to ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap. Get the README file in the directory above. o Contact : hrc@gea.lif.icnet.uk (Hugues Roest Crollius) ICRF, Lincoln's Inn Fields London, UK. o Last_update : August 94 o Database : AGsDB A Genus species Database o Species : Aspergillus nidulans o Species : Neurospora crassa o Species : cow w/ human anchor loci o Species : cotton (demo) o Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast o PI : Leland Ellis o Curator : Leland Ellis o Last_update : March 1994 o ACeDB_version : 3.0 (beta still), with extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe) yeast); interacting loci via defined Interactions for each locus o Models : as of 3.13.94 o Data : as of 3.13.94 o Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. o WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux (ducoux@moulon.inra.fr). o URL : http://keck.tamu.edu/ibt.html o Contact : leland@straylight.tamu.edu o Database : BeanGenes o Species : Phaseolus and Vigna species o PI : Phillip E. McCLean o Email : mcclean@beangenes.cws.ndsu.nodak.edu o WWW : http://probe.nalusda.gov:8300 o Gopher: probe.nalusda.gov o Database : ChlamyDB o Species : Chlamydomonas o PI : Elizabeth Harris o Contact : chlamy@acpub.duke.edu o Availability : ChlamyDB 1.0, using ACEDB 3.0, is now on WWW and gopher (probe.nalusda.gov). Complete version using ACECB 3.0 now available by ftp from probe.nalusda.gov in the pub/chlamydirectory. o URL : http://probe.nalusda.gov:8300 o Last_update : 25 Oct, 1994 o Database : CottonDB o Species : Gossypium hirsutum (cotton) and related species o PI : Russell J. Kohel USDA-ARS Southern Crops Research Laboratory Route 5, Box 805, College Station, Texas 77845 o Curator : Gerard R. Lazo o Curator : Sridhar Madhavan o Last_update : January, 1995 (version 95.1) o ACEDB_version : 3.0 o Contact : glazo@tam2000.tamu.edu (Gerard R. Lazo) o Contact : rjk0339@zeus.tamu.edu (Russell J. Kohel) o URL : http://probe.nalusda.gov:8000/index.html o Phone : 409-260-9311 o Fax : 409-260-9333 o Database : CSNDB o Focus : Cell Signalling Molecules and Interactions o Contact : Takako Igarashi National Insitute of Health Sciences Division of Chem-Bio Informatics Setagaya-ku, Tokyo, Japan 158 taka@nihs.go.jp o Database : EcoDB o Species : E. coli o PI : Staffan Bergh o Contact : staffan@biochem.kth.se o Availability : Proposed o Last_update : Aug. 1994 o Database : 11DB o Species : Homo sapiens o Focus : Physical mapping of chromosome 11 o Availability : under development o Curator : Benedict Arnold o PI : Peter Little o Contact : Benedict Arnold Dept. Biochemistry, Imperial College, London, SW7 2AZ b.arnold@ic.ac.uk o Database : The Encyclopaedia of the Drosophila Genome. o Acronym : (none) o Species : Drosophilidae (primarily D. melanogaster) o Availability : MacFly/FlyDB-based distribution by ftp and CD-ROM due early 1995 o Developer : Suzanna Lewis o Contact : suzi@fly2.berkeley.edu o Developer : Cyrus Harmon o Contact : sly@fly2.berkeley.edu o Developer : Edward Welbourne o Contact : eddy@gen.cam.ac.uk o Curation : Data is provided by the collaborating organisations: o Collaborator : The FlyBase Consortium, flybase@morgan.harvard.edu o Collaborator : The Berkeley Drosophila Genome Project o URL : gopher://fly.bio.indiana.edu:70+/11/Flybase o Database : Flydb o Species : Drosophila melanogaster o Curator : Suzanna Lewis o Contact : suzi@fly2.berkeley.edu o Database : GrainGenes o Species : Wheat, barley, oats, relatives o Availability : Anonymous ftp from probe.nalusda.gov:pub/grains o Availability : Gopher greengenes.cit.cornell.edu port 70 o Availability : Gopher probe.nalusda.gov port 7002 o Curator : David E. Matthews o PI : Olin D. Anderson o Contact : matthews@greengenes.cit.cornell.edu o Contact : oandersn@wheat.usda.gov o URL : gopher://greengenes.cit.cornell.edu/1/ o Data_version : 1.3 o Released : 12 Jan 1994 o Based_on : acedb.1-10 o Availability : See following WWW URL o URL : http://probe.nalusda.gov:8300 o Last_update : Feb. 1994 o Database : human.c17 o Species : Homo sapiens o Availability : the database is under development o Contact : lsprilus@weizmann.weizmann.ac.il o Focus : mapping & sequencing of Human Chromosome 17 o Based_on: acedb.3-0 o Last_update : Jan. 1994 o Database : IGD - the Integrated Genomic Database o Species : Homo sapiens (later mouse and other mammalian species) o Availability : September 1994 by ftp, on-line server October 1994 o Contact : Otto Ritter [ o.ritter@dkfz-heidelberg.de ] o Curator : tba o Description : IGD - the Integrated Genomic Database - aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. o Database : LIGM-DB o Curator : Veronique Giudicelli o Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors o PI : Marie_paule Lefranc o Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr o Database : Maize o Species : Zea mays L. ssp. mays o Focus : Maize genome o Acedb_version : 1.9 o FTP : probe.nalusda.gov, pub directory; anonymous ftp o Comment : Maize is an acedb front end for the Maize Genome Database, MaizeDB, a SYBASE database. o Comment : MaizeDB is updated daily and has WWW connectivity to external databases: GenBank (loci, alleles and probes), SwissProt (gene products) and the E. coli Stock Center (loci). o Data : Major data categories: 4522 mapped loci (located to chromosome or better) including 684 mapped genes and 1423 mapped probed sites (gene candidates); 982 probes; 1850 map scores; 1533 gel patterns (Probe/Enzyme/Stock); 4231 stocks; 5105 Variations (alleles, DNA polymorphisms, rearrangements, etc); 465 phenotypes; 223 traits; 547 gene products; 5314 bibliographic references; 1979 persons with addresses. o Gopher : host = teosinte.agron.missouri.edu, port = 70 o Telnet : telnet teosinte.agron.missouri.edu login as guest, use password 'corncob' o HTTP : http://teosinte.agron.missouri/top.html o HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant Genome Database o Comment : Genera is a software toolkit for creating and extracting data from Sybase databases; used to create MaizeDB and Worldwide Web connectivity. o HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html o Funding : MaizeDB USDA/ARS to E. Coe o Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn o Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu o Curator : Pat Byrne byrne@teosinte.agron.missouri.edu o Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu o Curator : Mary Polacco maryp@teosinte.agron.missouri.edu o Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu o Curator : Christiane Fauron FAURON@GENE1.med.utah.edu o Curator : Carolyn Wetzel cmwetzel@iastate.edu o Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU o Design : Stan Letovsky letovsky-stan@CS.YALE.EDU o Design : Mary Berlyn mary@fetalpig.biology.yale.edu o Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu o Contact : db_request@teosinte.agron.missouri.edu o Last_update : 25 April 1994 o Database : MycDB o Species : Mycobacteria o Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. o PI : Staffan Bergh o PI : Stewart Cole o PI : Doug Smith o Curator : Staffan Bergh o Contact : staffan@biochem.kth.se o Last_update : Apr. 1994 o WWW : http://kiev.physchem.kth.se/MycDB.html o ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB o ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB o ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb o Database : PomBase o Curator : Sean Walsh o Curator : Marie-Adele Rajendream o PI : Bart Barrell o Species : Schizosaccharomyces pombe o Contact : svw@sanger.ac.uk o Contact : barrell@sanger.ac.uk o Comment : Not yet available for distribution o DataBase : Mousedb o Species : Musculus Musculus o Species : Homo Sapiens o ACEDB_version : 3.0 with extensions to define and display cytogenetic data. o Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. o Curator : Michelle Kirby o Curator : Rachael Selley o PI : Mary Lyon o PI : Jo Peters o Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 For other information contact Michelle Kirby. o Contact : kirbym@har-rbu.mrc.ac.uk (or mkirby@hgmp.mrc.ac.uk) rselley@har-rbu.mrc.ac.uk MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD o Last_update : October 1994 o Database : RiceGenes o Species : Rice (O. sativa) o Availability : Anonymous ftp from probe.nalusda.gov:pub/rice o Availability : Gopher nightshade.cit.cornell.edu port 70 o Availability : Gopher probe.nalusda.gov port 7007 o Curator : Edie Paul o PI : Susah McCouch o Contact : epaul@nightshade.cit.cornell.edu o Release : ACEDB 1-10 o Last_update : May 1994 o Database : SacchDB o Species : Saccharomyces cerevisiae o Focus : Budding (common baker's) Yeast Genome o ACEDB_version : UNIX 2.0, MacAce 2.0b4 o FTP : genome-ftp.stanford.edu in /pub/SacchDB o FTP : ncbi.nlm.nih.gov in /repository/SacchDB o Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. o Gopher : host = genome-gopher.stanford.edu, port = 70 o HTTP : http://genome-www.stanford.edu/ o Funding : National Center for Human Genome Research, NIH o PI : David Botstein, botstein@genome.stanford.edu o Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu o Curator : Selena Dwight, dwight@genome.stanford.edu o Curator : Cathy Ball, ball@genome.stanford.edu o Curator : Rita Schmidt, bleb@genome.stanford.edu o Programmer : Karen Davis, karen@genome.stanford.edu o Sys. Admin : Mark Schroeder, mark@genome.stanford.edu o Contact : yeast-curator@genome.stanford.edu o Data_Submission : yeast-curator@genome.stanford.edu o Last_update : 2 February 1995 o Database : SolGenes o Coverage: Solanaceae - tomato, potato, pepper o Availability : Anonymous ftp from probe.nalusda.gov:pub/solgenes o Availability : Gopher nightshade.cit.cornell.edu port 71 o Availability : Gopher probe.nalusda.gov port 7006 o Curator : Clare Nelson o PI : Steve Tanksley o Contact : cnelson@nightshade.cit.cornell.edu o Release : ACEDB 3.0 o Last_update : May 1994 o Database : SorghumDB o Species : Sorghum bicolor (L.) Moench o PI : Keith F. Schertz USDA-ARS Dept. of Soil & Crop Sciences Texas A&M University College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 E_mail : schertz@tamvm1.tamu.edu o Curator : Najeeb U. Siddiqui Southern Crop Improvement Facility Crop Biotechnology Center Texas A&M University College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 E_mail : nus6389@tamsun.tamu.edu o Last_update : July 1994 o ACEDB_version : 3.0 o Availability : Under Development o Database : SoyBase o Species : Soybeans o Curator : Lisa Lorenzen o PI : Randy Shoemaker o Contact : lorenzen@mendel.agron.iastate.edu o Phone : 515-294-0421 o Fax : 515-294-2299 o Last_update : Sept. 1993 o Gopher : probe.nalusda.gov port 7005 o Database : Sybace o Species : Homo sapiens o Creator : Detlef Wolf o Comment : Custom software --ACEDB front-end to SYBASE data o Contact : D.Wolf@dfkz-heidelberg.de o See_also : IGD o Database : TreeGenes o Species : Forest trees o ACEDB_version : 3.0 o Curator : Bradley K. Sherman o PI : David B. Neale o Contact : Dendrome@s27w007.pswfs.gov o Contact : bks@s27w007.pswfs.gov o Contact : dbn@s27w007.pswfs.gov o Last_update : March 1994 o Gopher: s27w007.pswfs.gov o WWW: http://s27w007.pswfs.gov/ o FTP: probe.nalusda.gov in /pub/trees o Database : 21Bdb o Species : Homo sapiens o Focus : STS content mapping & sequencing of Human Chromosome 21 o Availability : by request, via ftp, world-wide-web o Based_on : acedb.1-10 plus moulon server o URL: ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z o URL: http://genome.lbl.gov/Genome/acepage.html o Curator : Donn F. Davy o Contact : DFDavy@lbl.gov o Contact : aggarwal@genome.lbl.gov o Focus : STS content mapping & sequencing of Human Chromosome 21 o PI : Michael Palazzolo o PI : Chris Martin o PI : Jan-Fang Cheng o Last_update : Apr. 1994 o Database : 22ace o Species : Homo sapiens o Curator : Ian Dunham o Focus : Physical mapping of chromosome 22 o PI : Ian Dunham o Contact : Ian Dunham Sanger Centre Hinxton Hall, Cambs. UK. id1@sanger.ac.uk o Database : VoxPop o Species : Populus spp. o Availability : contact curator o Curator : Carl G. Riches o PI : Reinhard F. Stettler o Contact : cgr@poplar1.cfr.washington.edu o Contact : STETTLER@coyote.cfr.washington.edu o Gopher : poplar1.crf.washington.edu o Last_update : Sept. 1993 o Database : Xace o Species : Homo sapiens o Curator : Gareth Maslen o Focus : Physical mapping of chromosome X o PI : David Bentley o Contact : Gareth Maslen Sanger Centre Hinxton Hall, Cambs. UK. glm@sanger.ac.uk o Database : ? o Species : Homo sapiens o Focus : Physical mapping of human chromosome 6. o Curator : Ioannis Ragoussis o Availability : Unknown o Contact : Guy's hospital o Database : ? o PI : Scott Chasalow o Species : Potato o Contact : Scottish Crop Institute, Dundee o Last_update : Sept. 1993 o Database : ? o PI : George Murphy o PI : David Flanders o Species : Arabidopsis thaliana o Contact : John Innes Center, Norwich, England o Last_update : Sept. 1993 o Database : ? o Species : Homo Sapiens o Focus : Physical and linkage mapping of chromosome 8 o Availability : o Curator : Stephen Wood o PI : Stephen Wood o Contact : Stephen Wood Dept. Medical Genetics University of B. C. Vancouver, B. C. Canada swood@unixg.ubc.cq Return to List of Questions Q5: What written documentation exists for ACEDB? ================================================ A5: From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000 . Primary documents from the developers are: o acedb -- A C. elegans Database: I. Users' Guide. o acedb -- A C. elegans Database: II. Installation Guide. o acedb -- A C. elegans Database: III. Configuration Guide. o Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z and ftp://weeds.mgh.harvard.edu/acedb_doc The files are in tex (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. Japanese language guides: _Japanese ACEDB Guide Ver.1.2._ _ACEDB ver.2 for NEC engineering workstation EWS4800 series_ are available in PostScript via anonymous ftp at ftp.nec.co.jp as /pub/packages/acedb/acemanjp.1_2.ps.Z . You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angisturte.ps and angistute.hqx available by anonymous ftp at ncbi.hih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Return to List of Questions Q6: Where can I find further information about ACEDB? ===================================================== A6: There is a Usenet/Biosci conference titled bionet.software.acedb. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. All of the articles are archived on the gopher at net.bio.net . Mike Cherry has set up an ACEDB Developer's archive. For anonymous ftp use the hostname weeds.mgh.harvard.edu and look in the acedb_dev directory. If you wish to contribute you can put files in the incoming directory. Send a message to Mike (cherry@genome.stanford.edu) that you have put something in that directory then Mike will move it out for general access. For gopher you can connect to weeds.mgh.harvard.edu (132.183.190.21) and ... --> N. FTP Archives for Molecular Biology/ then --> M. ACEDB Developer's archive/ [N and M are integers which are subject to change.] The bionet.software. acedb.conference is archived and can be searched using WAIS. Here is a Gopher-style link to the WAIS archive. (This is also courtesy of Mike Cherry.): # Type=7 Name=ACEDB BioSci Electronic Conference Path=7/.index/acedb-biosci Host=genome-gopher.stanford.edu Port=70 The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: o http://moulon.inra.fr/acedb/acedb.html for C. elegans data o http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data o http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html The Genome Computing Group, Lawrence Berkeley Laboratory has an anonymous ftp service at machine genome.lbl.gov (131.243.224.80) which contains: o flydb - LBL's Drosophila Acedb-style database o 21bdb - LBL's Human Chromosome 21 Acedb-style database o querdb - LBL's query-language extensions to Acedb o metadata - LBL's compendium of Acedb database schema variants o macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version o There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to dataabases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: o 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). o 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier Jean Thierry-Mieg et al), and the Interated Genome Database project in Heidelburg (Otto Ritter, Detlef Wolf et al). Return to List of Questions Q7: How should ACEDB be cited? ============================== A7: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions Q8: Is ACEDB object-oriented? ============================= A8: From the ACEDB User's Guide: A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions Q9: What's all this about Gopher, WAIS, FTP, WWW, URL, ... ========================================================== A9: These terms all refer to Internet protocols. An excellent introduction to the Internet is: _The Whole Internet User's Guide & Catalog_, by Ed Krol, O'Reilly & Associates, 1992. Or ask your system administrator to provide you with a gopher client or mosaic client and begin navigating on your own. URL is a Universal Resource Locator on the World-Wide Web (WWW). There are many free Internet browsers available that allow you to use an Internet connection and a URL to access services. Mosaic may be the most popular and it is available for Mac, PC or Unix via anonymous ftp from ftp.ncsa.uiuc.edu. Return to List of Questions Q10: How can I get on/off the ACEDB announcements mailing list? =============================================================== A10: To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q6 for details] is on the mailing list. Return to List of Questions Q11: When and where is the Next ACEDB Workshop? =============================================== The 1995 ACEDB Conference and Workshop will be held May 14-27, 1995, at the Isis Oasis, a small retreat center in Geyserville, about 80 miles north of SanFrancisco in Sonoma County, California. We will have exclusive use of the entire retreat center, including the theater (for workstations and primary sessions), dining room, lodge, and other residential facilities. For more information send email to ace95@genome.lbl.gov or vist URL http://genome.lbl.gov/ace95.html on the WWW. If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, there are online collections: o by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; o by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; o and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions Q411:Who prepared this document & where is the current version? =============================================================== A411: (Note to international readers: 411 is the phone number for information in the USA.) This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu as pub/usenet/news.answers/acedb-faq . If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html and http://s27w007.pswfs.gov/Homepage/acedbfaq.html Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov Major contributions in getting this FAQ off the ground were made by John McCarthy and Mike Cherry. Other contributors include: o Lisa Lorenzen o David Matthews o Edie Paul o Donn Davy o Eric De Mund o Sam Cartinhour Please cite as: Sherman,B.K., ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993,1994,1995 approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome Research Program. Return to List of Questions End of ACEDB FAQ --bks From owner-acedb@net.bio.net Tue Mar 07 22:00:00 1995 Path: biosci!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: A few changes in the FAQ Date: 7 Mar 1995 19:48:54 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 32 Distribution: world Message-ID: <3jidb6$duo@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov I will be sending out the new FAQ for this conference in a few minutes. I have made the HTML version the primary version and, henceforth, the text copy will be programmatically derived from that. This makes the layout a bit different, but it makes my life easier. I think that the new HTML version is much nicer. It can be accessed at: or Curators of ACEDB projects: please take a second and check your entries. You might want to check all of the links on the HTML version to make sure that they're oriented correctly. You can send new or modified paragraphs at any time to: acedbfaq@s27w007.pswfs.gov I will try to prepare a special version of the FAQ for handout at the upcoming Workshop. This is a good time to update your entries. (My apologies to anyone whose entry has been corrupted by my revising.) --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project From owner-acedb@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!omega.ludd.luth.se!news.ifm.liu.se!news.kth.se!sibirien.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Warning: Trying to open an ace3.6 (ace4) database with (x|t)ace3 Date: 9 Mar 1995 17:08:54 +0100 Organization: Biochemistry, KTH, Stockholm Lines: 24 Sender: staffan@biochem.kth.se Distribution: world Message-ID: <3jn96m$65o@sibirien.physchem.kth.se> NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Just a friendly warning to those of you that have both xace3 and xace4 (xace3.6) installed on your system: If you try to open an ace4-format database with ace3 (xace or tace) (ace will protest about the format and die) you will 'destroy' it - when next trying ace4 on it it will give a FATAL ERROR: System error 2 No such file or directory The old 24.25 and new 4 values of key Bat differ Better keep a backup (or the ace files)! /staffan Staffan Bergh Biochemistry, KTH, S-100 44 Stockholm, Sweden email: staffan@biochem.kth.se + Don't let that horse eat that violin phone: int+46 8 790 9230 + cried Chagall's mother fax: int+46 8 24 54 52 + but he kept right on painting + -- Lawrence Ferlinghetti Webmaster and MycDB maintainer From owner-acedb@net.bio.net Thu Mar 16 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!spool.mu.edu!uwm.edu!fnnews.fnal.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Mosaic 2.5 CCI and Pick_me_to_call Date: 17 Mar 1995 18:24:22 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 38 Distribution: world Message-ID: <3kck4m$ikt@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov How to use ACEDB to show stuff via Mosaic: Here's a URL http://s27w007.pswfs.gov/Homepage/acedb-faq.html Here's a fragment of a .ace file Paper : acedb-faq.html Pick_me_to_call : cci "http:\/\/s27w007.pswfs.gov/Homepage/acedb-faq.html" Here's the script .../externalFiles/cci #!/bin/csh sshow -host my.machine's.FQDN -port 9999 -url $1 Now get Mosaic version 2.5 and retrieve sshow (see http://www.ncsa.uiuc.edu/SDG/Software/Mosaic/CCI/cci-spec.html). Start up Mosaic (v2.5) and pull down the file menu and select "CCI...". Now start the program listening on port 9999 (say). Now click on "Pick_me_to_call" and acedb will cause Mosaic to display the FAQ. (n.b. ACEDB thinks that // starts a comment, even within double quotes! Is this a bug or a feature?) Nice for image display, too. You can get the library used to create sshow for your own imaginative www-client-remote-control-by-TCP/IP pleasure. --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project From owner-acedb@net.bio.net Mon Mar 20 22:00:00 1995 Path: biosci!GENOME.LBL.GOV!workshop From: workshop@GENOME.LBL.GOV (John McCarthy) Newsgroups: bionet.software.acedb Subject: ACEDB 1995 Request for Papers and Posters Date: 21 Mar 1995 10:14:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <199503211804.KAA28650@ux5.lbl.gov> NNTP-Posting-Host: net.bio.net REQUEST FOR PAPERS AND POSTERS The ACEDB 1995 Conference and Workshop is using World Wide Web facilities to share ideas before, during, and after our meetings. With those meetings just two months away, we'd like to invite everyone in the ACEDB community -- those who cannot attend this year's meetings as well as those who will be there in person -- to share any past or present work that might contribute to our meetings and the ongoing evolution of ACEDB. In order to make papers and posters available to everyone in the community, we would like to make them accessible as World Wide Web documents. There are at least three ways to do this, in order of preference as follows: 1. Send the URL for a paper/poster on your own WWW server; 2. Send your HTML paper/poster and we'll put it on an ACE95 WWW server; 3. Send a plain text paper/poster and we'll put it up as preformatted text. For an example, see file://genome.lbl.gov/pub/outline_mosaic/paper.html If you have not used HTML, but would like to try, its not too difficult. Take a look at the example source and the copy of the "Beginner's Guide to HTML" at http://genome.lbl.gov/ace95/HTML_Beginner's_Guide.html Please send your contributions to ace95@genome.lbl.gov. If you have questions, please contact Donn Davy (davy@genome.lbl.gov). From owner-acedb@net.bio.net Tue Mar 21 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!usenet From: yichena@ifi.uio.no (YichengAn) Newsgroups: bionet.software.acedb Subject: looking for bio-www programming projects Date: 22 Mar 1995 12:27:42 GMT Organization: Bio Center Lines: 14 Message-ID: <3kp53u$kkq@hermod.uio.no> NNTP-Posting-Host: biotek04.uio.no X-Newsreader: WinVN 0.92.3 Hello, all, The title says what I'm intended to. Here is the abridged version of my CV: Biochemistry Master Program student at Biotechnology Center of Oslo, my project has to do with "CANP inhibitors". Have had lots of Chemistry, Math, Computer C language programming and some Assembly language background. Have been successfully doing WWW programming that utilizes C language. Routinely use UNIX sun4, PC and Macintosh. Sincerely, Yicheng An From owner-acedb@net.bio.net Thu Mar 23 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!mojo.eng.umd.edu!cs.umd.edu!news.umbc.edu!haven.umd.edu!purdue!yuma!klab3.agsci.colostate.edu!user From: martinf@lamar.colostate.edu (Martin Ferguson) Newsgroups: bionet.software.acedb Subject: How to upgrade database to ver. 4 Date: Thu, 23 Mar 1995 16:15:12 -0600 Organization: Colorado State University Lines: 9 Distribution: world Message-ID: Reply-To: martinf@lamar.colostate.edu NNTP-Posting-Host: klab3.agsci.colostate.edu Greetings, I just compile version 3.6 and 3.7 on my Sun. I get an error indicating that I must upgrade my database to version 4, or use the correct (version 3, I assume) binary. How do I upgrade the database? Thanks. /s/ M From owner-acedb@net.bio.net Sun Mar 26 23:00:00 1995 Path: biosci!ksu.ksu.edu!dzolek From: dzolek@ksu.ksu.edu (Daniel Z. Skinner) Newsgroups: bionet.software.acedb Subject: Re: can't get Write Access in ACEDB Date: 27 Mar 1995 11:09:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <199503271909.NAA01992@grunt.ksu.ksu.edu> NNTP-Posting-Host: net.bio.net >I've never really had trouble getting "Write Access" to show up on the main >menu before (since the first ACEDB I installed), but this time I'm stumped. >I'm installing a copy of GrainGenes (ACEDB version 3.0) on an SGI in >Denmark. I changed passwd.wrm to contain my login name here, which is also >the name of the owner of all the directories and files. That name is >listed directly in /etc/passwd. The default shell for it is ksh instead of >csh, could that make a difference? (I'm running ace from a csh subshell.) > >I did setenv ACEDB_SU. The database directory and blocks.wrm exist, and are >writeable by the owner. Uncommenting "getLoginFailed" in passwd.wrm has no >effect. > >Some other folks have complained of this problem before. Did you fix it, or >give up on ACEDB? > >- Dave Matthews I was one of those to complain before. In my case, the problem was in where I was when I entered the setenv ACEDB_SU. To make a long story short, in my system I have to enter it _before_ I start X-Windows. So the sequence is, logon, setenv, xinit, start acedb. Good luck! Daniel Z. Skinner USDA-ARS and Agronomy Department Throckmorton Hall Kansas State University Manhattan, KS 66506-5501 E-mail dzolek@ksu.ksu.edu Telephone (913) 532-7247 Fax (913) 532-6094 From owner-acedb@net.bio.net Sun Mar 26 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Write-Access deja vu Date: 27 Mar 1995 11:48:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503271947.AA15021@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net >I've never really had trouble getting "Write Access" to show up on the main >menu before (since the first ACEDB I installed), but this time I'm stumped. >... For some reason bionet is just now posting this 3-week-old message of mine to some locations. Strange. Anyway, in the interim I figured out yet another work-around. In my case Jo Dicks's "whoami" vs. "who i am" test turned out to be the most relevant. Whenever I couldn't get Write Access, "who i am" didn't know who I was. Usually it thought I was somebody else from /etc/passwd but once it thought I was "telnet". "whoami" was always correct. The work-around was to create a new xterm window and try again. Saying "xterm" in a bad-who-i-am xterm window usually (always, I think) produced a good-who-i-am window. - Dave From owner-acedb@net.bio.net Mon Mar 27 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!ag24 From: ag24@mole.bio.cam.ac.uk (Aubrey de Grey (Genetics)) Newsgroups: bionet.software.acedb Subject: MothBase ideas Date: 28 Mar 1995 15:25:56 GMT Organization: U. of Cambridge, England Lines: 24 Distribution: world Message-ID: <3l99q4$fqs@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk I am looking into the possibility of setting up a database for the Lepidoptera ('MothBase'?) using ACeDB. The immediate impetus is that serious molecular linkage mapping is now going on using the domesticated silkworm, Bombyx mori, aimed toward eventual positional cloning of known mutations (200 mapped), quantitative trait locus mapping, and comparative genome analysis, and we need to organize this information and make it available to others. Right now I do not expect anyone to undertake large-scale sequencing, but would also like to keep track of clones, sequences, pesticide resistance mutations, etc. that are being picked up from other leps, as well as the broader literature in lepidopteran genetics, molecular biology, and development. Is anyone interested in a job as a part-time programmer for 1 or 2 years to set up such a database? It would be especially good to have someone who already knows something about leps or at least insects in general, but this isn't necessary. Funds aren't yet available; I'm just trying to get the lay of the land. I am now on sabbatical in Europe but am usually based at the University of Rhode Island, Kingston, RI, a small town near the coast about 30 miles from Providence, the major city in the state (where Brown U. is located). Boston, Woods Hole, and New Haven are about 90 mi to the north, northeast, and south respectively. Please respond to: Marian Goldsmith, e-mail: mki101@uriacc.uri.edu From owner-acedb@net.bio.net Tue Mar 28 23:00:00 1995 Path: biosci!rutgers!uwm.edu!news.moneng.mei.com!news.ecn.bgu.edu!usenet.ins.cwru.edu!howland.reston.ans.net!news.sprintlink.net!news1.channel1.com!news.channel1.com!channel1!chuck.frieser Distribution: world Newsgroups: bionet.software.acedb Subject: Attention Shareware Autho From: chuck.frieser@channel1.com (Chuck Frieser) Message-ID: <40.304.3163@channel1.com> Date: Mon, 27 Mar 1995 22:32:00 -0500 Organization: Channel 1(R) 617-864-0100 Info Lines: 76 Second Annual Ziff-Davis Shareware Awards *** DEADLINE: APRIL 1, 1995 *** Attention all shareware authors! Ziff-Davis Interactive (ZDI), PC Magazine, Computer Life and Computer Gaming World are sponsoring the second annual Ziff-Davis Shareware Awards, honoring the best PC-based shareware written or significantly upgraded between June 1, 1994 and April 1, 1995. The awards will be presented at a banquet during this year's Summer Shareware Seminar. Judges for the awards will include editors from the sponsoring magazines and Ziff-Davis Interactive. Ziff-Davis Shareware Award winning programs will be featured in special editorial coverage by the sponsoring magazine. The winning programs will also be posted in highly visible sections of the software libraries on ZiffNet and Interchange Computing. Authors who want to submit their shareware for the awards can enter by posting their programs in a special section of the Ziff-Davis Interactive Author Upload Center or by mailing the submissions on disk. Submissions will be accepted beginning on February 1, 1995. The submission deadline is April 1, 1995. Finalists will be announced on April 15, 1995. INSTRUCTIONS FOR SUBMITTING YOUR PROGRAMS A special section of Ziff-Davis Interactive's Author Upload Center has been established to allow authors to submit their programs electronically. To send your programs, just dial: 1-800-426-3425 8 lines/2400-28.8k baud/24 hour access Follow the instructions on-screen to upload your program. The deadline for all submissions is midnight April 1, 1995. International callers can send their products for entry by calling the Author Upload Center BBS (617) 252-5510 or sending disk-based material to: ZDI Shareware Awards 25 First St. Cambridge, Ma. 02141 Submission Criteria: - All entries must be shareware programs first released or significantly upgraded between June 1, 1994 and April 1, 1995. - All programs must be compressed using PKZip v2.04g. - All entries must be in a single package: please do not upload multi-part ZIPs (such as FILEA.ZIP, FILEB.ZIP, FILEC.ZIP, etc.). - Please submit the unregistered evaluation version of your program. Problems? Questions? If you are having difficulty uploading your submission, or have questions about the Ziff-Davis Shareware Awards, please call our Shareware Author Hotline at (617) 252-5527. Mail-In Submissions For directions on submitting your programs by mail, please call our Shareware Author Hotline at (617) 252-5527. From owner-acedb@net.bio.net Fri Mar 31 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 1 Apr 1995 02:00:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 347 Sender: daemon@net.bio.net Distribution: world Message-ID: <199504011000.CAA23694@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions on how to subscribe/unsubscribe will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. Any text placed on the Subject: line of your message will be ignored, so be sure to put the "help" command in the body of the message. If you need personal assistance, a BIOSCI staff member can be contacted at either of the following addresses. Please contact the address designated for your location. Support Address Location --------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim **** SEARCHING BIOSCI ARCHIVES **** The easiest way to search the BIOSCI archives is to use Mosaic or another World Wide Web browser and connect to the BIOSCI WWW home page at URL http://www.bio.net/. Select the hypertext link to the BIOSCI archives. This gives you read access to all newsgroup messages and the ability to search the indexes described below. You can also use gopher software and connect over the Internet to net.bio.net, the U.S. BIOSCI computer. We maintain three indexes which are searchable from the main gopher menu on net.bio.net: (1) an index of all BIOSCI postings; (2) an index of individual journal article references from the Table of Contents postings on the BIO-JOURNALS newsgroup; and (3) an index of BIOSCI users including regular mail and e-mail addresses, phone/FAX numbers, research interests, and newsgroup participation. 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 (anything entered on the Subject: line is ignored). WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). Finally, the BIOSCI archive files are accessible by anonymous FTP to net.bio.net [134.172.2.69] in the directory pub/BIOSCI. **** 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 fix problems that you might encounter in using the newsgroups. The FAQ and other BIOSCI documentation is available through our WWW home page at URL http://www.bio.net/. It is also available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. 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, waismail, gopher, and WWW access (the URL is http://www.bio.net). If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). 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 your database entry from time-to-time to see if your address information is still up-to-date. 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: > > --> 14. 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. > > > 6. Information in English/ > > 5. Scientific and other topics/ > > 1. Finnish EMBnet BioBox/ > > 9. FAQ Files/ > > 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). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. 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., 15-05-93 for 15 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., 15-05-93, not 15-5-93. 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 ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs 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 BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses 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 MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish 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: