From owner-acedb@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!cea.fr!usenet From: cisitm@albert.cad.cea.fr (Pierre Didierjean) Newsgroups: bionet.software.acedb Subject: *** Q: WHAT KIND OF PEOPLE ON THE NET ? Date: 3 Nov 1994 16:17:35 GMT Organization: SSII Lines: 28 Sender: cisitm@albert.cad.cea.fr Message-ID: <39b2ev$9qm@anemone.saclay.cea.fr> NNTP-Posting-Host: nyassa.cad.cea.fr I'd like to know what kind of people i find on the net. Students, Commercials, Adminitrations, Scientifics or what ?? Is anybody knows that or have statistical results ? What are YOU doing in life ? I am a system administrator. Thanks for the answers and sorry for my english ..... Bye +-----------------------------------------------------------------------------+ | Pierre DIDIERJEAN | | | | Administrateur Systeme UNIX | | Cisi, Aix-en-Provence | | France | +-----------------------------------------------------------------------------+ | email : cisitm@albert.cad.cea.fr | +-----------------------------------------------------------------------------+ From owner-acedb@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!morpheus.lif.icnet.uk!user From: mike@bison.lif.icnet.uk (Mike Mitchell) Newsgroups: bionet.software.acedb Subject: Re: *** Q: WHAT KIND OF PEOPLE ON THE NET ? Date: Thu, 03 Nov 1994 20:16:22 +0100 Organization: Imperial Cancer Research Fund Lines: 52 Message-ID: References: <39b2ev$9qm@anemone.saclay.cea.fr> NNTP-Posting-Host: morpheus.lif.icnet.uk In article <39b2ev$9qm@anemone.saclay.cea.fr>, cisitm@albert.cad.cea.fr (Pierre Didierjean) wrote: > I'd like to know what kind of people i find on the net. > > Students, Commercials, Adminitrations, Scientifics or what ?? > > Is anybody knows that or have statistical results ? > > > What are YOU doing in life ? > > I am a system administrator. > > > Thanks for the answers and sorry for my english ..... > > > > Bye > > > +-----------------------------------------------------------------------------+ > | Pierre DIDIERJEAN | > | | > | Administrateur Systeme UNIX | > | Cisi, Aix-en-Provence | > | France | > +-----------------------------------------------------------------------------+ > | email : cisitm@albert.cad.cea.fr | > +-----------------------------------------------------------------------------+ The sort of people who post a stupid message to every newsgroup available! -- * ***************************************************************** * *Michael Mitchell *"All I know about babies is that you * *User Support * are not supposed to put them into * *Molecular Biology Software * washing machines. Makes the colours * *Imperial Cancer Research Fund* run, presumably." * *+44 (0)71 269 3115 * Tom Holt - Here Comes The Sun - 1994* * ***************************************************************** * From owner-acedb@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!rutgers!gatech!news-feed-1.peachnet.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: ACEDB version 3.3? Date: 4 Nov 1994 21:53:24 GMT Organization: University of Georgia, Athens Lines: 20 Message-ID: <39eagk$1np@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi all: We're working on a genetic database for peanuts (arachis) and the template we're working from is SoyBase 1.9. We've imported our data into ACEDB 3.3 (after making the necessary backwards-compatible modifications to ACEDB 3.3's wspec files). In 3.3, double clicking on a linkage group opens a tree display instead of the graphic gMap. We'd like the graphic gMap instead. Before I plunge heedlessly into the code, is anyone else working on porting SoyBase-style systems to ACEDB 3.3? And more generally, how has version 3.3 caught on? I haven't seen anything about it on the net (except the source!). -- Paul Brunk Botany Department University of Georgia pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Fri Nov 04 22:00:00 1994 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mieg@watson.wustl.edu (Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: ACEDB version 3.3? Date: 5 Nov 1994 00:29:50 -0000 Lines: 37 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39ejlu$2vv@mserv1.dl.ac.uk> Original-To: pbrunk@dogwood.botany.uga.edu 3.3 was for developpers it is beeing used with fixes for IGD, the human genome project the code as on ncbi had some errors in configuration files etc you want that for your linkage group in options.wrm to say -D VMAP actually all the -D GMAP should go there to -DVMAP except for class _gMap I just did put on ncbi 3.4 with the following README Known bug in this code: the online help now calls mosaic and immediatly crashes this is beeing looked and this is why this code is here the rest is supposed to work Improvements over 3.3 the tags.wrm and classes.wrm files are gone this means that directa dditions to models work and that this program can run on different databases say nematode and IGD without problem the table maker bug to access matrices of data is fixed the table maker know supports constarints between columns this will be documented soon the speed of the lexique is much increased however THIS IS NOT a fullfledged distribution **** please let me know if you use this code From owner-acedb@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!rutgers!gatech!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!yuma!usenet From: mferguso@klab.agsci.colostate.edu (Martin L. Ferguson) Newsgroups: bionet.software.acedb Subject: Getting WWW/Mosaic interface to display map graphics?? Date: 7 Nov 1994 19:40:07 GMT Organization: csu Lines: 17 Distribution: world Message-ID: <39lvqn$39ca@yuma.ACNS.ColoState.EDU> Reply-To: mferguso@klab.agsci.colostate.edu NNTP-Posting-Host: klab.agsci.colostate.edu Greetings all, I just set up a www interface to our ACeDB Aedes aegypti database. I've noticed that when accessing AAtDB or ACeDB vi Mosaic, and looking at a chromosome map, you see the graphic. On the one I set up (http://klab.agsci.colostate.edu) you only get a list of the loci on that particular chromosome map. My question: how do I get Mosaic to display the chromosome map graphic? Thanks to any and all. /s/ Martin From owner-acedb@net.bio.net Mon Nov 07 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!sunic!news.kth.se!kiev.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: Getting WWW/Mosaic interface to display map graphics?? Followup-To: bionet.software.acedb Date: 8 Nov 1994 08:11:23 +0100 Organization: Biochemistry, KTH, Stockholm Lines: 40 Sender: staffan@biochem.kth.se Distribution: world Message-ID: <39n8ar$79i@kiev.physchem.kth.se> References: <39lvqn$39ca@yuma.acns.colostate.edu> NNTP-Posting-Host: kiev.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Keywords: WWW In article <39lvqn$39ca@yuma.acns.colostate.edu> Martin Ferguson (mferguso@klab.agsci.colostate.edu) writes: >I just set up a www interface to our ACeDB Aedes aegypti database. Welcome to the gang, Martin! >I've noticed that when accessing AAtDB or ACeDB vi Mosaic, and looking >at a chromosome map, you see the graphic. On the one I set up >(http://klab.agsci.colostate.edu) you only get a list of the loci on >that particular chromosome map. > >My question: how do I get Mosaic to display the chromosome map >graphic? Briefly: you need to set up GhostScript to translate the graphics into GIF, and (possibly) set a few environmental variables. The defaults are such that if you have GS installed in the 'right' place and do nothing else, then you get clickable maps. My guess is that you're missing ghostscript! It's a GNU program, available from many places. This is described in Guy's installation instructions, at URL: http://moulon.inra.fr/acedb_tech_eng.fr >Thanks to any and all. > >/s/ Martin /staffan Staffan Bergh Biochemistry, KTH, S-100 44 Stockholm, Sweden MycDB, The mycobacterial database -- http://kiev.physchem.kth.se/MycDB.html AboutDB, The database about ACEDB -- http://kiev.physchem.kth.se/AboutDB.html email: staffan@biochem.kth.se + Don't let that horse eat that violin phone: int+46 8 790 8758 + cried Chagall's mother fax: int+46 8 24 54 52 + but he kept right on painting + -- Lawrence Ferlinghetti From owner-acedb@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mieg@watson.wustl.edu (Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: change models and classes Date: 10 Nov 1994 23:01:21 -0000 Lines: 1 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39u8o1$3nu@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk you NEED NOT recompile in Unix nor in Mac to add classes and change models From owner-acedb@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!daresbury!trane.uninett.no!eunet.no!nuug!nac.no!nntp.uio.no!rodrigol From: rodrigol@biomaster.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.acedb Subject: IGD problem Date: 10 Nov 1994 14:54:55 GMT Organization: University of Oslo Lines: 28 Message-ID: <39tc7v$fsb@hermod.uio.no> NNTP-Posting-Host: biomaster.uio.no X-Newsreader: TIN [version 1.2 PL2] Hello, I'm having a problem using IGD (the mosaic interface+AceDB) on my site. After installation under my user name or root everything I've tested so far seems to work. Mosaic fires up ok and cliking on the links brings up the appropriate client. Now for the problem: When I log in as another user and start igd and click on the link all I get is the contents of the csh file the link is composed of. All user what rx permission on all directories where I installed fred 1.0. So the question is: What an I doing wrong? Thanks in advance, R:) -- *************************************************************************** * RODRIGO LOPEZ SERRANO rodrigol@biotek.uio.no * * Norwegian EMBnet node Tel:xx-47-22958756 Fax:xx-47-22694130 * * gopher= biomaster.uio.no 70 WWW= http://biomaster.uio.no/ * *************************************************************************** From owner-acedb@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!sgiblab!spool.mu.edu!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: macace recompile? Date: 10 Nov 1994 19:20:01 GMT Organization: University of Georgia, Athens Lines: 13 Message-ID: <39trp1$rgv@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi all: If I want to add models/classes/tags to macace 2.0, can I do this and recompile as I can in UNIX? Has anyone done this? Which compiler did you use? Thanks again! -- Paul Brunk Botany Department University of Georgia pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Thu Nov 10 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: macace recompile? Date: 11 Nov 1994 13:31:50 -0000 Lines: 7 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39vro6$kqs@mserv1.dl.ac.uk> Original-To: pbrunk@dogwood.botany.uga.edu You don't need to recompile if you just add classes, tags and models, and you don't use them in the code, e.g. if you just want to look at them in tree/text form. You only need to recompile if you change the code. This is true of both the Unix and Macintosh versions. Richard From owner-acedb@net.bio.net Sun Nov 13 22:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: compiling ace3.4a on SGI Date: 14 Nov 1994 10:14:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411141815.AA08938@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net compiling ace3.4a on SGI; I suggest to change 3 things: 1. cc -Wf,-XNh2000 -g -DNO_LEFT_CASTING -I../wh -I../whooks -DACEDB -DSGI -c -c parse.c cfe: Error: parse.c, line 642: Type void of returning expression is incompatible with type void of function return type { return openCprsFile(0) ; --^ cfe: Error: parse.c, line 646: Type void of returning expression is incompatible with type void of function return type { return openCprsFile('Z') ; --^ cfe: Error: parse.c, line 650: Type void of returning expression is incompatible with type void of function return type { return openCprsFile('g') ; --^ please remove the "return" because there is nothing returned. 2. Since the object file for disknew.c was so empty, I added -DACEDB3 to wmake/SGI_DEF 3. in truemake: \rm abi should be changed into \rm -f abi otherwise you get an error on the first time and abi is not set up as a link. -------------------------------- now a am loading the GDB data from a compressed file :-) However, the user interface is confusing: in the ".ace file parser" window, after selecting a .Z file, this .Z extension is not reflected in the filename shown -- it is still .ace. Anyway I would prefer the file chooser to display .ace, .ace.gz and .ace.Z and ACEDB would recognize by the filename extension how to open the file instead of having three different buttons. I think we can make computers that smart ;-) best wishes Detlef From owner-acedb@net.bio.net Sun Nov 13 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!lll-winken.llnl.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 14 Nov 1994 22:17:29 GMT Organization: Dendrome, A genome database for forest trees Lines: 1124 Approved: news-answers-request@MIT.Edu Message-ID: <3a8nlp$ee6@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:480 news.answers:26818 Archive-name: acedb-faq Last-modified: 11/14/94 Version: 1.16 ---------------------------------------------------------------------- Common Questions, with Answers, about ACEDB. 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|ftp|WWW|URL ... Q10: How can I get on/off the ACEDB announcements mailing list? Q11: When and where is the next ACEDB Workshop? Q411: Who prepared this document & where is the current version? 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 [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. 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.] Currently there are two threads of the ACEDB kernel: the 2.x series which represents the C. elegans project under the tutelage of Richard Durbin, and the 3.x series from Jean Thierry-Mieg. However, the differences in the code are slight and the two authors committed to a single kernel at the ACEDB workshop in July, 1994. The most recent release is an experimental version 3.3 which is available from the repositories. 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: Unix and X11: Sun/SunOS 4.x Sun/Solaris DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series 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. 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. NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu MSDOS/Windows/NT: A port to NT is rumored to be in the works. Macintosh: [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. To retrieve the software see Q3. For cost savings, a combination of a high-end Intel platform with Linux appears very attractive. [Though the port does not seem robust, yet --bks] 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. 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: 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. MacAce is available from: genome.lbl.gov (131.243.224.80) in pub/macace cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb/macace Linux; ACEDB version 2.0 for Linux 2-10: trog.mbb.sfu.ca /pub/acedb as linux.2_10.tar.Z 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 Return to List of Questions ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alphabetic order by Database name. Curators, submit changes as new paragraphs.--bks] Database : AAnDB-1.0 Species : Aspergillus nidulans PI : Leland Ellis Last_update : February 1994 ACEDB_version : 3.0 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : AAtDB Species : Arabidopsis thaliana Current version : 3-3 Last_update : June 1994 Curator : John Morris Contact : curator@frodo.mgh.harvard.edu Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x Availability : Macintosh version in /aatdb/MacAAtDB directory URL : gopher://weeds.mgh.harvard.edu/ URL : http://weeds.mgh.harvard.edu:80/index.html Database : ABtDB-1.0 Species : Bovine, Bos taurus ACEDB_version : 3.0 extended PI : Leland Ellis Last_update : February 1994 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : AboutDB Curator : Staffan Bergh PI : Staffan Bergh Subject : ACEDB itself (Is this meta-meta-metadata) ACEDB 3.0 Contact : staffan@biochem.kth.se URL http://kiev.physchem.kth.se/AboutDB.html Database : ACeDB Species : Caenorhabditis elegans Current version: 2-10 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@mrc-lmb.cam.ac.uk Contact : mieg@kaa.crbm.cnrs-mop.fr Last_update : May 1994 DataBase : AceMap Species : Homo sapiens (Mus musculus under development) Focus : Physical mapping of human chromsome X and 21 ACEDB_version : 3.0 Curator : Hugues Roest Crollius PI : Hans Lehrach 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. Contact : hrc@gea.lif.icnet.uk (Hugues Roest Crollius) ICRF, Lincoln's Inn Fields London, UK. Last_update : August 94 Database : AGsDB A Genus species Database Species : Aspergillus nidulans Species : Neurospora crassa Species : cow w/ human anchor loci Species : cotton (demo) Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast PI : Leland Ellis Curator : Leland Ellis Last_update : March 1994 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 Models : as of 3.13.94 Data : as of 3.13.94 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. WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux (ducoux@moulon.inra.fr). URL : http://keck.tamu.edu/ibt.html Contact : leland@straylight.tamu.edu Database : ChlamyDB Species : Chlamydomonas PI : Elizabeth Harris Contact : chlamy@acpub.duke.edu Availability : ChlamyDB 1.0, using ACEDB 3.0, is now on WWW and gopher (probe.nalusda.gov). Complete version using ACECB 3.3 will be available soon by ftp. URL : http://probe.nalusda.gov:8300 Last_update : 25 Oct, 1994 Database : CottonDB Species : Gossypium hirsutum (cotton) PI : Russell J. Kohel USDA-ARS Southern Crops Research Laboratory Route 5, Box 805, College Station, Texas 77845 Curator : Gerard R. Lazo Curator : Sridhar Madhavan Last_update : July, 1994 ACEDB_version : 3.0 Contact : rjk0339@zeus.tamu.edu (Russell Kohel) Contact : lazo@genome.tamu.edu (Gerard Lazo) Availability : still under construction Phone : 409-260-9311 Fax : 409-260-9333 Database : CSNDB Focus : Cell Signalling Molecules and Interactions Contact : Takako Igarashi National Insitute of Health Sciences Division of Chem-Bio Informatics Setagaya-ku, Tokyo, Japan 158 taka@nihs.go.jp Database : EcoDB Species : E. coli PI : Staffan Bergh Contact : staffan@biochem.kth.se Availability : Proposed Last_update : Aug. 1994 Database : 11DB Species : Homo sapiens Focus : Physical mapping of chromosome 11 Availability : under development Curator : Benedict Arnold PI : Peter Little Contact : Benedict Arnold Dept. Biochemistry, Imperial College, London, SW7 2AZ b.arnold@ic.ac.uk Database : The Encyclopaedia of the Drosophila Genome. Acronym : (none) Species : Drosophilidae (primarily D. melanogaster) Availability : MacFly/FlyDB-based distribution by ftp and CD-ROM due early 1995 Developer : Suzanna Lewis Contact : suzi@fly2.berkeley.edu Developer : Cyrus Harmon Contact : sly@fly2.berkeley.edu Developer : Edward Welbourne Contact : eddy@gen.cam.ac.uk Curation : Data is provided by the collaborating organisations: Collaborator : The FlyBase Consortium, flybase@morgan.harvard.edu Collaborator : The Berkeley Drosophila Genome Project URL : gopher://fly.bio.indiana.edu:70+/11/Flybase Database : Flydb Species : Drosophila melanogaster Curator : Suzanna Lewis Contact : suzi@fly2.berkeley.edu Database : GrainGenes Species : Wheat, barley, oats, relatives Availability : Anonymous ftp from probe.nalusda.gov:pub/grains Availability : Gopher greengenes.cit.cornell.edu port 70 Availability : Gopher probe.nalusda.gov port 7002 Curator : David E. Matthews PI : Olin D. Anderson Contact : matthews@greengenes.cit.cornell.edu Contact : oandersn@wheat.usda.gov URL : gopher://greengenes.cit.cornell.edu/1/ Data_version : 1.3 Released : 12 Jan 1994 Based_on : acedb.1-10 Availability : See following WWW URL URL : http://probe.nalusda.gov:8300 Last_update : Feb. 1994 Database : human.c17 Species : Homo sapiens Availability : the database is under development Contact : lsprilus@weizmann.weizmann.ac.il Focus : mapping & sequencing of Human Chromosome 17 Based_on: acedb.3-0 Last_update : Jan. 1994 Database : IGD - the Integrated Genomic Database Species : Homo sapiens (later mouse and other mammalian species) Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter [ o.ritter@dkfz-heidelberg.de ] Curator : tba 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. Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie_paule Lefranc Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr Database : Maize Species : Zea mays L. ssp. mays Focus : Maize genome Acedb_version : 1.9 FTP : probe.nalusda.gov, pub directory; anonymous ftp Comment : Maize is an acedb front end for the Maize Genome Database, MaizeDB, a SYBASE database. 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). 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. Gopher : host = teosinte.agron.missouri.edu, port = 70 Telnet : telnet teosinte.agron.missouri.edu login as guest, use password 'corncob' HTTP : http://teosinte.agron.missouri/top.html HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant Genome Database Comment : Genera is a software toolkit for creating and extracting data from Sybase databases; used to create MaizeDB and Worldwide Web connectivity. HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu Curator : Pat Byrne byrne@teosinte.agron.missouri.edu Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu Curator : Mary Polacco maryp@teosinte.agron.missouri.edu Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Curator : Christiane Fauron FAURON@GENE1.med.utah.edu Curator : Carolyn Wetzel cmwetzel@iastate.edu Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU Design : Stan Letovsky letovsky-stan@CS.YALE.EDU Design : Mary Berlyn mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 25 April 1994 Database : MycDB Species : Mycobacteria 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. PI : Staffan Bergh PI : Stewart Cole PI : Doug Smith Curator : Staffan Bergh Contact : staffan@biochem.kth.se Last_update : Apr. 1994 WWW : http://kiev.physchem.kth.se/MycDB.html ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb Database : PomBase Curator : Sean Walsh Curator : Marie-Adele Rajendream PI : Bart Barrell Species : Schizosaccharomyces pombe Contact : svw@sanger.ac.uk Contact : barrell@sanger.ac.uk Comment : Not yet available for distribution DataBase : Mousedb Species : Musculus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. 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. Curator : Michelle Kirby Curator : Rachael Selley PI : Mary Lyon PI : Jo Peters 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. 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 Last_update : October 1994 Database : RiceGenes Species : Rice (O. sativa) Availability : Anonymous ftp from probe.nalusda.gov:pub/rice Availability : Gopher nightshade.cit.cornell.edu port 70 Availability : Gopher probe.nalusda.gov port 7007 Curator : Edie Paul PI : Susah McCouch Contact : epaul@nightshade.cit.cornell.edu Release : ACEDB 1-10 Last_update : May 1994 Database : SacchDB Species : Saccharomyces cerevisiae Focus : Budding Yeast Genome Acedb_version : 2.0, MacAce FTP : genome-ftp.stanford.edu, not available yet. Comment : The database is in beta test by a small number of yeast labs. The WWW-ACEDB gateway version is currently available, see HTTP below. The Gopher server contains only the Olson restriction map information and views of the resulting Clone (Physical) Map. Data : Olson/Riles Physical Map, Mortimer Genetic Maps and Information, Sequences from GenBank, Gene/Clone associations using the Wash Univ. prime clone filters. Gopher : host = genome-gopher.stanford.edu, port = 70 HTTP : URL http://genome-www.stanford.edu Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Fred Dietrich, dietrich@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Systems : Dan Mosedale, mosedale@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Last_update : 9 August 1994 Database : SolGenes Coverage: Solanaceae - tomato, potato, pepper Availability : Anonymous ftp from probe.nalusda.gov:pub/solgenes Availability : Gopher nightshade.cit.cornell.edu port 71 Availability : Gopher probe.nalusda.gov port 7006 Curator : Edie Paul PI : Steve Tanksley Contact : epaul@nightshade.cit.cornell.edu Release : ACEDB 3.0 Last_update : May 1994 Database : SorghumDB Species : Sorghum bicolor (L.) Moench 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 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 Last_update : July 1994 ACEDB_version : 3.0 Availability : Under Development Database : SoyBase Species : Soybeans Curator : Lisa Lorenzen PI : Randy Shoemaker Contact : lorenzen@mendel.agron.iastate.edu Phone : 515-294-0421 Fax : 515-294-2299 Last_update : Sept. 1993 Database : Sybace Species : Homo sapiens Creator : Detlef Wolf Comment : Custom software --ACEDB front-end to SYBASE data Contact : D.Wolf@dfkz-heidelberg.de See_also : IGD Database : TreeGenes Species : Forest trees Availability : alpha, contact curator ACEDB_version : 1-10 Curator : Bradley K. Sherman PI : David B. Neale Contact : Dendrome@s27w007.pswfs.gov Contact : bks@s27w007.pswfs.gov Contact : dbn@s27w007.pswfs.gov Last_update : March 1994 URL : gopher://s27w007.pswfs.gov/ URL : http://s27w007.pswfs.gov/ URL : ftp://probe.nalusda.gov/pub/trees Database : 21Bdb Species : Homo sapiens Focus : STS content mapping & sequencing of Human Chromosome 21 Availability : by request, via ftp, world-wide-web Based_on : acedb.1-10 plus moulon server URL : ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z URL : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy Contact : DFDavy@lbl.gov Contact : aggarwal@genome.lbl.gov Focus : STS content mapping & sequencing of Human Chromosome 21 PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng Last_update : Apr. 1994 Database : 22ace Species : Homo sapiens Curator : Ian Dunham Focus : Physical mapping of chromosome 22 PI : Ian Dunham Contact : Ian Dunham Sanger Centre Hinxton Hall, Cambs. UK. id1@sanger.ac.uk 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 : Xace Species : Homo sapiens Curator : Gareth Maslen Focus : Physical mapping of chromosome X PI : David Bentley Contact : Gareth Maslen Sanger Centre Hinxton Hall, Cambs. UK. glm@sanger.ac.uk Database : ? Species : Homo sapiens Focus : Physical mapping of human chromosome 6. Curator : Ioannis Ragoussis Availability : Unknown Contact : Guy's hospital 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 and linkage mapping of chromosome 8 Availability : Curator : Stephen Wood PI : Stephen Wood 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: 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-) Get By anonymous ftp from ncbi.nlm.nih.gov (130.14.20.1) 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 and postscript. [I have had some difficulty printing these. Jean Thierry-Mieg suggests latex xxxx.tex, dvi2ps xxxx.dvi > xxxx.ps, lpr xxxx.ps.] 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: http://moulon.inra.fr/acedb/acedb.html for C. elegans data http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html http://moulon.inra.fr/acedb_conf.html (en francais) The Genome Computing Group, Lawrence Berkeley Laboratory has an anonymous ftp service at machine genome.lbl.gov (131.243.224.80) which contains: flydb - LBL's Drosophila Acedb-style database 21bdb - LBL's Human Chromosome 21 Acedb-style database querdb - LBL's query-language extensions to Acedb metadata - LBL's compendium of Acedb database schema variants macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version There is also a repository of contributed software for data conversions and the like. [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: 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). 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 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. 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 ... 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 is on the mailing list. Return to List of Questions ---------------------------------------------------------------------- Q11: When and where is the Next ACEDB Workshop? In planning, California 1995. [Contact information to appear here. --bks] If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers taken by Mike Cherry with the camera on an SGI workstation, the URL is: http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html. John Morris has provided some more at URL: http://weeds.mgh.harvard.edu/ace94/ace94.image.html. Return to List of Questions ---------------------------------------------------------------------- Q411:Who prepared this document & where is the current version? [Note to international readers: 411 is the phone number for information in the USA. --bks] 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. 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/acedocs/acedbfaq.html 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: Lisa Lorenzen David Matthews Edie Paul Donn Davy Eric De Mund 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, 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. --bks Return to List of Questions ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Mon Nov 14 22:00:00 1994 Path: biosci!ic.ac.uk!b.arnold From: b.arnold@ic.ac.uk Newsgroups: bionet.software.acedb Subject: A puzzle with graphBoxDim. Date: 15 Nov 1994 03:37:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <16837.9411151135@bccsc.bc.ic.ac.uk> NNTP-Posting-Host: net.bio.net Hi there, I'm having a problem with a call to graphBoxDim. The code looks as follows in MapDrawAnyLocus : for (i = 0 ; i < arrayMax(look->segs) ; ++i) { seg = arrp(look->segs,i,SEG) ; if (seg->flag & FLAG_HIDE) continue ; if (!(seg->flag & (FLAG_ANY_LOCUS | FLAG_MULTIPLE_LOCUS))) continue ; y = MAP2GRAPH(look->map,seg->x) ; if (y > topMargin && y < graphHeight-1) { array(look->boxIndex,ibox=graphBoxStart(),int) = i; x = errorScale*seg->dx ; bumpItem (bump, strlen(name(seg->symbol)), 0.6, &x, &y) ; graphText (name(seg->symbol), *offset+x, y-0.3) ; graphBoxDraw (ibox, BLACK, WHITE) ; graphBoxEnd () ; graphBoxMenu (ibox, nGeneMenu) ; } The problem I have is that I now want to make a call as follows graphBoxDim(ibox,&x1,&y1,&x2,&y2); As the code above suggests that ibox has been drawn, and the code compiles ok, why when I run abi and try and select a map from my list do I get the message FATAL ERROR: Cannot get box x - index out of range. It seems most odd that following a graphBoxEnd() I can then not do a graphBoxDim() call. Another interesting item to add to this is that this only appears to happen if the map consists of information that has boxes drawn around in the MapDrawAnyLocus function. If any boxes are drawn leftward of the start of this function then the map draws ok and the graphBoxDim call works without problem. I hope someone can explain this I'm completely stumped. Benedict Arnold. From owner-acedb@net.bio.net Mon Nov 14 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!morpheus.lif.icnet.uk!user From: mike@bison.lif.icnet.uk (Mike Mitchell) Newsgroups: bionet.software.acedb Subject: Trouble with MacACedb Date: Tue, 15 Nov 1994 15:58:57 +0100 Organization: Imperial Cancer Research Fund Lines: 16 Message-ID: NNTP-Posting-Host: morpheus.lif.icnet.uk We are having difficulty locally getting the Multimaps displayed when running macace3.nt, there is an error message:- A fatal Error has just occurred: textBounds called on invalid graph type 2 HELP!!! please. -- * ***************************************************************** * *Michael Mitchell *"All I know about babies is that you * *User Support * are not supposed to put them into * *Molecular Biology Software * washing machines. Makes the colours * *Imperial Cancer Research Fund* run, presumably." * *+44 (0)71 269 3115 * Tom Holt - Here Comes The Sun - 1994* * ***************************************************************** * From owner-acedb@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uunet!olivea!sgigate.sgi.com!enews.sgi.com!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!unixg.ubc.ca!unixg.ubc.ca!swood From: swood@unixg.ubc.ca (Stephen Wood) Newsgroups: bionet.software.acedb Subject: Re: IGD problem Date: 16 Nov 94 06:49:13 GMT Organization: The University of British Columbia Lines: 21 Message-ID: References: <39tc7v$fsb@hermod.uio.no> NNTP-Posting-Host: unixg.ubc.ca rodrigol@biomaster.uio.no (Rodrigo Lopez) writes: >Hello, >I'm having a problem using IGD (the mosaic interface+AceDB) on my site. >When I log in as another user and start igd and click on the link all >I get is the contents of the csh file the link is composed of. >All user what rx permission on all directories where I installed fred 1.0. >So the question is: What an I doing wrong? I encountered the same problem. The answer from genome.dkfz-heidelberg.de is to copy the .mailcap and .mime.types files from your home directory to /usr/local/lib/mosaic and rename them mailcap and mime.types i.e. they should no longer be .files. Worked for me. Stephen Wood From owner-acedb@net.bio.net Mon Nov 21 22:00:00 1994 Path: biosci!agate!gmrubin5.berkeley.edu!user From: sly@fly2.berkeley.edu (Cyrus Harmon) Newsgroups: bionet.software.acedb Subject: Re: font of macace Date: 22 Nov 1994 21:11:59 GMT Organization: UC Berkeley Lines: 16 Distribution: world Message-ID: References: <9411220850.AA11347@nihs> NNTP-Posting-Host: gmrubin5.berkeley.edu In article <9411220850.AA11347@nihs>, taka@nihs.go.jp (Takako Igarashi 296) wrote: > > I am a macace user,and I have one question. > Can I change the size of a font of macace? > I can change fonts in X11-acedb by editing the > "xfonts.wrm" file, but in macace that does not work. > The fonts are currently hard-coded in the application. This is a bad thing and will hopefully be fixed one of these days. Cyrus Harmon Berkeley Drosophila Genome Project sly@fly2.berkeley.edu From owner-acedb@net.bio.net Mon Nov 21 22:00:00 1994 Path: biosci!nihs.go.jp!taka From: taka@nihs.go.jp (Takako Igarashi 296) Newsgroups: bionet.software.acedb Subject: font of macace Date: 22 Nov 1994 00:52:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411220850.AA11347@nihs> NNTP-Posting-Host: net.bio.net Hello, I am a macace user,and I have one question. Can I change the size of a font of macace? I can change fonts in X11-acedb by editing the "xfonts.wrm" file, but in macace that does not work. I am sorry to bother you with such a trivial question, but my assistant is so short-sighted that she is hard to look at the letters of macace. Thank you in advance, Takako Igarashi National Institute of Health Sciences taka@nihs.go.jp From owner-acedb@net.bio.net Thu Nov 24 22:00:00 1994 Path: biosci!agate!ames!enews.sgi.com!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!unixg.ubc.ca!port45.annex1.net.ubc.ca!user From: seow@unixg.ubc.ca (Kah-Tong, Seow) Newsgroups: bionet.software.acedb Subject: (Q) How to set up MycDB Followup-To: bionet.software.acedb Date: Thu, 24 Nov 1994 21:19:49 -0800 Organization: West East Centre, UBC Lines: 20 Message-ID: NNTP-Posting-Host: port45.annex1.net.ubc.ca I am interested to set up MycDB in a centris 650. I have tried to understand the procedure of setting it up by reading the MycDBretrieved.doc. I have a few questions. (1) What is the newest version of Macace which will work with the version 3 of MycDB . Which site has it?. (2) The MycDB is availabe as update3_1.tar.z to update 3_5.tar.z. Do I retrieved all of them into Mac and what utility programs should I use to decrompress them Thanks in advance. -- Kah-Tong, Seow West East Centre Univ of British Columbia Vancouver seow@unixg.ubc.ca From owner-acedb@net.bio.net Sun Nov 27 22:00:00 1994 Path: biosci!FLY2.BERKELEY.EDU!suzi From: suzi@FLY2.BERKELEY.EDU (Suzanna Lewis) Newsgroups: bionet.software.acedb Subject: Re: Pick_me_to_call twice or more Date: 28 Nov 1994 10:27:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411281823.KAA00861@fly2.berkeley.edu> NNTP-Posting-Host: net.bio.net > > sorry this cannot be done as is > but Otto ah been suggesting for along time a more powerful > ?Action class which would do that sort of things or invke > external progrmas in a generic way > we should implement taht some day > > some us already have... -suzi From owner-acedb@net.bio.net Sun Nov 27 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mieg@watson.wustl.edu (Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Pick_me_to_call twice or more Date: 28 Nov 1994 17:59:31 -0000 Lines: 6 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3bd5q3$nkv@mserv1.dl.ac.uk> Original-To: @wugate.wustl.edu@dl.ac.uk, @.ib.rl.ac.uk@dl.ac.uk, @pserv1.dl.ac.uk:server-daemon@dl.ac.uk sorry this cannot be done as is but Otto ah been suggesting for along time a more powerful ?Action class which would do that sort of things or invke external progrmas in a generic way we should implement taht some day From owner-acedb@net.bio.net Sun Nov 27 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!newsserver.cshl.org!pjm From: pjm@isis.cshl.org (Pat Monardo) Newsgroups: bionet.software.acedb Subject: ACEDB bugs Date: 28 Nov 1994 17:15:01 GMT Organization: Cold Spring Harbor Labs Lines: 10 Message-ID: <3bd36lINN6i4@phage.cshl.org> NNTP-Posting-Host: lilith.cshl.org I shouldn't be too surprised if software created for worms has bugs. If someone could fill me in on the best way to discuss acedb bugs, that would be nice. I keep getting 'Fatal Error: lost a chromosome' when working with physical maps. I have to admit it was a very interesting error message. Anyway, happy bug hunting ... Fun software! From owner-acedb@net.bio.net Sun Nov 27 22:00:00 1994 Path: biosci!nihs.go.jp!taka From: taka@nihs.go.jp (Takako Igarashi 296) Newsgroups: bionet.software.acedb Subject: use pick_me_to_call twice or more Date: 28 Nov 1994 01:26:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411280924.AA04726@nihs> NNTP-Posting-Host: net.bio.net Hello, I would like to use Pick_me_to_call facility twice or more in one class. Of course, because Pick_me_to_call is a tag, it can be used only once per class definition. To circumvent this restriction, I tried to apply "constructed type" facility and "attach" facility. (I got code_3.3 from ncbi mirror site in Japan.) But both of them do not work. They give the same error message as follows: Sorry, a program its parameters are expected here. And this is the class definition that I tried: ?Structural_Data Schematic_Structure ?View @">Pick;Pick_me_to_call" 3D_Structure #View ?View Pick Pick_me_to_call UNIQUE Text UNIQUE Text Isn't it possible to use Pick_me_to_call facility twice or more in one class by any means? Thank you in advance, Takako Igarashi National Institute of Health Sciences taka@nihs.go.jp From owner-acedb@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mieg@watson.wustl.edu (Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Problem compiling ace 3.5 Date: 29 Nov 1994 05:14:41 -0000 Lines: 6 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3bedc1$3ov@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk i already replied to that one you have a different include stuff from your gcc edit wh/mystdlib.h so as to jump the definition of flsbuf From owner-acedb@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunic!news.kth.se!kiev.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: Problem compiling ace 3.5 Date: 29 Nov 1994 08:12:32 +0100 Organization: Biochemistry, KTH, Stockholm Lines: 28 Distribution: world Message-ID: <3bek90$2c4@kiev.physchem.kth.se> References: NNTP-Posting-Host: kiev.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article jvu@CHROM5.HSIS.UCI.EDU (John Vu) writes: > >Hi acedb users, > >We are having a problem in compiling ace 3.5 (from ftp//ncbi.nih.gov). >We are running SPARCstation IPX, SUN OS 4.1.3, with 32 MB RAM. [...stuff deleted...] >/dcs/packages/gnu/lib/gcc-lib/sparc-sun-sunos4.1.1/2.5.8/include/stdio.h:28: previous declaration of `_flsbuf' ^^^^^ My suggestion is to upgrade to latest version of gcc = 2.6.2, seems the 2.5.8 includes have some problems with Sun's non-standard includes. I've compiled 3.4e with 2.6.2 on SunOS4.1.3 with none of these errors. (I'll have a go at 3.5 today ...) /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 8758 + cried Chagall's mother fax: int+46 8 24 54 52 + but he kept right on painting + -- Lawrence Ferlinghetti From owner-acedb@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!CHROM5.HSIS.UCI.EDU!jvu From: jvu@CHROM5.HSIS.UCI.EDU (John Vu) Newsgroups: bionet.software.acedb Subject: Problem compiling ace 3.5 Date: 28 Nov 1994 17:38:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi acedb users, We are having a problem in compiling ace 3.5 (from ftp//ncbi.nih.gov). We are running SPARCstation IPX, SUN OS 4.1.3, with 32 MB RAM. Here is the error message we get after setting ACEDB_MACHINE to SUN and attempting to "make": ------------------- chrom5% make ACeDB source directory: /data/ace3.4 making xace for SUN_STATIC cp ../w1/freesubs.c . chmod u+w freesubs.c gcc -Wreturn-type -Wimplicit -Wunused -Wcomment -O -fwritable-strings -DWCS -g -I../wh -I../whooks -DACEDB -DSUN -c freesubs.c In file included from ../wh/regular.h:8, from freesubs.c:19: ../wh/mystdlib.h:185: conflicting types for `_flsbuf' ../wh/mystdlib.h:185: An argument type that has a default promotion ../wh/mystdlib.h:185: can't match an empty parameter name list declaration. /dcs/packages/gnu/lib/gcc-lib/sparc-sun-sunos4.1.1/2.5.8/include/stdio.h:28: previous declaration of `_flsbuf' *** Error code 1 make: Fatal error: Command failed for target `freesubs.o' Current working directory /data/ace3.4/bin.SUN_STATIC *** Error code 1 The following command caused the error: cd /data/ace3.4/bin.SUN_STATIC ; make xace make: Fatal error: Command failed for target `xace' ------------------------- We would appreciate any input/advice. Thank you. Regards, John D. Vu INTERNET: JDVU@UCI.EDU National Human Genome Research Center Phone : (714) 824 - 7447 UCI College of Medicine, Medical Sciences I, Rm D240 Irvine, CA 92717 From owner-acedb@net.bio.net Tue Nov 29 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!csulb.edu!nic-nac.CSU.net!charnel.ecst.csuchico.edu!waldorf.csc.calpoly.edu!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!unixg.ubc.ca!port19.annex4.net.ubc.ca!user From: seow@unixg.ubc.ca (Kah-Tong, Seow) Newsgroups: bionet.software.acedb Subject: MacAce 3.0 Followup-To: bionet.software.acedb Date: Tue, 29 Nov 1994 23:42:16 -0800 Organization: West East Centre, UBC Lines: 9 Message-ID: NNTP-Posting-Host: port19.annex4.net.ubc.ca I would like to know where I could download the latest version of MacAce 3.0. Most sites offer MacAce 2.04. Thanks very much. -- Kah-Tong, Seow West East Centre Univ of British Columbia Vancouver seow@unixg.ubc.ca From owner-acedb@net.bio.net Wed Nov 30 22:00:00 1994 Path: biosci!rutgers!gatech!newsfeed.pitt.edu!godot.cc.duq.edu!news.duke.edu!glh From: glh@acpub.duke.edu (Geoff Hughes) Newsgroups: bionet.software.acedb Subject: ACEDB for HPUX? Date: 1 Dec 1994 18:44:52 GMT Organization: Duke University, Durham, NC, USA Lines: 21 Message-ID: <3bl5j4$qvs@news.duke.edu> NNTP-Posting-Host: bio6.acpub.duke.edu X-Newsreader: TIN [version 1.2 PL2] Hello again everybody- Its been a year since I had the pleasure of working with acedb, and now I am hoping I can use it at my new job. If anyone knows of a source code that will run on HPUX, or if the standard version will run on HPUX, I would greatly appreciate hearing about it. Please don't post or email as this is an account due to expire in a few days. If anyone is feeling particularly friendly, please call me at (919)406-1669. This is a North Carolina phone number. Thanks in advance, Geoff Hughes System Administrator Compuchem Environmental Corporation 3306 Chapel Hill/Nelson Hwy PO box 14998 Research Triangle Park, NC 27709-4998 (919)406-1669 j