From owner-acedb@net.bio.net Mon Aug 01 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: ace3.3 DEC compil. Date: 2 Aug 1994 12:08:28 +0100 Lines: 5 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <31l9fc$dch@mserv1.dl.ac.uk> Original-To: hrc@gea.lif.icnet.uk to compile my code 3.3 either have a -DACEDB2 make xace or -DACEDB3 make abi not make xace, sorry for this erro jean From owner-acedb@net.bio.net Mon Aug 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!trane.uninett.no!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: compiling 3.3 code Date: 2 Aug 1994 12:14:03 +0100 Lines: 64 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <31l9pr$dpe@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk This is a correct example of DEF as included in the 3.3 tar file: ################################################################# ############### acedb: R.Durbin and J.Thierry-Mieg ############## ########### wmake/DEC_ALPHA_DEF March-18-1993 ########## ################################################################# ################################################################# ########## Machine dependant compiler modification ############## ####### for the DEC-Alpha 3000 model 500 running Unix ########### ################################################################# ########### This file is included by wmake/truemake ############# ###### Edit this file to adapt the ACeDB to a new machine ###### ##### following the explanations given in wmake/truemake ##### ################################################################# NAME = ALPHA COMPILER = cc -g -std1 -DACEDB3 LINKER = cc -g LIBS = -lm ..c.o: $(CC) -c $*.c ################################################################# ################################################################# notice the line -DACEDB3 a similar define is needed for SUN etc this beeing done you can make: make xabi make tace make aceserver %%%%%%%%%%%%%%%%% alternativelly use NAME = ALPHA COMPILER = cc -O2 -DACEDB2 LINKER = cc LIBS = -lm ..c.o: $(CC) -c $*.c %%%%%%% then you can make xace make tace most probably, but i did not check aceserver/client From owner-acedb@net.bio.net Mon Aug 01 23:00:00 1994 Path: biosci!agate!library.ucla.edu!news.mic.ucla.edu!news.bc.net!newsserver.sfu.ca!sfu.ca!baillie From: baillie@beaufort.sfu.ca (Dave Leonard Baillie) Newsgroups: bionet.software.acedb Subject: Re: Help installing ace2 on LINUX Date: 30 Jul 94 23:53:42 GMT Organization: Simon Fraser University Lines: 9 Message-ID: References: <31cfmi$dq6@quartz.ucs.ualberta.ca> NNTP-Posting-Host: beaufort.sfu.ca Ken Clark has done the port of ace2 to Linux, it runs fine. I have been using it on my portable for last month or so. The binaries should be at ncbi site, if not one can pick them up from ftp trog.mbb.sfu.ca dave baillie ps ken said he was doing ace3 also, but I haven't checked to see if he put it in out anonymous ftp site. From owner-acedb@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: tace dump whole database? Date: 4 Aug 1994 04:33:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408041134.AA16373@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net is it possbible to dump a whole database non-interactively? I did not find such a command in tace. Thanks Detlef From owner-acedb@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: kirbym@har-rbu.mrc.ac.uk Newsgroups: bionet.software.acedb Subject: acedb3.3 reinitialisation bug Date: 4 Aug 1994 15:59:13 +0100 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <31qvo1$anh@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Has anyone noticed the following bug in the new acedb3.3? The system crashes if an attempt is made to reinitialise it by removing the database/ACEDB.wrm file only. !! FATAL ERROR 0: !! Bad Block Address in partition Increasing the DISK size in wspec/cachesize.wrm improves the situation temporarily but only until the next time ACEDB.wrm is removed. Deleting the whole of the database/* directory each time the system is reinitialised removes the problem as far as I can tell. Michelle email: kirbym@har-rbu.mrc.ac.uk From owner-acedb@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!agate!doc.ic.ac.uk!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Maps in 3.3 Date: 4 Aug 1994 16:50:37 +0100 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <31r2od$dtl@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk You should be able to compile either a version 2 compatible binary or a version 3 compatible binary from 3.3. For version 2 define -DACEDB2 during compilation as in ALPHA_2_DEF, and use GMAP to display maps. For version 3 define -DACEDB3, make abi, not xace, and use VMAP for your maps. i.e. the version 3 GMAP has been renamed VMAP (vertical map of any type) to avoid name clashes. In a future version 4 it is possible this will become MAP. As Jean has mailed, there may be some bugs in the 3.3 display handling -- the aim was to get something out reflecting the current state after the workshop, not a rock-solid distribution including all the new developments, which will take some time. Richard From owner-acedb@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: kirbym@har-rbu.mrc.ac.uk Newsgroups: bionet.software.acedb Subject: Is acedb3.3 for acedb2 only?? Date: 4 Aug 1994 16:11:28 +0100 Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <31r0f0$bgg@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Is acedb3.3 intended for acedb2 and acedb3 or is it meant to combine both these codes into a single system? I compiled acedb3.3 with the -DACEDB3 option but found my existing models and data (for acedb3) caused a system crash and core dump when a Map was picked for display. The w7/gmapdisp.c code appears to find map positions based on the models used for the acedb2 map display. There is no version provided for acedb3 models which define positions differently. That is, maps are generated in acedb3.3 (as in acedb2) with Position UNIQUE Map ?Map XREF Locus UNIQUE Float UNIQUE Float rather than the acedb3 definition of Location Map ?Map XREF Locus #map_location As there are differences between the acedb3 and acedb3.3 versions of gmapdisp.c this rules out using the older version of the file. Incidentally this problem has picked up on an existing bug which was: If a map is defined (either explicitly or through XREF's) but has no data provided, it will cause a system crash when that map is selected. Michelle email: kirbym@har-rbu.mrc.ac.uk From owner-acedb@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!couloir From: couloir@u.washington.edu (Chris Abajian) Newsgroups: bionet.software.acedb Subject: Sequence assembly software under devel? Date: 4 Aug 1994 23:26:44 GMT Organization: University of Washington Lines: 6 Message-ID: <31rtfk$a01@news.u.washington.edu> NNTP-Posting-Host: stein3.u.washington.edu Summary: Is there a new sequence assembly program in the offing? Keywords: sequence assembly I've been told that Jean Thierry-Mieg (and others) are currently working on a new sequence assembly program with an X interface that will support /use acedb files. True? Any estimates of time to beta release? Please email: chrisa@bozeman.mbt.washington.edu From owner-acedb@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: kirbym@har-rbu.mrc.ac.uk Newsgroups: bionet.software.acedb Subject: Re: Maps in 3.3 Date: 4 Aug 1994 19:00:29 +0100 Lines: 22 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <31rabt$mtp@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Richard says: >> You should be able to compile either a version 2 compatible binary or >> a version 3 compatible binary from 3.3. For version 2 define -DACEDB2 >> during compilation as in ALPHA_2_DEF, and use GMAP to display maps. >> For version 3 define -DACEDB3, make abi, not xace, and use VMAP for >> your maps. i.e. the version 3 GMAP has been renamed VMAP (vertical >> map of any type) to avoid name clashes. In a future version 4 it is >> possible this will become MAP. Having tried "make abi" with the -DACEDB3 compiler option set and changed the -GMAP flags in the options.wrm file to -VMAP, it does not make any difference. It still core dumps. The problem (at least initially) appears to be some missing bsPushObjs where it should be finding the map locations. Hence, I don't think it does produce a binary that is compatible with version 3. If anyone can suggest anything further I will try it. If not, I shall wait for acedb4. Michelle From owner-acedb@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: summary: tace dump whole database? Date: 4 Aug 1994 09:05:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408041606.AA00580@cvx12.inet.dkfz-heidelberg.de> References: <9408041524.AA05450@cele.mrc-lmb.cam.ac.uk> NNTP-Posting-Host: net.bio.net Thanks for all the responses. The current method of choice is: > Just write a tace script to dump it class by class. In fact this is more > flexible and useful. > Richard However, xace has a dump database command which is quite useful, so I agree only with the first part of Richard's argument. Detlef From owner-acedb@net.bio.net Thu Aug 04 23:00:00 1994 Path: biosci!biosci!not-for-mail From: kckim@phantom.com (Kim Konrad) Newsgroups: bionet.software,bionet.cellbiol,bionet.general,bionet.molbio.methds-reagnts,bionet.software.acedb,bionet.software.gcg Subject: Scanning Cell Culture Colonies Date: 5 Aug 1994 15:35:48 -0700 Organization: [MindVox] / Phantom Access Technologies / (+1 800-MindVox) Lines: 14 Sender: kristoff@net.bio.net Distribution: world Message-ID: <31u5n2$r52@dockmaster.phantom.com> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:8949 bionet.cellbiol:788 bionet.general:10597 bionet.molbio.methds-reagnts:16997 bionet.software.acedb:370 bionet.software.gcg:692 Hi, I'm wondering if there exisits scanning software(for Mac or PC) to count colonies on a given cell culture bottle. This is especially helpful if one counts large amounts of cell cultures colonies. Tell me what you use and what's the best (fastest, most functions, can export to favorite spreadsheet) on the market. Thanks, all suggestions are welcome. :) Konrad C. Kim Senior Lab Tech From owner-acedb@net.bio.net Sun Aug 07 23:00:00 1994 Path: biosci!ic.ac.uk!b.arnold From: b.arnold@ic.ac.uk Newsgroups: bionet.software.acedb Subject: ACEDB 3.3 Date: 8 Aug 1994 03:08:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <2136.9408081007@bccsc.bc.ic.ac.uk> NNTP-Posting-Host: net.bio.net Hi there Having got a copy of the ACEDB 3.3 code to compile and run I would like to know how to use the columns control on the vertical map. Specifically, has the columns cotrol code been integrated into ACEBD 3.3 fully and what needs to be included in configuration files (models.wrm etc) as from what i can gather from the resume Simon sent to the ace94 group he (you) seems to say that the code allows columns to become objects, if this is so, do they do this automatically or do they need to be told to do this ? At the moment, what i get when I run the system, what I get is a normal VMAP display with no pointers/tips or anything indicating where,what or how the columns control has been implemented or is usedand set up. Hope the above makes some sense to you simon and anyone else out there who may be able to help me. thanks in advance Benedict Arnold. From owner-acedb@net.bio.net Sun Aug 07 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 8 Aug 1994 19:41:13 GMT Organization: Dendrome, A genome database for forest trees Lines: 1053 Approved: news-answers-request@MIT.Edu Message-ID: <3261op$5r4@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.pswfs.gov Summary: Frequently Asked Questions about finding and getting started with the database system ACEDB. ACEDB is used to collect information regarding the molecular biology of the genome. Archive-name: acedb-faq Last-modified: 8/8/94 Version: 1.13 Xref: biosci bionet.software.acedb:372 news.answers:21167 ---------------------------------------------------------------------- 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) 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 (version 1-10 is available in repository/aatdb) 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 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 (S. pombe, M. musculus in development) Focus : Physical mapping of human chromosomes X and 21 Availability : PI : Hans Lehrach PI : Hugues Roest Crollius Curator : Hugues Roest Crollius Contact : hrc@gea.lif.icnet.uk ICRF, Lincolns Inn Fields, London. UK. Last_update : 22 Feb 1994 Database : ace11 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 (this address seems wrong--bks) 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 : mps2@acpub.duke.edu Curator : Maulin P. Shah Availability : Under development (Est. Sept. 94) Last_update : 30 Sept. 1993 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 : EcoDB Species : E. coli PI : Staffan Bergh Contact : staffan@biochem.kth.se Availability : Still under construction Last_update : Aug. 1994 Database : FlyBase Species : Drosophila melanogaster Availability : gopher or gopher+ ftp.bio.indiana.edu Availability : ACeDB-style interface to SyBase server due by end of 1994 Curator : Edward Welbourne Contact : eddy@gen.cam.ac.uk Contact : flybase@morgan.harvard.edu PI : William Gelbart PI : Michael Ashburner PI : Thomas Kaufman PI : Kathy Matthews PI : John Merriam Database : Flydb Species : Drosophila melanogaster 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:8000/acedbs/acedbs/graingenes/index.html 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 : 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 : SaccDB Species : Saccharomyces cerevisiae Focus : Budding Yeast Genome Acedb_version : 2.0 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. primer 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 Systems : Dan Mosedale, mosedale@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Last_update : 7 May 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 1-10 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 mapping of human chromosomes 22 and X Curator : Ian Dunham Contact : idunham@crc.ac.uk id1@sanger.ac.uk PI : Ian Dunham PI : David Bentley Last_update : 28 Sep 1993 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. (1993) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press (in press). [text is available through ftp or gopher from weeds.mgh.harvard.edu] Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1993) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. (Academic Press) (review, in press). [text is available through ftp or gopher from weeds.mgh.harvard.edu] 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) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. Mike Cherry has set up an ACEDB Developer's archive. For anonymous ftp use the hostname weeds.mgh.harvard.edu and look in the acedb_dev directory. If you wish to contribute you can put files in the incoming directory. Send a message to Mike (cherry@genome.stanford.edu) that you have put something in that directory then Mike will move it out for general access. For gopher you can connect to weeds.mgh.harvard.edu (132.183.190.21) and ... --> N. FTP Archives for Molecular Biology/ then --> M. ACEDB Developer's archive/ [N and M are integers which are subject to change.] The bionet.software. acedb.conference is archived and can be searched using WAIS. Here is a Gopher-style link to the WAIS archive. (This is also courtesy of Mike Cherry.): # Type=7 Name=ACEDB BioSci Electronic Conference Path=7/.index/acedb-biosci Host=genome-gopher.stanford.edu Port=70 The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. Other URL's that readers with mosaic clients might want to examine are: http://moulon.inra.fr/acedb/acedb.html for C. elegans data http://moulon.inra.fr/acedb/mycdb.html for Mycobacterium data http://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. Return to List of Questions ---------------------------------------------------------------------- Q11: When and where is the Next ACEDB Workshop? Unannounced. 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, Bradley K. (1994) "ACEDB Genome Database FAQ." Usenet news.answers. Available via Universal Resource Locators ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq and http://probe.nalusda.gov:8000/acedocs/acedbfaq.html. 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 Aug 08 23:00:00 1994 Path: biosci!UX5.LBL.GOV!mccarthy From: mccarthy@UX5.LBL.GOV (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: ACEDB 95 Conference and Workshop Date: 8 Aug 1994 19:19:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 99 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408090219.TAA06532@ux5.lbl.gov> Reply-To: JLMcCarthy@lbl.gov NNTP-Posting-Host: net.bio.net 8 August 1994 TO: Potential Participants for ACEDB 95 Conference and Workshop FR: John McCarthy, Lawrence Berkeley Laboratory RE: Time, Place, Format, etc. ---------------------------------------------------------- At the very successful ACEDB 94 Workshop last month in Montpellier, LBL was asked to help arrange next year's Workshop in California. In order to begin this planning effort, I'd like to learn who might want to attend, and what preferences you might have as to dates, location, and meeting format, even though we may be constrained by site availability and other factors. We are also exploring the possibility of getting financial support from DoE, NIH, NSF, USDA, and the European Community to help offset some of our costs, including scholarships and some travel support. Could you please fill out the brief questionnaire below and return it to me as soon as possible? (this week would be best, if you're not on vacation). If more than one person from your organization would like to attend, please get each person to fill out and return a separate questionnaire. Thanks, -John ======================================================== To: jlmccarthy@lbl.gov Subject: ACEDB 95 Conference and Workshop Please fill out information following colons (:) and put X's in brackets [X] Name: Organization: A. CONFERENCE V. WORKSHOP The 1992 and 1993 ACEDB Conferences were three days long. This year, 1994, the ACEDB Workshop was two weeks long, modeled on Physics workshops. Some people have suggested that next year we might try to do both. What would you prefer? Please indicate one or both you would like to attend. [ ] I would like to attend a three day ACEDB 95 Conference [ ] I would like to attend a two week ACEDB 95 Workshop [ ] Other (please specify): [ ] the 2 week ACEDB Workshop should immediately follow the Conference [ ] a 3 day ACEDB Conference should be held at another time of year Conference Time Comments: B. DATES The 1992 Conference was held in May; the 1993 Conference was in August; and this year's workshop was the first two weeks of July. In 1995, the Cold Spring Harbor meetings will be the second week of May , and the Hilton Head meeting is scheduled for September 16-20. Would people like to have the ACEDB Workshop close to one of those meetings or at some other time? [ ] following Cold Spring Harbor meeting in mid May [ ] June [ ] July [ ] August [ ] September, prior to Hilton Head meeting [ ] September, following Hilton Head meeting Date Comments: C. LOCATION In 1992 our Conference was in Cambridge, in 1993 in Boston, and this year in a small village outside Montpellier. What would you prefer for 1995? (you can indicate 1,2,3 for first, second, and third choices if you wish) [ ] Lawrence Berkeley Laboratory [ ] Stanford [ ] Berkeley [ ] San Francisco Peninsula (towards Stanford) [ ] Marin County (north of San Francisco) [ ] Monterey Bay area [ ] Lake Tahoe [ ] Other (please specify): D. HOUSING ARRANGEMENTS We can probably save some money by sharing rooms. What would you like? (please check only one) [ ] single room (even if it costs more) [ ] willing to share with another person to save money [ ] willing to share with more than one person to save more money Housing Comments: E. GENERAL COMMENTS AND SUGGESTIONS Please add anything else that might be relevant to scheduling a time and place for next year's meeting(s). From owner-acedb@net.bio.net Mon Aug 08 23:00:00 1994 Path: biosci!UX5.LBL.GOV!mccarthy From: mccarthy@UX5.LBL.GOV (John McCarthy) Newsgroups: bionet.software.acedb Subject: ACEDB 95 Conference v. Workshop distinctions Date: 9 Aug 1994 06:46:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408091346.GAA18105@ux5.lbl.gov> Reply-To: jlmccarthy@lbl.gov NNTP-Posting-Host: net.bio.net After sending out the questionnaire yesterday, I realized it probably should have been accompanied by an explanation of the distinction between a three day conference and a two week workshop (aside from time). As originally promoted by Jean and exemplified in this year's Montpellier workshop, a two week workshop ideally should let people collaborate on various types of ACEDB work, including: - database curators building, revising, and augmenting individual databases; - programmers working on various display and analysis modules; - system developers working on kernal enhancements; - other people working on related tools, scripts, etc. - writers working on development of different types of documentation; - discussion of possible future enhancements; - tutorials in ACEDB programming, style, etc. The two week format allows sufficient time for productive work. We can undoubtedly improve on the details, especially for database curators. I think a three day conference would be a more standard sort of thing, with talks on new features, introductory tutorials, round-table discussions, etc. Three days is too short a time to expect to get much actual work done. Unfortunately, Asilomar is not available for two week periods except in December/January, so we are investigating other possible locations. Other suggestions would be welcome. -John From owner-acedb@net.bio.net Mon Aug 08 23:00:00 1994 Path: biosci!sanger.ac.uk!srk From: srk@sanger.ac.uk Newsgroups: bionet.software.acedb Subject: Re: ACEDB 3.3 Date: 9 Aug 1994 09:00:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408091701.AA11555@handa> References: <2136.9408081007@bccsc.bc.ic.ac.uk> NNTP-Posting-Host: net.bio.net Benedict, The new columns control for the vertical map is not in the 3.3 release, mainly as it currently only suports the gmap display, but partially because A bug was found in it just before release, while I was on holiday. Current plans are to have it for vmap and gmap in ACEDB 4.0 It is intended to allow the current column configuration of a display to be stored in database objects, but it' not done yet. Hope this helps, Simon. ------------------------------------------------------------------------------- Simon Kelley. srk@sanger.ac.uk work: +44 223 494980 home: +44 223 832411 From owner-acedb@net.bio.net Mon Aug 08 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: bug in querying multivalued vectors fixed yet? Date: 9 Aug 1994 09:15:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408091614.AA20645@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Does anyone who's seen ace 3.3 know if the multivalued-vector query bug is fixed yet? The one that causes the record TShirt : "sam05" Remarks 1990 "Great Shirt!" 1991 "Sarah dislikes color" to be found by the query 'find tshirt remarks AND NEXT = "great*"' but not by 'find tshirt remarks AND NEXT = "sarah*" because only the first value is examined by the query mechanism? - Dave From owner-acedb@net.bio.net Tue Aug 09 23:00:00 1994 Path: biosci!agate!library.ucla.edu!news.mic.ucla.edu!news.bc.net!newsserver.sfu.ca!darwin.mbb.sfu.ca!jbryer From: jbryer@darwin.mbb.sfu.ca (Jeff Bryer) Newsgroups: bionet.software.acedb,bionet.celegans Subject: ACEDB 2-10 for Linux Date: 10 Aug 1994 02:24:23 GMT Organization: none Lines: 20 Distribution: world Message-ID: <329doo$qgl@seymour.sfu.ca> NNTP-Posting-Host: darwin.mbb.sfu.ca Xref: biosci bionet.software.acedb:377 bionet.celegans:54 Hi everyone, 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 (142.58.213.33) 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 did. Jeff Bryer jbryer@darwin.mbb.sfu.ca From owner-acedb@net.bio.net Thu Aug 11 23:00:00 1994 Path: biosci!headwall.Stanford.EDU!hsdndev!cvlb29.harvard.edu!user From: system@cvlab.harvard.edu (TJR) Newsgroups: bionet.software,bionet.cellbiol,bionet.general,bionet.molbio.methds-reagnts,bionet.software.acedb,bionet.software.gcg Subject: Re: Scanning Cell Culture Colonies Date: 12 Aug 1994 14:21:32 GMT Organization: HSPH Lines: 4 Distribution: world Message-ID: References: <31u5n2$r52@dockmaster.phantom.com> NNTP-Posting-Host: cvlb29.harvard.edu Xref: biosci bionet.software:9008 bionet.cellbiol:810 bionet.general:10658 bionet.molbio.methds-reagnts:17221 bionet.software.acedb:378 bionet.software.gcg:702 Try using NIH Image --- using anonymous ftp, download NIH Image from zippy.nlm.nih.gov. TJR From owner-acedb@net.bio.net Sun Aug 14 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!uni-muenster.de!asterix.uni-muenster.de!schapej From: schapej@asterix.uni-muenster.de (Jörg Schaper) Newsgroups: bionet.software.acedb Subject: Programmers guide? Date: 15 Aug 1994 15:09:31 GMT Organization: Westfaelische Wilhelms-Universitaet Muenster, Germany Lines: 14 Message-ID: <32o0fb$1ets@obelix.uni-muenster.de> NNTP-Posting-Host: asterix.uni-muenster.de X-Newsreader: TIN [version 1.2 PL2] Hi, working with ACEDB 2.0 at the moment I've seen some remarks about a programmers / curators guide. On the ftp servers given in the faq I can only find the installation, configuration and users guide. Where can I get the programmers guide? Can anyone send me a ftp adress? Thanks in advance. JS --------------------------------------------------------------------------- - Jörg Schaper schapej@uni-muenster.de -- --------------------------------------------------------------------------- From owner-acedb@net.bio.net Mon Aug 15 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: Programmers guide? Date: 16 Aug 1994 09:03:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408161603.AA15309@cvx12.inet.dkfz-heidelberg.de> References: <32o0fb$1ets@obelix.uni-muenster.de> NNTP-Posting-Host: net.bio.net here is some old version, hope this helps. ftp> open igd-ftp.inet.dkfz-heidelberg.de Connected to igd-ftp. 220 sun09a FTP server (SunOS 4.1) ready. Name : anonymous 331 Guest login ok, send ident as password. Password: 230 Guest login ok, access restrictions apply. ftp> cd pub/acedb/doc 250 CWD command successful. ftp> ls 200 PORT command successful. 150 ASCII data connection for /bin/ls (193.174.54.111,32998) (0 bytes). programmers.guide.apr-92.tar.Z Detlef ----------------------------------------------------------------------------- Detlef Wolf, European Data Resource for Human Genome Research eMail: D.Wolf@dkfz-heidelberg.de phone: +49 6221 42 -2331 fax: -2333 sMail: DKFZ (German Cancer Research Centre), Abt. Molekulare Biophysik (0810) Im Neuenheimer Feld 280, 69120 Heidelberg, Germany From owner-acedb@net.bio.net Tue Aug 16 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!scsing.switch.ch!news.dfn.de!uni-muenster.de!asterix.uni-muenster.de!schapej From: schapej@asterix.uni-muenster.de (Jörg Schaper) Newsgroups: bionet.software.acedb Subject: Re: Programmers guide? Date: 17 Aug 1994 13:08:27 GMT Organization: Westfaelische Wilhelms-Universitaet Muenster, Germany Lines: 37 Distribution: world Message-ID: <32t24b$19vf@obelix.uni-muenster.de> References: <32o0fb$1ets@obelix.uni-muenster.de> <199408161603.AA15309@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: asterix.uni-muenster.de X-Newsreader: TIN [version 1.2 PL2] Detlef Wolf (D.Wolf@dkfz-heidelberg.de) wrote: : here is some old version, hope this helps. : ftp> open igd-ftp.inet.dkfz-heidelberg.de : Connected to igd-ftp. : 220 sun09a FTP server (SunOS 4.1) ready. : Name : anonymous : 331 Guest login ok, send ident as password. : Password: : 230 Guest login ok, access restrictions apply. : ftp> cd pub/acedb/doc : 250 CWD command successful. : ftp> ls : 200 PORT command successful. : 150 ASCII data connection for /bin/ls (193.174.54.111,32998) (0 bytes). : programmers.guide.apr-92.tar.Z : Detlef : ----------------------------------------------------------------------------- : Detlef Wolf, European Data Resource for Human Genome Research : eMail: D.Wolf@dkfz-heidelberg.de phone: +49 6221 42 -2331 fax: -2333 : sMail: DKFZ (German Cancer Research Centre), Abt. Molekulare Biophysik (0810) : Im Neuenheimer Feld 280, 69120 Heidelberg, Germany -- Hi, thanks a lot for enabling us to get the programmers guide. We could not connect to the server given above, we had to skip the .inet JS --------------------------------------------------------------------------- - Jörg Schaper schapej@uni-muenster.de -- --------------------------------------------------------------------------- From owner-acedb@net.bio.net Sun Aug 21 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!P.Kocab From: P.Kocab@dkfz-heidelberg.de (Petr Koca'b) Newsgroups: bionet.software.acedb Subject: Re: ACEDB 95 Conference and Workshop Date: 22 Aug 1994 00:30:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 84 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408220729.AA17768@sun09b.inet.dkfz-heidelberg.de> References: <199408090219.TAA06532@ux5.lbl.gov> NNTP-Posting-Host: net.bio.net Please fill out information following colons (:) and put X's in brackets [X] Name: Petr Kocab Organization: DKFZ Heidelberg, Germany A. CONFERENCE V. WORKSHOP The 1992 and 1993 ACEDB Conferences were three days long. This year, 1994, the ACEDB Workshop was two weeks long, modeled on Physics workshops. Some people have suggested that next year we might try to do both. What would you prefer? Please indicate one or both you would like to attend. [X] I would like to attend a three day ACEDB 95 Conference [X] I would like to attend a two week ACEDB 95 Workshop [ ] Other (please specify): [X] the 2 week ACEDB Workshop should immediately follow the Conference [ ] a 3 day ACEDB Conference should be held at another time of year Conference Time Comments: B. DATES The 1992 Conference was held in May; the 1993 Conference was in August; and this year's workshop was the first two weeks of July. In 1995, the Cold Spring Harbor meetings will be the second week of May , and the Hilton Head meeting is scheduled for September 16-20. Would people like to have the ACEDB Workshop close to one of those meetings or at some other time? [X] following Cold Spring Harbor meeting in mid May [ ] June [ ] July [ ] August [ ] September, prior to Hilton Head meeting [ ] September, following Hilton Head meeting Date Comments: C. LOCATION In 1992 our Conference was in Cambridge, in 1993 in Boston, and this year in a small village outside Montpellier. What would you prefer for 1995? (you can indicate 1,2,3 for first, second, and third choices if you wish) [X] Lawrence Berkeley Laboratory [ ] Stanford [ ] Berkeley [ ] San Francisco Peninsula (towards Stanford) [ ] Marin County (north of San Francisco) [ ] Monterey Bay area [ ] Lake Tahoe [ ] Other (please specify): D. HOUSING ARRANGEMENTS We can probably save some money by sharing rooms. What would you like? (please check only one) [X] single room (even if it costs more) [ ] willing to share with another person to save money [ ] willing to share with more than one person to save more money Housing Comments: E. GENERAL COMMENTS AND SUGGESTIONS Please add anything else that might be relevant to scheduling a time and place for next year's meeting(s). ____________________________________________________ | | | Petr Kocab || | German Cancer Research Center (DKFZ) || | Molecular Biophysics Group || | Im Neuenheimer Feld 280 || | D-69120 Heidelberg, Germany || | || | email: P.Kocab@dkfz-heidelberg.de || | voice: (+49-6221) 42 2340 || | fax : (+49-6221) 42 2333 || |____________________________________________________|| |____________________________________________________| From owner-acedb@net.bio.net Wed Aug 24 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: .ace and doube quotes Date: 25 Aug 1994 09:32:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 69 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408251632.AA21627@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net Thu Aug 25 17:55:44 MDT 1994 dok256 .ace and doube quotes -- a nightmare Summary: do not use double quotes in .ace data. Reason: if there are double quotes in the data it is not possible to dump the database and get back to same state by reloading that dump Method: using ACEDB 3.1 as of 14.July 94 or the with ACEDB 3.3 from_ncbi as of 94-07-30 with: the model: ?Sequence other_features ?Text Text Text Text or ?Motif Text Text Text (from ACEDB 3.3) read .ace file: Sequence "a1" other_features "1a" "2" "3" other_features "\"1b" "2" "\"3" other_features "\""1c" "2" "\""3" displayed as: a1 Attach... Quit Features other_features 1a 2 3 1b 2 3 "1c 2 "3 dumped as: // data dumped from tree display Sequence : "a1" other_features "1a" "2" "3" other_features "1b" "2" "3" other_features ""1c" "2" ""3" reading that dump is displayed as: a2 Attach... Quit Features other_features 1a 2 3 1b 2 3 EMBL data contains a lot of double quotes which I would like to keep. I think this is such a silly bug and should be fixed. The problem is probably with these lines in w1/freesubs.c: else if (*in == '"') /* restore backslash for freeword to read */ { *in = '\\' ; *++in = '"' ; } why is " replaced by \ in the current position and the next position set to " ? Detlef ----------------------------------------------------------------------------- Detlef Wolf, European Data Resource for Human Genome Research eMail: D.Wolf@dkfz-heidelberg.de phone: +49 6221 42 -2331 fax: -2333 sMail: DKFZ (German Cancer Research Centre), Abt. Molekulare Biophysik (0810) Im Neuenheimer Feld 280, 69120 Heidelberg, Germany From owner-acedb@net.bio.net Fri Aug 26 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: minimal ACEDB classes.wrm file Date: 27 Aug 1994 09:14:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 308 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408271611.AA11055@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net If you want to add many classes (150) to an ACEDB database, then read this else skip it. --------------------------- probably this comes a bit late now, since Jean will release a code that does not need this anymore. But for the time being: Starting from the code as of 94-07-14 for ACEDB 3.1 from the Montpellier workshop (this most probably also applies to ACEDB 3.3), I wanted to add a lot of classes to ACEDB, so I had to leave out some of the old ones. Since I needed a contiguous space of class numbers I had to recompile. But which user-defined classes are needed by the code? All classes used in ACEDB source code: perl -ne '/(_V\w+)/ && print $1,"\n"' w?/*.c w?/*.h | sort | uniq Then I form the intersection with the classes in the orginal classes.wrm file. The tags file I keep, because many tags are used and new tags are cheap. The options.wrm is adapted to classes.wrm Thus having minimal {classes,tags,options}.wrm files for compiling, I use the "newspec" script from Otto that auguments the {classes,tags,options}.wrm with everything necessary for the current models.wrm I append all classes, options and newspec files, so you can use them. tags.wrm is from the distribution. Detlef ----------------------------------------------------------- ----------------------------------------------------------- /* minimal version Fri Aug 26 12:10:40 WET DST 1994 dok256 */ /* wspec/classes.wrm This file is read at compile and at execution time. It holds the enumaration of the application dependent classes. Classes necessary to the kernel are defined in a second file wspec/sysclasses.wrm, which should not be touched except in consultation with us. You can add new classes at will, but if you suppress one or renumber it, you must recompile and reconstruct the database from ace files. Class properties, formerly defined in this file, are now in wspec/options.wrm. If there is no entry there then classes are type B (tree), hidden, with display method TREE. Each #define line corresponds to a class. We require strlen(name) < 32. There must be no repetitions of class numbers. The total number of classes cannot exceed 255. The total number of display types cannot exceed 64. For now we allocate 0-100 for system classes 101-199 for application classes 200-255 for subtypes The subytypes will not need class numbers when the ?Model class works fully. */ /* def _VClass_name Class_number */ #define _V2_point_data 101 #define _VAllele 102 #define _VChrom_Band 103 #define _VClone 104 #define _VClone_Grid 105 #define _VContig 106 #define _VDNA 107 #define _VDf_Dup_data 108 #define _VGene_Class 109 #define _VInterval 110 #define _VLocus 111 #define _VMap 112 #define _VMethod 113 #define _VMotif 114 #define _VMultiMap 115 #define _VMulti_pt_data 116 #define _VPaper 117 #define _VPeptide 118 #define _VPool 119 #define _VProbe 120 #define _VRestriction 121 #define _VSequence 122 #define _VgMap 123 #define _VpMap 124 #define _VvMap 125 /* --------- end of needed classes ----------- */ ----------------------------------------------------------- /* minimal version Fri Aug 26 12:10:40 WET DST 1994 dok256 */ /* wspec/options.wrm This file is read only at execution time It holds the class definitions necessary to the applications. The kernel classes are defined in wspec/sysoptions.wrm which can serve as a model when editing this one. You can freely edit this file without recompiling but it must remain consistent with the other wspec files and you must never change the type (A, B, X) of a class unless you reconstruct the database from ace files. Line starting with _VClassName are parsed, they are expected to contain a la Unix a set of -Option parameters. Class names must match their enumeration in wspec/classes.wrm The order in which classes appear here will be used in displays. Options names can be abbreviated, recognized options are -Hidden : this class will not be listed in the acedb Main Window. -Visible : this class will be listed in the acedb Main Window. -Array : this class is of type A, (Array or tuple). -Btree : this class is of type B, it must be further defined in models.wrm -XREF : Auto cross referencing Hidden B system class. Do not use. -Display displayType : The preferred display type of the class, as enumerated in wspec/disptype.wrm -Title Tag : Tag must be a tag name listed in wspec/tags.wrm (or systags) If present in some object of that class, the text following it will be used preferentially when referring to that object. -Symbol Tag : Tag must be a tag name listed in wspec/tags.wrm (or systags) If present in some object of that class, the text or key following it will be used preferentially when referring to that object in Maps. -Rename otherName : Other name will show in lists, old and new name will be recognized in ace files and queries, old is used in the code. In case some newName matches some old name, the new name takes precedence. -CaseSensitive : The names in this class will be case sensitive. Never undo this option once it has been used. -Sybase : Experimental external storage in sybase. -Known : Prevents indirect creation of new object in ace files You can't enter a new object in this class directly but not by quoting it in another object. Classes default as -B -H -D TREE A classes further default as -H -D ZERO Displays: Every display type needs a display function. Parsers: Special code must be provided for A Classes Dumps: Special code must be provided to dump A classes These routines must be registered in file wspec/quovadis.h before recompilation. */ // _VAA -A -H _VChrom_Band -V -D VMAP _VClone -V -D PMAP _VContig -V -D PMAP _VDNA -A -V -D FMAP // _VFragment -V -D VMAP // _VGDB_id -V -Protected _VLocus -V -D VMAP _VMap -V -D VMAP _VMotif -V _VMultiMap -V -D DtMULTIMAP _VPaper -V -T Title _VProbe -V -T Name // _VSTS -V -D VMAP _VSequence -V -D FMAP -T Title // _VYAC -V -D DtPmapFingerprint _VgMap -A -H -D GMAP _VpMap -A -H -D PMAP _VvMap -A -H -D VMAP /* ------------ minimal version ends here ----------------- */ ----------------------------------------------------------- #!/usr/local/bin/gawk -f # ^ # use nawk or gawk, but NOT awk # # filename: newspec # by Otto Ritter, DKFZ, Germany [o.ritter@dkfz-heidelberg.de] # created Nov 3 93 # last modif Apr 23 94 SGI # purpose; parse models.wrm and generate new {tags|classes|options} # syntax: setenv ACEDB ; newspec # -- no command line arguments # Fri Aug 26 12:49:58 WET DST 1994 dok256 -- classes are no tags ######################################################################## BEGIN { ### check the environment & backup some files if ( ENVIRON["ACEDB"] == "") { print "newspec error:: ACEDB variable not defined." ; exit 1 } path = ( ENVIRON["ACEDB"] "/wspec/" ) print "echo newspec :: " path "models.wrm" if ( system("cd " path "; \cp tags.wrm tags.wrm.bak") != 0 ) { print "newspec error:: cannot backup tags.wrn" ; exit 1 } if ( system("cd " path "; \cp classes.wrm classes.wrm.bak") != 0 ) { print "newspec error:: cannot backup classes.wrn" ; exit 1 } ### now we are working in $ACEDB/wspec logfile = path "newspec.log" ### parse sys files first print "// newspec.log\n" > logfile ff = (path "sysclass.wrm") while ((getline < ff ) >0) if ($1=="#define") class[tolower($2)] = $2; close(ff); ff = (path "classes.wrm") while ((getline < ff ) >0) if ($1=="#define"){ if (tolower($2) in class) { printf "## warning: %s both in sysclass.wrm and classes.wrm ", tolower($2) ;} else class[tolower($2)] = $2; ClassNr =$3+1; } close(ff); ff = (path "systags.wrm") while ((getline < ff ) >0) if ($1=="#define") tag[tolower($2)] = $2; close(ff); ff = (path "tags.wrm") while ((getline < ff ) >0) if ($1=="#define") { if (tolower($2) in tag ) { printf "## warning: %s both in systags.wrm and tags.wrm", tolower(tg); } else tag[tolower($2)] = $2; TagNr = $3+1; } close(ff); ff = (path "options.wrm") while ((getline < ff ) >0) if (substr($1,1,2) =="_V") in_options[$1] = 1; close(ff); if (ClassNr < 110 ) ClassNr = 110 if ( TagNr < 1000) TagNr = 1000 ### parse models.wrm ff = (path "models.wrm") while ((getline < ff ) > 0 ){ gsub("#","?"); gsub(/\/\/.*$/,""); gsub(/@.*$/,""); for (i=1;i<=NF;i++) { if (substr($i,1,1) == "?" ) { # classname cl = "_V" substr($i,2) ; if (tolower(cl) in class) { if ( class[tolower(cl)] != cl ) print "## warning: case mismatch ", cl, class[tolower(cl)] ; } else {class[tolower(cl)] = cl; print ("#define",cl,ClassNr++) >> (path "classes.wrm"); newclass = newclass SUBSEP cl;} if (!(cl in in_options) && !(cl in newoptions)) {print cl " -V" >> "options.wrm"; newoptions[cl] = ++nopt; }; continue; # detlef thinks classes are no tags } # classname tg = "_" $i; # tag name gsub(/\?/,"",tg); if ( tolower(tg) in tag ) { if ( tag[tolower(tg)] != tg ) print "case mismatch ", tg, tag[tolower(tg)] ; } else { tag[tolower(tg)] = tg; print ("#define",tg,TagNr++) >> (path "tags.wrm"); newtag = newtag SUBSEP tg; } }#for } #while close(ff); ### generate report { ncl = split(newclass,arr,SUBSEP); print "======== added classes ======" > logfile for ( x in arr ) print arr[x] > logfile ntg = split(newtag,arr,SUBSEP); print "\n======== added tags =========" > logfile for ( x in arr ) print arr[x] > logfile print "\n======== added options ======" > logfile for (x in newoptions) print x, "-V" > logfile printf "## newspec added:\n%i to %s\n%i to %s\n%i to %s\nsee the logfile %s\n\n", ncl,"classess.wrm",\ ntg, "tags.wrm", nopt,"options.wrm", logfile ; } exit 0 }#BEGIN {} # empty main From owner-acedb@net.bio.net Sun Aug 28 23:00:00 1994 Path: biosci!nihs.nihs.go.jp!taka From: taka@nihs.nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: gif display program Date: 29 Aug 1994 01:39:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408290838.AA07585@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net I am a researcher of National Institute of Health Sciences in Japan. I am working on reconfiguring ACEDB for our new database. I would like to know how to display "gif files" from ACEDB. Does anyone know any appropriate program ? Thank you for your attention of this question. Takako Igarashi National Institute of Health Sciences Division of Chem-Bio Informatics taka@nihs.go.jp From owner-acedb@net.bio.net Sun Aug 28 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: "follow" into a vector? Date: 29 Aug 1994 11:34:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408291658.AA25428@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Is there a way to use the query command "follow" to follow the second field of a vector instead of the first? e.g. for ?Germplasm Collection_and_ID ?Collection ?Germplasm , example Germplasm : "Abilene" Collection_and_ID "USDA" "PI12345" , I'd like to follow to the PI12345 etc. values of such records. "find germplasm; follow collection_and_id NEXT" didn't work, still returned the Collection's. - Dave Matthews From owner-acedb@net.bio.net Mon Aug 29 23:00:00 1994 Path: biosci!agate!news.Stanford.EDU!stout.Stanford.EDU!cherry From: cherry@stout.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: gif display program Date: 30 Aug 1994 03:42:58 GMT Organization: Stanford University Genetics Department Lines: 32 Message-ID: <33u9s2$d0n@nntp2.Stanford.EDU> References: <9408290838.AA07585@nihs.nihs.go.jp> NNTP-Posting-Host: stout.stanford.edu In article <9408290838.AA07585@nihs.nihs.go.jp>, Takako Igarashi wrote: >I would like to know how to display "gif files" from ACEDB. >Does anyone know any appropriate program ? >Thank you for your attention of this question. You can use the Pick_me_to_call facility. In your models file add the following within the class you want to contain the reference to the image: Pick_me_to_call UNIQUE Text UNIQUE Text Then in the info in the ace file like this example from AAtDB: Image : "1a5" Locus "1a5" Autorad "1a5" Caption "Photo by Nottingham Stock Centre" Pick_me_to_call "xv" "1A5.gif" The first Text item is the name of the graphic viewer and the second is the filename of the image. When the Pick_me_to_call is clicked, in the above example, on twice xace will do the following via a system call: cd $ACEDB/externalFiles; xv 1A5.gif You should be able to use a different viewer, but I have only used xv for GIF images on UNIX. You can get a copy of xv version 2.x from ncbi.nlm.nih.gov in repository/acedb or weeds.mgh.harvard.edu in aatdb/aatdb.1x Mike From owner-acedb@net.bio.net Mon Aug 29 23:00:00 1994 Path: biosci!CADEV6.INTEL.COM!ptagare From: ptagare@CADEV6.INTEL.COM Newsgroups: bionet.software.acedb Subject: date and time comparision in ACEDB Date: 30 Aug 1994 08:29:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408301524.AA11571@cad553.intel.com> NNTP-Posting-Host: net.bio.net Hi! I'm looking at some of ACEDB's data management capabilities, and I was wondering if ACEDB supports the concept of date and time as basic data types? In other words, can I do a query that finds me all the authors of papers published after 08/22/94 (mm/dd/yr) AND 13:00:00 (hrs:mnts:secs)? Also, when are the set operations going to be implemented in tace? They are not in 3.1, as far as I could tell. Thank you. -- pradeep *************************************************************** * Pradeep Tagare ptagare@scdt.intel.com * * CAD Engineer * * Intel Corp. * * Santa Clara, CA. * * (408) 765-6461 FAX: (408) 765-4716 * *************************************************************** * "It might be in the basement, I'll go upstairs and check..."* * M. C. Escher * * ************************************************************* From owner-acedb@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: date and time comparision in ACEDB Date: 31 Aug 1994 10:36:12 +0100 Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <341iuc$9je@mserv1.dl.ac.uk> Original-To: ptagare@cadev6.intel.com We now have a DateType as a basic type like Int, Float, Text. This was implemented during the 1994 ACEDB workshop, and will be in the next main release, later this fall. It shows the date and time to the second, and can parse in just a date, just the time (implicit todays date -- I think this is there!) and "now" (current date/time). '>' and '<' will work with items from this type. I'm not so sure about set operations in queries. I'll leave that to Jean. Richard From owner-acedb@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!nihs.nihs.go.jp!taka From: taka@nihs.nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: RE: RE: gif display program Date: 31 Aug 1994 02:46:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408310945.AA13905@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net Thank you. I could display gif files. I could also know how to use Pick_me_to_call facility of ACEDB. Thank you again. Takako Igarashi National Institute of Health Sciences taka@nihs.nihs.go.jp From owner-acedb@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: date and time comparision in ACEDB Date: 31 Aug 1994 05:33:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408311233.AA00224@cvx12.inet.dkfz-heidelberg.de> References: <341iuc$9je@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net I tried the dateType in queries, but think it is not parsed yet. Using ACEDB 3.3 code from ncbi as of 94-07-30 compiled on an SGI. the model: ?Locus GDB Name UNIQUE Text Add_date UNIQUE DateType Modification_date UNIQUE DateType the data: // data dumped from keyset display Locus : "1" Name "test" Add_date 1994-08-31_00:00:00 Modification_date 1994-08-30_00:00:00 the queries: >?Locus Add_date < "1994-09-30_00:00:00" >?Locus Add_date < 1994-09-30_00:00:00 >?Locus Add_date = 1994-08-31_00:00:00 >?Locus Add_date = "1994-08-31_00:00:00" >?Locus Add_date = "1*" none of the queries retrieves the locus. Did anyone get it working? From owner-acedb@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: date in queries Date: 31 Aug 1994 19:52:06 +0100 Lines: 1 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <342jgm$drg@mserv1.dl.ac.uk> Original-To: net@cnusc.fr i am sorry i thought it did work, i ll check soon. From owner-acedb@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!CS.Arizona.EDU!uunet!EU.net!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: A weird idea ... Date: 31 Aug 1994 20:07:00 +0100 Lines: 43 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <342kck$eu4@mserv1.dl.ac.uk> Original-To: net@cnusc.fr i (mieg) strongly supports this use of the tree system by Eddy: pondering Aberrations (again) and thought of something that makes controlled vocabularies happen in a rather neat way. Suppose we're really after, say, Type UNIQUE Deficiency Duplication Inversion Ring Other because our software needs to know which of these classes to display an object as belonging to, but our source of information supplies a broader (still controlled) vocabulary which, in effect, subdivides each of the above; we could say (I'm sorry, I don't know a suitable subdivision so I'm just using synonyms instead): Type UNIQUE Deficiency deficient lacking short Duplication multivalent copied polymerised Inversion backwards inverted reversed Ring cycle circle Other anomalous strange and so on. Then supplying the relevant word to an object fills in that tag and all the intervening ones (Type and one of the UNIQUE set) so that code which really wants one of the narrowed CV to work from can find the right version. Users would still get the variety of synonyms (which might, after all, be a classification within the relevant sub-heading and, therefore, useful). Not relevant to anything at the moment, but possibly worth sharing ... Eddy. From owner-acedb@net.bio.net Wed Aug 31 23:00:00 1994 Path: biosci!FLY2.BERKELEY.EDU!suzi From: suzi@FLY2.BERKELEY.EDU (Suzanna Lewis) Newsgroups: bionet.software.acedb Subject: one querybuilder bug Date: 31 Aug 1994 22:55:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409010553.WAA26080@fly2.berkeley.edu> NNTP-Posting-Host: net.bio.net a nitty-gritty picyune detail There is (at least) one bug in query builder. You will only notice this one if you have tag names greater than 24 chars in length and have the memory checking turned on. The bug is in several places, whereever a menu is being generated. Before newMenu->text = (char *) arrayCreate (BUFFER_SIZE, char); strcpy(newMenu->text, "menu item string"); This was copying the string into the array structure (length 24) It should be newMenu->text (char *) messalloc (BUFFER_SIZE) ; strcpy (newMenu->text, "menu item string") ; Likewise the destroy has to be changed to do a messfree. -s From owner-acedb@net.bio.net Wed Aug 31 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!news.kth.se!kiev.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: help with pc-486 and Linux Followup-To: poster Date: 1 Sep 1994 16:24:25 +0200 Organization: Biochemistry, KTH, Stockholm Lines: 65 Sender: staffan@biochem.kth.se Distribution: world Message-ID: <344o6p$aj5@kiev.physchem.kth.se> NNTP-Posting-Host: kiev.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Keywords: Linux, MycDB, PC486 Hi can anyone help with this? I don't have any experience with Linux at all, and I don't think we have any users currently using Linux. You can email me and I'll pass it on. TIA /staffan (staffan@biochem.kth.se) =================================== From ARCIB@delphi.com Thu Sep 1 15:52:00 1994 Received: from bos2a.delphi.com by kiev.physchem.kth.se (5.61-bind 1.4+ida/4.0) id AA10699; Thu, 1 Sep 94 15:51:56 +0200 Received: from delphi.com by delphi.com (PMDF V4.3-9 #7804) id <01HGL61ZT68W9ZMMSE@delphi.com>; Thu, 01 Sep 1994 06:08:21 -0400 (EDT) Date: Thu, 01 Sep 1994 06:08:21 -0400 (EDT) From: ARCIB@BIOTECHNET.COM Subject: Sender: ARCIB@delphi.com To: staffan@biochem.kth.se Message-Id: <01HGL61ZT68Y9ZMMSE@delphi.com> X-Vms-To: INTERNET::"staffan@biochem.kth.se" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Status: RO To: staffan@biochem.kth.se From: Dear Staffan, I, Tanmay Banerjee, would like your help in installing MycDB software running under Linux on PC-386. I am working with Dr. Indira Ghosh, who spoke to you regarding MycDB software on her last visit to Stockholm. Here are certain points on which I would like your comments: 1. We have not been able to get a Xwindow working with colour. We ran the the MycDB software on the Black & White mode (VGA mono) of Xwindow. We could read the header of each window, but the content of the window is not readable (as the black background,overlapped with the text in black). We looked into the Xconfig file under /usr/X386/lib/X11/. We found that RGBPath is given as usr/X386/lib/X11/rgb,but in the mentioned directory there are three files with starting with rgb. They are rgb.txt, rgb.dir & rgb.par. Amongst them, rgb.txt is a readable file, while others are not. We made a separate directory named "rgb" and put these three files in it, but it still did not read it. 2. Can you tell us how to use tvga9000 instead of VGAmono? 3. Can you provide us the name & e-mail of a person, who is using MycDB on PC-386 under Linux ? With this information,(I can provide more if required) Will you be able to help us in running MycDB in mono mode if not in colour? (We have a VGA color monitor). I would be grateful, if you can reply at your earliest. With regards, Tanmay Banerjee.