From owner-acedb@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!s.u-tokyo!news.tisn.ad.jp!news.u-tokyo.ac.jp!sinetnews!daffy!uwvax!uchinews!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!redstone.interpath.net!ddsw1!willis.cis.uab.edu!maze.dpo.uab.edu!ramermac.nrc.uab.edu!user From: ramer@nrc.uab.edu (Kevin W. Ramer) Newsgroups: bionet.software,bionet.software.acedb Subject: Re: Mac Printing (Was Visualisation of Postscript files in Macs?) Date: Mon, 03 Oct 1994 09:48:33 -0600 Organization: University of Alabama at Birmingham Lines: 27 Distribution: world Message-ID: References: <36cs42$jko@calvin.st-and.ac.uk> <36hd6l$ehm@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ramermac.nrc.uab.edu Xref: biosci bionet.software:9507 bionet.software.acedb:447 In article , flip@bogie2.bio.purdue.edu (Phillip D. Russell) wrote: > > I guess you don't have the laserwriter 8 extention. You can print > multiple pages on one sheet from any program. > > The laserwriter 8 extention should be at all FTP site with > Mac shareware. > I believe that your best bet is an Apple site. e.g ftp.apple.com:/dts/mac/sys.soft or ftp.austin.apple.com, et. al. I don't think that this software is permitted on most sites. > Flip > > -- > __@ Phillip "Flip" Russell | Purdue University __@ > _ -_,_-\<,_flip@bogie2.bio.purdue.edu | West Lafayette, IN _ -\<,_ > (_)-----/-(_) The important things... (_)-/-(_) > My bikes and my Macintosh -- Kevin W. Ramer ramer@nrc.uab.edu Programmer Analyst Neurobiology Research Center University of Alabama at Birmingham From owner-acedb@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!sunic!news.uni-c.dk!dkuug!eunet.no!nuug!trane.uninett.no!daresbury!hgmp.mrc.ac.uk!crc.ac.uk!dtailor From: dtailor@crc.ac.uk (Dilip Tailor x3296) Newsgroups: bionet.software.acedb Subject: ACeDB data update via cron/expect/tace Date: 30 Sep 1994 11:15:20 GMT Organization: MRC Human Genome Mapping Project Resource Centre, Harrow, UK Lines: 43 Distribution: world Message-ID: <36gs08$h7a@mercury.hgmp.mrc.ac.uk> Reply-To: dtailor@crc.ac.uk (Dilip Tailor x3296) NNTP-Posting-Host: krypton.hgmp.mrc.ac.uk Hello, I wish to update ACeDB databases via cron jobs and not via interactive means. Has anyone attempted to do this? tace with parse command almost does this but it's interactive. I have created a 'expect' script to drive the tace program to parse rawdata update files but it fails to update the database. I think its something to do with pawning a new shell??? expect script: #!/packages/expect/bin/expect set env(ACEDB) /packages/mbx/ACeDB set env(DBDIR) /packages/mbx/ACeDB/database spawn $env(ACEDB)/bin.SOLARIS/tace expect {acedb >} { send " ?\r"} expect {acedb >} { send "parse /packages/mbx/ACeDB/rawdata/update.3-1\r"} expect {acedb >} { send "quit\r"} The '?' or help works. The parse runs but fails to update DB. The 'quit' works. What am l doing wrong? Is it possible to run tace via options list? i.e tace -parse filename Regards, Dilip Tailor HGMP-RC From owner-acedb@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: ACeDB data update via cron/expect/tace Date: 3 Oct 1994 12:25:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410031925.AA04438@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > dtailor@crc.ac.uk says: > I wish to update ACeDB databases via cron jobs and not via interactive means. > Has anyone attempted to do this? Hi Dilip, I do this by sending tace the commands via the csh "<<" operator. (Not my idea, I saw other people using it.) E.g.: #!/bin/csh # ~/ggscrps/loadace, DEM 7/22/94 # "loadace " loads ~/xgraingenes/rawdata/ into the database. echo Loading file $file /home/grains/textxgg < References: <36gs08$h7a@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: net.bio.net Dilip Tailor writes: > > Hello, > > > I wish to update ACeDB databases via cron jobs and not via interactive means. > Has anyone attempted to do this? > I use a commands file to achieve this. My command file looks like this: Parse /home/myfile.ace Find Authors List Then, I invoke tace this way: tace < commandFile This loads the data in, and saves it when upon exit. Thanks, -- 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 Mon Oct 03 23:00:00 1994 Path: biosci!nihs.nihs.go.jp!taka From: taka@nihs.nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: Windows version Date: 4 Oct 1994 03:50:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410041049.AA00945@nihs.nihs.go.jp> Hello! Do you have any plan to produce Windows version of the acedb? And if anyone plans to produce Japanese version, or any other language versions of the acedb, please tell me about your plan. Thank you for your attention to this mail. Takako Igarashi National Institute of Health Sciences taka@nihs.go.jp From owner-acedb@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!europa.eng.gtefsd.com!sundog.tiac.net!wizard.pn.com!satisfied.elf.com!rpi!usenet!edickg From: edickg@rpi.edu (George F Edick) Newsgroups: bionet.software.acedb Subject: test Followup-To: bionet.software.acedb Date: Wed, 5 Oct 94 20:59:14 GMT Organization: Rensselaer Polytechnic Institute, Troy NY, USA Lines: 5 Message-ID: NNTP-Posting-Host: bio22.bio.rpi.edu X-Newsreader: VersaTerm Link v1.1.1 This is a test. Please ignore. George Edick RPI - Dept. Biology Troy, NY 12180 edickg@rpi.edu From owner-acedb@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!news.mic.ucla.edu!unixg.ubc.ca!news.bc.net!newsserver.sfu.ca!darwin.mbb.sfu.ca!dbaillie From: dbaillie@darwin.mbb.sfu.ca (David L. Baillie) Newsgroups: bionet.software.acedb Subject: Re: Windows version Date: 6 Oct 94 17:00:11 GMT Organization: Simon Fraser University Lines: 40 Message-ID: References: <9410041049.AA00945@nihs.nihs.go.jp> NNTP-Posting-Host: darwin.mbb.sfu.ca taka@nihs.nihs.go.jp (Takako Igarashi) writes: >Hello! >Do you have any plan to produce Windows version of >the acedb? Takako I do not know of any port to MS windows, although there have been romours of a windows NT port (MAYBE). If you want to run ACeDB on a Intel machine, try the LINUX port that Ken Clark has done, the 2.0 port is on ncbi.nlm.nih.gov in /repository/acedb/ace2 You have to set up a linux OS on your machine, but it can share disk with DOS, and OS2. The machine must be a 486 or highher for good performance and must have 12 -16 mb of RAM. Linux and ACeDB eat up about 150 mb of disk space with the C. e. data set. Also we run the power MAC version of ACeDB, it runs fine, but also needs 16 mb of RAM and works about the same as the Linux version on a comparable processor. dave baillie ps a BSD unix port was also done by Ken Clark, if that is of use let me know. It's ace 2.0 again. pps we will not do a port of ace3, but plan to port ace4 when it is available. . >And if anyone plans to produce Japanese version, >or any other language versions of the acedb, please >tell me about your plan. >Thank you for your attention to this mail. >Takako Igarashi >National Institute of Health Sciences >taka@nihs.go.jp From owner-acedb@net.bio.net Thu Oct 06 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Problems with 2-x on Solaris Message-ID: <1994Oct7.092731.16838@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 7 Oct 1994 09:27:31 GMT Lines: 26 Colleagues, we are still troubled on a Sparcstation which we try to maintain via network. The memory allocation failure I reported earlier on Solaris 4.1 still occured after upgrading the machine to 96 MB physical memory, and reloading the binaries. As there is no GCC installed recompilation is not an option. There- fore I installed everything from sratch (starting with 2-0) and surprisingly got an error in 2-8 stating 'internal system error: parse error near line 61557 in B0248: Unknown tag "Overlap_right"'. Aligning the maps manually gives a bus error. Any ideas and suggestions? The disk has 115 MB free, so disk space should not be a problem. Regards Reinhard Doelz for University Fribourg, Switzerland. -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-acedb@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!nihs.nihs.go.jp!taka From: taka@nihs.nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: Greek letters Date: 7 Oct 1994 02:28:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410070927.AA11154@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net Hello, I would like to use Greek letters in ACEDB. Is it possible? Thank you for your attention to this mail. Takako Igarashi National Institute of Health Sciences taka@nihs.go.jp From owner-acedb@net.bio.net Sat Oct 08 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: [SUMMARY] Solving Problems with 2-x on Solaris Message-ID: <1994Oct9.144613.14177@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <1994Oct7.092731.16838@comp.bioz.unibas.ch> Date: Sun, 9 Oct 1994 14:46:13 GMT Lines: 63 Thanks to all who replied. Key answers are summarized below. Reinhard Doelz (doelz@comp.bioz.unibas.ch) wrote: : we are still troubled on a Sparcstation which we try to maintain via network. : The memory allocation failure I reported earlier on Solaris 4.1 still occured [...] : got an error in 2-8 stating 'internal system error: parse error near line : 61557 in B0248: Unknown tag "Overlap_right"'. Aligning the maps manually : gives a bus error. |> -Cyrus Harmon |> sly@fly2.berkeley.edu suggested to change the cachesize in wspec/cache.wrm. The parameter 2048 for both caches proved to solve the memory allocation error. The software-set value of 4000 did not work. |> Tohru Sano |> sano@kirara.exp.cl.nec.co.jp suggested that the INSTALL script was an old one. actually, the solution to the problem with missing elements came |> From: " (Richard Durbin)" |> |> You are not using the 2-14 wspec/. Each update comes with its own wspec/ |> directory, and they evolve with time, so while you can read early updates |> with later wspec/'s, you can't do the opposite. The first version of |> INSTALL untarred in alphabetical order, so update.2-2 overwrote update.2-14. |> INSTALL scripts since 2-10 have done things in the numerical order. Anyway, |> you just need to untar wspec from update.2-14.tar.Z to cure your |> Overlap_right problem. The update ended in a bus error, which could be repaired using advice From letter 2-14: : After adding the update, as the administrator (the person who : installed ACEDB) : Select "Write Access" from the main menu : Select "Align Maps" from the main menu : Press the "Make pMaps" button to make the physical maps : Press the "Make gMaps" button to make the genetic maps : Select "Save" from the main menu. If I dare hitting 'Make cMaps' as well I get a Segmentation fault which I am not sure whether this is the expected behaviour. : -- : R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| : Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| : Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| : EMBnet Switzerland:info@ch.embnet.org -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-acedb@net.bio.net Mon Oct 10 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!csulb.edu!nic-nac.CSU.net!charnel.ecst.csuchico.edu!xmission!u.cc.utah.edu!not-for-mail From: kr5205@u.cc.utah.edu (Kerry Rowe) Newsgroups: bionet.software.acedb Subject: lost loci on maps? Date: 10 Oct 1994 17:56:24 -0600 Organization: University of Utah Computer Center, Salt Lake City, Ut. Lines: 18 Message-ID: <37ckb8$or7@u.cc.utah.edu> NNTP-Posting-Host: u.cc.utah.edu I have built a database using ACEDB 3.0 where I have defined an STS object in models.wrm that should work like a Locus on the genetic and physical maps (i.e., it should be displayed the way any other Locus would be). This works fine (the STSs are displayed on the map) unti I... 1. place them on more than one map; then they are displayed on only the first map on which they are defined to reside and are missing from others. 2. ask that the maps be "Recalculated"; afterward they disappear. 3. add Locus objects to the map; then all my STSs disappear. Can someone please tell me how to fix this? Please respond directly to the newsgroup or to the following email address: bayer@darwin.med.utah.edu Thanks in advance. bayer From owner-acedb@net.bio.net Mon Oct 10 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!acheng From: acheng@ncsa.uiuc.edu (Albert Cheng) Newsgroups: bionet.software.acedb Subject: Must read's for acedb programmer Date: 11 Oct 1994 19:31:46 GMT Organization: Nat'l Ctr for Supercomp App (NCSA) @ University of Illinois Lines: 12 Distribution: world Message-ID: <37ep72$bd1@vixen.cso.uiuc.edu> References: <37ckb8$or7@u.cc.utah.edu> NNTP-Posting-Host: shalom.ncsa.uiuc.edu Originator: acheng@shalom.ncsa.uiuc.edu Hello, I am considering to install a database using Acedb but wanting to make it a client-server type database, i.e. frontend display running on one machine while the database backend sits on another. Can you recommend some documents/papers/guides/etc that describe Acedb that I should read first before hacking the code like a fool? Thanks in advance. =Albert Cheng From owner-acedb@net.bio.net Tue Oct 11 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: Must read's for acedb programmer Date: 12 Oct 1994 13:28:22 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 28 Distribution: world Message-ID: <37go9m$dob@overload.lbl.gov> References: <37ckb8$or7@u.cc.utah.edu> <37ep72$bd1@vixen.cso.uiuc.edu> NNTP-Posting-Host: s27w007.pswfs.gov In article <37ep72$bd1@vixen.cso.uiuc.edu> acheng@ncsa.uiuc.edu (Albert Cheng) writes: > ... >Can you recommend some documents/papers/guides/etc that describe >Acedb From the ACEDB FAQ: The latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html http://s27w007.pswfs.gov/Homepage/acedbfaq.html And there will be a new FAQ posted here about the 6th of each month (we're running late this month.) --bks -- Bradley K. Sherman Computer Scientist Dendrome Project 510-559-6437 FAX: -6440 Institute of Forest Genetics bks@s27w007.pswfs.gov P.O. Box 245, Berkeley, CA 94701 http://s27w007.pswfs.gov/People/bks.html From owner-acedb@net.bio.net Tue Oct 11 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!zip.eecs.umich.edu!umn.edu!scrapie.med.umn.edu!nrd From: nrd@scrapie.med.umn.edu (Neal Dalton) Subject: Conversion tools for ACeDB Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: scrapie.med.umn.edu Organization: University of Minnesota, Twin Cities X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 12 Oct 1994 15:05:13 GMT Lines: 26 I have been scrounging for tools to convert various formats, I'm still looking for a medline to ACeDB converter. I was surprised that this wasn't a FAQ, may this can be used to add a new one. They may need some changes, since databases vary. If there are better locations or other utilities, please let me know. I will post a summary. At ftp://weeds.mgh.harvard.edu/acedb_dev/utilities I found blast2ace - Converts NCBI blast email server format gb2ace - Comvert GenBank format (there are 2) mapm2ace - Converts Mapmaker "map" or "print chromosomes" sortpmap - Constructs physical map contigs in text ace2go - Dumps classes from ACeDB and waisindexing the .ace-format ace2nal - Translate Data from ACeDB Database to Relational Tables At ftp://igd-ftp.dkfz-heidelberg.de/pub/igd-ted opm2aces - OPM (Oject-Protocol Model) to ACeDB ace2eers - Experimental translates ACeDB model files to .erd for ERDRAW Neal From owner-acedb@net.bio.net Wed Oct 12 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!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: 13 Oct 1994 19:05:24 GMT Organization: Dendrome, A genome database for forest trees Lines: 1095 Approved: news-answers-request@MIT.Edu Message-ID: <37k0dk$2bu@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:460 news.answers:24818 Archive-name: acedb-faq Last-modified: 10/13/94 Version: 1.15 ---------------------------------------------------------------------- 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 : 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 : 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 : Still under construction 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 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 : 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 Wed Oct 12 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Beware of type Text! Date: 13 Oct 1994 16:09:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 84 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410132309.AA18051@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net I just figured out a bug in GrainGenes that's plagued me for many months. Since March I've been unable to reload the database from a full dump. I had to load it from my original .ace files, and I had to load them in a particular order. If I didn't the usual error message was !!FATAL ERROR: system error 12 Not enough memory malloc failure in messalloc: requesting 29360128 bytes , though there were others, especially !! FATAL ERROR 0: !! Bnew node : block overflow The results were the same for ace1-10 through ace3.1, under SunOS, Solaris and Linux. On further investigation I found that there were certain objects in the database to which no new data could be added. No additional links, directly or by XREF, not even an additional few characters of Text. Such objects were found in at least three of my classes, Gene, Gene_Class and Gene_Set. Here is one of them. Gene_Set : "Glu-1" Reference "TAG-60-229" Reference "WGS-83-827" Reference "JCS-3-17" Reference "TAG-13-6833" Reference "NAR-13-8729" Reference "NAR-13-6817" Reference "TAG-67-87" Reference "BCG-24-579" Reference "WGP-84-111" Reference "TAG-75-651" Gene_class "Glutenins" Gene "Glu-D1 (Triticum)" Gene "Glu-A1 (Triticum)" Gene "Glu-B1 (Triticum)" Gene "Glu-E1 (Elytrigia)" Gene "Glu-H1 (Hordeum)" Gene "Glu-H^ch^1 (Hordeum)" Gene "Glu-R1 (Secale)" Gene "Glu-R^m^1 (Secale)" Gene "Glu-U1 (Aegilops)" Gene "Glu-V1 (Dasypyrum)" Gene "Glu-H^t^1 (Elymus)" Comment "The Glu-1 loci, which are compound, encode HMW glutenin \ subunits." Comment "Each Glu-1 locus in hexaploid wheat contains two genes, the \ products of which were described as 'x-type' and 'y-type' based on \ differences in molecular weight and isoelectric point (790). Other \ evidence has shown these gene products to differ in electrophoretic \ fingerprint pattern (798) and cysteine content (730), and the genes \ themselves to differ in nucleotide sequence (1068, 1034, 255). \ Although early evidence suggested up to 6 genes in total at each \ locus (1069, 255), it appears likely that only a single copy of each \ gene is present at the 1AL, 1BL, and 1DL loci (340)." Comment "The symbols for the genes within the Glu-1 loci encoding \ 'x-type' and 'y-type' proteins are Glu-1-1 and Glu-1-2, respectively \ [rather than Glu-1x and Glu-1y (1068)]. The genes are closely linked \ but recombination has been observed between Glu-B1-1 and Glu-B1-2 \ with a frequency of 3 in 3,450 (789). The gene order, relative to \ the centromere, has not been ascertained." Comment "A system of naming the Glu-A1-1, Glu-A1-2, Glu-B1-1 and \ Glu-B1-2 alleles in T. turgidum var. dicoccoides is given in 577." Numbered_reference 790 "TAG-60-229" Numbered_reference 798 "WGS-83-827" Numbered_reference 730 "JCS-3-17" Numbered_reference 1068 "TAG-13-6833" Numbered_reference 1034 "NAR-13-8729" Numbered_reference 255 "NAR-13-6817" Numbered_reference 1069 "TAG-67-87" Numbered_reference 340 "BCG-24-579" Numbered_reference 789 "WGP-84-111" Numbered_reference 577 "TAG-75-651" To make a long story short, the problem turned out to be that those Comment fields were of type Text. I changed them to ?Text, and now everything is working. A question: Is Text a recommended type for any situations? As I recall it used to be required for the arguments of Pick_me_to_call, ?Text didn't work. Anything else? - Dave From owner-acedb@net.bio.net Sun Oct 16 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: model trees Date: 17 Oct 1994 22:11:20 +0100 Lines: 46 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <37up9o$6h@mserv1.dl.ac.uk> Original-To: ptv@druid.epm.ornl.gov > Logically, it is sufficient to avoid identical pathes in model trees: the same > tag may appear several times iff different labeled pathes from the root lead to > every occurence of the tag. You are correct. We could always use complete paths, and then only require that tags are unique to the right of any one node, so that paths are unique. This would be implementable, though it would mean that all requests to the object package would have to pass a path of tags, rather than just a single tag as now. It would mean changing a lot of code. I suppose I feel that the lack of a requirement for knowledge about previous layers is part of the philosophy. It certainly allows us to dump out data, rearrange the inner structure of a model, and read the data back in again. Also, it allows the map code to refer to the "Map" subtree for example, without it being necessary for the tag "Map" to always be in the same place in the complete model. Of course the correct answer is that you can achieve exactly what you want with constructed subtypes, i.e. the '#' construction. e.g. the model ?Box Forecol #Colour Backcol #Colour ?Colour UNIQUE Red Blue Green amounts to ?Box Forecol UNIQUE Red Blue Green Backcol UNIQUE Red Blue Green except that you can obviously not just query on Red for a box, you must use "Forecol # Red" instead. Subtypes don't get used much, I suspect because they are a pain. Richard From owner-acedb@net.bio.net Sun Oct 16 23:00:00 1994 Path: biosci!CADEV6.INTEL.COM!ptagare From: ptagare@CADEV6.INTEL.COM Newsgroups: bionet.software.acedb Subject: Bug in TableMaker? Date: 17 Oct 1994 08:55:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410171524.AA08704@cad553.intel.com> NNTP-Posting-Host: net.bio.net Hi! I can't seem to get the "Condition" field in the TableMaker to work. When I hit the button to search, the condition field is totally ignored (This field remains yellow even after I hit return). However, if I save the tablemaker.def file, and use it for textace, it works! This is in ACEDB 3.0 on SUN OS4.1.3. Any clues? Thanks, -- 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 Sun Oct 16 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swrinde!emory!cs.utk.edu!stc06.CTD.ORNL.GOV!druid!ptv From: ptv@druid.epm.ornl.gov (Sergey Petrov) Newsgroups: bionet.software.acedb Subject: model trees Date: 17 Oct 1994 14:54:06 GMT Organization: Oak Ridge National Lab/CESAR Lines: 18 Distribution: world Message-ID: <37u36e$p6l@stc06.CTD.ORNL.GOV> Reply-To: ptv@druid.epm.ornl.gov NNTP-Posting-Host: druid.epm.ornl.gov Keywords: tags repetition I wonder how deep the restriction on tags repetitions is hardwired into acedb software. Logically, it is sufficient to avoid identical pathes in model trees: the same tag may appear several times iff different labeled pathes from the root lead to every occurence of the tag. The restriction helps to create .ace files: instead of the whole tree, one needs to use only 'leaf tags'. The restriction is tiresome in case, for example, of spatial relationships expressions in a model: one needs separate tags 'inside_yac' and 'contains_yac' instead of three tags: 'contains', 'inside', and 'yac', 'clone', 'locus', etc. Is there anybody who is interested in the subject? Sergey Petrov From owner-acedb@net.bio.net Sun Oct 16 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!agate!howland.reston.ans.net!pipex!uunet!EU.net!sun4nl!news.nic.surfnet.nl!rug.nl!ppsw131250.ppsw.rug.nl!tdewit From: tdewit@ppsw.rug.nl (Toine de Wit) Subject: Conference: Social Science Information Technology Message-ID: Keywords: statistics, psychology, software, market research Lines: 46 Sender: root@rug.nl (Operator) Nntp-Posting-Host: ppsw131250.ppsw.rug.nl Organization: Faculty Social Sciences Rijksuniversiteit Groningen Date: Mon, 17 Oct 1994 12:44:10 GMT ************** SSIT 94 *************** SECOND INTERNATIONAL CONFERENCE ON SOCIAL SCIENCE INFORMATION TECHNOLOGY DATES: 7-8-9 December 1994 PLACE: RAI Congress Centre Amsterdam, the Netherlands PROGRAM: 7 December WORKSHOPS (confirmed as of October 1994) * Structural Equation Modeling * Scaling * Experimentation and Observation * Content and Text Analysis 8-9 December SESSIONS (confirmed as of October 1994) * Social Network Analysis * Statistical Computer Applications * Innovative Educational Systems * Decision Challenges and the Role of Knowledge * Brain Research and Task Performance * Psychological Assessment * Content and Text Analysis * Simulation * Computer-Assisted Data Collection * Neural Networks and Self-Organizing Networks * Visualization * Advanced Statistical Techniques * Behavioral Research and Applications * Analysis and Diffusion of Information CONTACT: SSIT 94 Organizing Committee iec ProGAMMA P.O. Box 841 9700 AV Groningen The Netherlands Tel.: +31 50 636 900 Fax: +31 50 636 687 Email: gamma.post@gamma.rug.nl ** PLEASE FEEL FREE TO REPOST THIS ANNOUNCEMENT ** From owner-acedb@net.bio.net Sun Oct 16 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: Bug in TableMaker? Date: 17 Oct 1994 22:04:35 +0100 Lines: 18 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <37uot3$t11@mserv1.dl.ac.uk> Original-To: ptagare@cadev6.intel.com > I can't seem to get the "Condition" field in the TableMaker to work. > When I hit the button to search, the condition field is totally > ignored (This field remains yellow even after I hit return). You certainly have to hit return in the field for the condition to register. I remember problems with this, but I have used the field in xace. Normally I use prestored tables. What if you save a table and reload it back into xace? Jean has added significantly to Table_maker for the next version of ACEDB. First it now handles correctly items that are not immediately adjacent to a tag, so you can make a table of all pairs. Second, you can now set a condition on a column involving other columns as parameters in the query. This in effect allows relational join-type operations. Unfortunately there is a fatal bug we must find before it is released. Richard From owner-acedb@net.bio.net Sun Oct 23 22:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: storing comments on the IGD-schema Date: 24 Oct 1994 10:18:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410241718.AA12313@cvx12.inet.dkfz-heidelberg.de> References: <28897.9410241548@iron.hgmp.mrc.ac.uk> NNTP-Posting-Host: net.bio.net I remember John McCarthy having a Meta Data handling system integrated into ACEDB. However, we could also use a normal ACEDB to handle the schema description. I tried a 10-minute test: 1. add a class (to {models,classes,options}.wrm): ?Meta KW ?LongText REPEAT 2. run this awk-script on models.wrm: '/^ *\/\// {next} /^ *$/ {print; next} /^\?/ {print "Meta :",$1; $1=""; print "KW",$0; next} {print "KW",$0} and redirect its output into a file models.ace 3. in ACEDB, read models (from main menu), then read models.ace Now for each tag and each pointer a long text can be entered, altough the text must be a summary on all the places the tag is used in the model. 2 sample "Long"Texts: LongText : Full_name the full name for an Author comes from GDB Mon Oct 24 18:02:49 MET 1994 dok256 ***LongTextEnd*** LongText : ?Clone Clones come from GDB and RLDB ***LongTextEnd*** And the main work -- writing the text -- remains, of course. Greetings Detlef From owner-acedb@net.bio.net Sun Oct 23 22:00:00 1994 Path: biosci!UX5.LBL.GOV!mccarthy From: mccarthy@UX5.LBL.GOV (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Re: storing comments on the IGD-schema Date: 24 Oct 1994 12:09:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410241909.MAA20826@ux5.lbl.gov> Reply-To: JLMcCarthy@lbl.gov NNTP-Posting-Host: net.bio.net I like Detlef's awk script to capture information on tags, but I think it needs a bit more: 1. tags need to be associated with classes, since a tag may have different semantic meanings in different classes; and 2. likewise, pointers need to be associated with a particular ?Class/tag, since there can even be multiple pointers to the same class from different tags within a single class -- each with different semantic meaning. At the ACEDB Workshop, we demonstrated that it is possible to invoke Mosaic from within ACEDB, and to pass it information on what class and tag are currently selected, so that one could provide context sensitive help on individual elements (?Class, tag, pointer, data value, etc.). -John