From owner-acedb@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!dave_s From: dave_s@iastate.edu (David A Schrader) Newsgroups: bionet.software.acedb Subject: environment variable for images Date: 1 Jun 1995 16:38:52 GMT Organization: Iowa State University, Ames, Iowa USA Lines: 10 Message-ID: <3qkqes$6dg@news.iastate.edu> NNTP-Posting-Host: isum1.iastate.edu I would like to suggest that there should be an environment variable that can be set to indicate the location of the image files which are accessed when the user presses the Pick_me_to_call area in images. Dave S. -- =============================================================================== | Dave Schrader | But remember, as you stare into the abyss,| |schrader@mendel.agron.iastate.edu| so the abyss also stares into you. | | (515) 294-0421 | -Nietzsche | =============================================================================== From owner-acedb@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!world!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!news From: Brian Fristensky Newsgroups: bionet.software.acedb Subject: XREF Date: 5 Jun 1995 23:24:57 GMT Organization: University of Manitoba Lines: 34 Message-ID: <3r03o9$jfc@canopus.cc.umanitoba.ca> NNTP-Posting-Host: antares.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3 sun4m) X-URL: news:bionet.software.acedb I would like some clarification on the user of XREF in ACEDB. For example, ?Author Name Text Paper ?Paper ?Paper Title Text Author ?Author The example above should create a 2-way link between Author and paper. However the syntactic definitions for ACEDB (Dec. 10 1992) gives an example (edited here for brevity) that reads ?Author Name Text Paper ?Paper XREF Author ?Paper Title Text Author ?Author XREF Paper What does the XREF accomplish? What can you do that would otherwise be impossible without the XREF? Can someone illustrate this point with an example? -- =============================================================================== Brian Fristensky | Department of Plant Science | Life doesn't imitate art, University of Manitoba | it imitates bad television. Winnipeg, MB R3T 2N2 CANADA | frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Woody Allen, HUSBANDS AND WIVES FAX: 204-261-5732 | http://www.umanitoba.ca/Agriculture/Plant_Science/Fristensky/Fristensky.html =============================================================================== From owner-acedb@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!NCBI.NLM.NIH.GOV!mieg From: mieg@NCBI.NLM.NIH.GOV (Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: ACEDB 4 distribution Date: 5 Jun 1995 22:12:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506060512.AA20893@ncbi.nlm.nih.gov> NNTP-Posting-Host: net.bio.net We want to confirm the situation with respect to the ACEDB 4 distribution. The present code distribution was renamed to ace4.test following a number of bug reports. It can be used for viewing data, but should be considered only as test code for data management, and should not be used for production purposes. The code was released at the end of the ACE95 2-week workshop, during which many improvements had been made and bugs fixed. Unfortunately we did not have time to fully test this version before the C. elegans meeting (June 3-7). Acedb 4 supports the new C. elegans data release, and we will fix bugs in it, and develop from it in the future. As always, we welcome your comments, and in particular bug reports. Jean Thierry-Mieg Richard Durbin From owner-acedb@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: XREF Date: 6 Jun 1995 04:54:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 111 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506061154.AA01391@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Brian Fristensky, frist@cc.umanitoba.ca, asks: > the syntactic definitions for ACEDB (Dec. 10 1992) gives an > example (edited here for brevity) that reads > > ?Author Name Text > Paper ?Paper XREF Author > > ?Paper Title Text > Author ?Author XREF Paper > > What does the XREF accomplish? The purpose of the XREF command in models.wrm is to instruct ACEDB to create an automatic back-reference when the .ace file is loaded. For example, loading a .ace file containing only the record, Paper : TAG-87-697 Title "Cultivar discrimination of Brassica napus using RAPDs" Author Mailer-RJ Author Scarth-R Author Fristensky-B , will create in the database not only that Paper object but also the Author objects Author Mailer-RJ Paper TAG-87-697 Author Scarth-R Paper TAG-87-697 Author Fristensky-B Paper TAG-87-697 That's the basic answer. It's a very useful function. Now for the Appendix to the answer. APPENDIX: "Remove the XREF from ?Author Paper ?Paper XREF Author!" It turns out that the example used in this syntactic definitions document is a particularly poor one, and the document should be updated. Although in many cases it is convenient to set up reciprocal XREFs so that two- way links are automatically created regardless of which class of objects are loaded, this leads to trouble in the case of ?Paper <-> ?Author. The problem is that the Authors of a given Paper will be listed in the order loaded, so if all the Author objects are loaded before all the Paper objects (as happens when the database is re-loaded from a dump file) the presence of an XREF in the ?Author Paper field scrambles the Author orders. Below is a fuller description of this problem (found by searching the acedb newsgroup archive, gopher://genome-gopher.stanford.edu/77/.index/ acedb-biosci, for "xref"). regards, - Dave :::::::: >From BIOSCI-REQUEST Mon Apr 24 14:09:23 1995 To: acedb@net.bio.net >From: Subject: Author order Original-To: acedb@dl.ac.uk > We're running version 3.0 on a SUN. I've noticed that after several days > of use, our database has changed the order of Author's names inside of > Paper objects. Have others experienced this? Has it been addressed in > later versions? I doubt the order is changing. The order in a column is determined by the order in which items are entered. If they are there already then they are not reentered. People have had problems with Author order before, for the following reason. If you XREF from Author to ?Paper, e.g. your models contain something like ?Author Address ... Paper ?Paper XREF Author // <1> ?Paper Reference Title ?Text Author ?Author XREF Paper // <2> then if you add Author objects before the Paper objects, the Paper object will be created by the XREF <1>, and the author list in position <2> in the paper object will be determined by the order in which the Author objects are read in, not the order of authors in the Paper object. This was a problem with the very early models used by the C. elegans database, and hence unfortunately propagated around the world. The solution is to remove XREF <1>, so the models look like: ?Author Address ... Paper ?Paper ?Paper Reference Title ?Text Author ?Author XREF Paper Now the authors in the Paper object will only be added when the Paper object is read, and will be in the order specified there. I hope this is both clear, and also the cause of the reported problem. Richard From owner-acedb@net.bio.net Fri Jun 09 23:00:00 1995 Newsgroups: bionet.software.acedb Path: biosci!agate!howland.reston.ans.net!torn!newshub.ccs.yorku.ca!newshub.ariel.cs.yorku.ca!cs911196 From: cs911196@ariel.cs.yorku.ca (AIK KHOON EUGENE LEE) Subject: LOOKING FOR EDUCATIONAL SOFTWARE Message-ID: Sender: news@ariel.cs.yorku.ca Organization: York University, Dept. of Computer Science Date: Fri, 9 Jun 1995 19:49:34 GMT Lines: 31 Hello: I am currently looking for some educational software for the kids, teenagers and adults learning centre. I would like to know which programs are the best to use and where I can download those complete set of programs. Anyone who has information about this, please help me out. Thank in advanced. 1.) English courses: ---------------- ** Level: from kindergarten to high school ** Dos & windows version 2.) Mathematics courses: -------------------- ** Level: from kindergarten to high school ** Dos & windows version 3.) Computer courses: ----------------- ** Introduction to personal computer. Basic ideas of how to operate windows and simple DOS commands. ** If anyone have related programs for sale, please feel free to contact me. Thank you very much. Eugene. e-mail: cs911196@ariel.cs.yorku.ca From owner-acedb@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: ?2_Point_Data vs. ?2_point_data Date: 12 Jun 1995 09:42:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506121631.AA10787@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net In xace4_0b4, trying to load a ?2_Point_Data object gives "Unrecognized Class 2_Point_Data", whereas ?2_point_data objects load fine. My models.wrm and options.wrm specify the Upper_Case version; "?2_point_data" doesn't exist in my wspec directory. Is this a reserved class name? - Dave From owner-acedb@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!sol.ctr.columbia.edu!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: ?2_Point_Data vs. ?2_point_data Date: 12 Jun 1995 19:57:48 +0100 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3ri2nc$952@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk The code since last October (version 3.5?) has installed 2_point_data as a class (lower case version), and this is what is used in the map display routines. I guess the code that reads options.wrm is not case sensitive, and reads your ?2_Point_Data as referring to the already existing ?2_point_data class. But the parser code is apparently case sensitive. So for now you will have to use the lower case version. To avoid this type of problem, we should be consistent, and either always make class name recognition case sensitive, or case insensitive. I propose it should be case insensitive -- it would be very confusing to have two classes whose names differed only by case. Any objections from anyone? Richard From owner-acedb@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: ?2_Point_Data vs. ?2_point_data Date: 12 Jun 1995 13:28:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506122028.AA11464@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > I propose it > should be case insensitive -- it would be very confusing to have two > classes whose names differed only by case. Any objections from > anyone? Fine with me. The next question is which case will be shown in the displays, in case of a conflict. Use the one in models.wrm in preference to options.wrm or other, code-installed versions? - Dave From owner-acedb@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!dave_s From: dave_s@iastate.edu (David A Schrader) Newsgroups: bionet.software.acedb Subject: metabolic pathways problem Date: 12 Jun 1995 20:30:18 GMT Organization: Iowa State University, Ames, Iowa USA Lines: 15 Message-ID: <3ri84q$966@news.iastate.edu> NNTP-Posting-Host: isum1.iastate.edu I am setting up our metabolic pathways and can read in the data & models just fine, but when I try to bring up a diagram, I get : !! FATAL ERROR 0: !! textBounds called on invalid graph type 2 and then acedb exits. Any insights into the cause of this ? Dave S. -- =============================================================================== | Dave Schrader | But remember, as you stare into the abyss,| |schrader@mendel.agron.iastate.edu| so the abyss also stares into you. | | (515) 294-0421 | -Nietzsche | =============================================================================== From owner-acedb@net.bio.net Mon Jun 12 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Re: metabolic pathways problem Date: 13 Jun 1995 10:23:08 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3rjlds$leu@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk > I am setting up our metabolic pathways and can read in the data & models just > fine, but when I try to bring up a diagram, I get : > > !! FATAL ERROR 0: !! textBounds called on invalid graph type 2 > > and then acedb exits. Any insights into the cause of this ? You should have a line _DMETAB -g TEXT_FULL_SCROLL -t "Pathways" -width .6 -height .4 -help Pathways in your wspec/displays.wrm file. Richard From owner-acedb@net.bio.net Mon Jun 12 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!usenet.eel.ufl.edu!noc.netcom.net!news.sprintlink.net!aimnet1.aimnet.com!aimnet.aimnet.com!not-for-mail From: chinabus@aimnet.com (Michael Lee) Newsgroups: schule.software,bionet.software.srs,bionet.software.acedb,bionet.software.gcg Subject: Chinese Computer Digest http://www.gy.com Date: 13 Jun 1995 02:32:29 -0700 Organization: AIMNet Corp. Lines: 28 Message-ID: <3rjlvd$gb3@aimnet.aimnet.com> NNTP-Posting-Host: aimnet.aimnet.com Xref: biosci bionet.software.srs:85 bionet.software.acedb:627 bionet.software.gcg:1222 [Chinese Computer Digest] http://www.gy.com Chinese Computer Digest is the first Chinese Computing Magazine on the internet , it has own domain name: gy.com, the homepage of Chinese Computer Digest is at: http://www.gy.com Chinese Computer Digest is the bilingual magazine , it has both English and Chinese version, for the Chinese version, it has both GB Code and Big5 Code. Chinese Computer Digest covers following area: Apple Chinese Software Chinese Windows Software Chinese Educational Software Chinese Computer CD-Title Chinese English Translation Software Chinese Computer Fonts Chinese Personal Digital Assistant Chinese Speaking & Input Software Chinese OCR Software Computer News From China Chinese Software Company Chinese Speaking & Input Software ...... Welcome to Chinese Computer Digest, any suggestion or comments please contact with: Chinese Computer Digest 10787-A South Blany Ave., Cupertino, CA 95014 USA Tel: 408-257-9480 Email: chinabus@gy.com From owner-acedb@net.bio.net Mon Jun 12 23:00:00 1995 Path: biosci!rutgers!uwm.edu!newsspool.doit.wisc.edu!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!news From: Brian Fristensky Newsgroups: bionet.software.acedb Subject: (no subject) Date: 13 Jun 1995 22:16:25 GMT Organization: University of Manitoba Lines: 43 Message-ID: <3rl2np$roh@canopus.cc.umanitoba.ca> NNTP-Posting-Host: antares.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3 sun4m) To: calling,external,programs X-URL: news:bionet.software.acedb#9506131040.AA12553@greengenes.cit.cornell.edu I am implementing an ACEDB database for my lab in a group-readable directory, allowing users to log in on their own accounts, but still use ACEDB as a read-only database. (This is being done on a SUN, by the way.) However, I have encountered a problem in running external programs such as xv. For example, I have an image defined as Pick_me_to_call xv Clones/pI176.gif which sends the following command to the system: acedb call: cd /home/u12/frist/drr/lab/externalFiles ; xv Clones/pI176.gif & When I run ACEDB from my account (I am the owner of the directory), the command works fine. When another user chooses this command, xv starts up, but gives the message "Can't open file 'getwd: can't open ./Clones/pI176.gif'. No such file or directory. (Bummer!)" The root of the problem here seems to be that ACEDB automatically changes to the externalFiles directory, and either fails to pass the path along, or fails to tell the new shell that it has permission to read in that group-readable directory. I can solve the problem by redefining the image as Pick_me_to_call cd; xv $ACEDB/externalFiles/Clones/pI176.gif but that's kind of messy, since every object has to have these fixes explicitly spelled out. Recognizing that Unix groups are kind of tricky, I wonder if anyone else has encountered and solved this problem before? =============================================================================== Brian Fristensky | Department of Plant Science | Life doesn't imitate art, University of Manitoba | it imitates bad television. Winnipeg, MB R3T 2N2 CANADA | frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Woody Allen, HUSBANDS AND WIVES FAX: 204-261-5732 | http://www.umanitoba.ca/Agriculture/Plant_Science/Fristensky/Fristensky.html =============================================================================== From owner-acedb@net.bio.net Mon Jun 12 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: announcing SampleDB release 1.0 Date: 13 Jun 1995 07:18:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506131417.AA13082@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net The first release of SampleDB, described below, is now available for anonymous ftp from probe.nalusda.gov:pub/acedocs/sampledb*. ~~~~~~~~ SampleDB, version 1.0, 12 June 1995 A sample database to demonstrate features of ACEDB, especially map and sequence displays. FEATURES INCLUDED The GMAP C. elegans chromosome V and its neighbors To view, pick Map "V". There is a "guided tour" available via the online help; click the "Help" button in the main window. The PMAP ctg313 and ctg893, from C. elegans chromosome V, and their neighbors To view, pick Map "V" and double-click on the yellow "Contigs" bars The Sequence Display C. elegans sequence B0272 and some of its neighbors To view, pick Sequence "B0272". The MultiMap Rice chromosome 1 vs. maize chromosomes 3 and 8 To view, examine MultiMaps "Rice 1, Maize 3,8" and "Rice 1, Maize 3,8 Anchored" Developers and documenters are encouraged to add more features to SampleDB, by submitting - concise .ace datasets, - description of any models.wrm changes needed, relative to AC.elegansDB, and - suggested objects to look at to exercise the features. SampleDB 1.0 is distributed with a SunOS 4.x executable of ACEDB version 4_0b4. It is not necessarily expected to work with any other version of ACEDB. Dave Matthews matthews@greengenes.cit.cornell.edu From owner-acedb@net.bio.net Mon Jun 12 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: ?2_Point_Data vs. ?2_point_data Date: 13 Jun 1995 03:40:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506131040.AA12553@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > From rd@sanger.ac.uk Tue Jun 13 05:17:50 1995 > To: matthews@greengenes.cit.cornell.edu > Subject: Re: ?2_Point_Data vs. ?2_point_data > > Currently the internal version would win out for display. I would > prefer that the version in options.wrm wins. That is the per-class file. > models.wrm is about models, not classes. You can have an array class > with no model, and a model for a subtype with no class. > > Richard Okay. I hadn't been sensitive to that difference or the philosophies to be drawn from it. - Dave From owner-acedb@net.bio.net Mon Jun 12 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!gaia.ucs.orst.edu!nostromo.OES.ORST.EDU!uriber From: uriber@nostromo.OES.ORST.EDU (Ricardo Uribe) Newsgroups: bionet.software.acedb Subject: Problem with Ace4 Under Solaris 2.4 Date: 13 Jun 1995 22:59:46 GMT Organization: Oregon Extension Service Lines: 13 Message-ID: <3rl592$9gv@gaia.ucs.orst.edu> NNTP-Posting-Host: nostromo.oes.orst.edu Hello, I got the binaries for Solaris, but everytime I tried to run the xace4 I get this error: ld.so.1: /data/yuca4/bin/xace: fatal: libXaw.so.5.0: can't open file: errno=2 Killed I know I have my X libraries in my LD path set correctly, could some one help me on this? Thanks Ricardo Uribe CIAT From owner-acedb@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!trane.uninett.no!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: sets Date: 14 Jun 1995 17:09:06 +0100 Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3rn1j2$pf3@mserv1.dl.ac.uk> Original-To: scartinh@coyote.tamu.edu the command { >?Map_set Human; >Map; >Locus } $& { >?Map_set Mouse; >Map; >Locus } does not work because of a problem in the parser of the query language the parser breaks on ; evn though the ; is embedded inside a {} sorry about that, it is a slghtly difficult problem needing one extra level of recursivity in the system i paln to do that someday, but with a rather low priority jean From owner-acedb@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!usenet From: Akemi Yagi Newsgroups: schule.software,bionet.software.srs,bionet.software.acedb,bionet.software.gcg Subject: Re: Chinese Computer Digest http://www.gy.com Date: 14 Jun 1995 14:57:23 GMT Organization: The Scripps Research Institute Lines: 17 Message-ID: <3rmtcj$ev5@riscsm.scripps.edu> References: <3rjlvd$gb3@aimnet.aimnet.com> NNTP-Posting-Host: energy_pc.scripps.edu Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="-------------------------------16884454920067" X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: echan@gcrc Xref: biosci bionet.software.srs:86 bionet.software.acedb:633 bionet.software.gcg:1224 This is a multi-part message in MIME format. ---------------------------------16884454920067 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Hi Ed, Heard about this? Akemi ---------------------------------16884454920067 Content-Transfer-Encoding: 7bit Content-Type: ---------------------------------16884454920067-- From owner-acedb@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!dave_s From: dave_s@iastate.edu (David A Schrader) Newsgroups: bionet.software.acedb Subject: Re: (no subject) Date: 14 Jun 1995 13:10:55 GMT Organization: Iowa State University, Ames, Iowa USA Lines: 50 Message-ID: <3rmn4v$hd0@news.iastate.edu> References: <3rl2np$roh@canopus.cc.umanitoba.ca> NNTP-Posting-Host: isum1.iastate.edu I have had the same problem and got around it by changing program name from something like xv to my own wrapper which then calls xv or whatever. I wrote the wrapper in perl and it allows you to set a couple of environment variables which point to where you want the images to reside and where you want the program to be. BTW another suggestion that I got when asking this question was to use a soft link from the externalfiles directory to where ever your images actually reside. Here is the perl script that does the work. As you can see it is very simple: #!/usr/local/bin/perl # # This perl script was written to allow multiple version of acedatabase to access# a single set of image files. Normally, acedb insists that it has subdirectory # beneath the present working directory which contains the images. This would # be very inefficient in terms of disk usage. This script allows the user to # preset environment variables that specify the image viewer ( and its full # path ), and the path to the image files. xv_hack takes as its arguement, the # name of the file that is to be passed to the image viewing program. # # VARIABLES : # IMG_SRC -full path to directory containing images # # VIEWER_PATH -full path to the image viewing program. THis MUST end # in / so that the image filename can be appended neatly. # # # get the environement variables and command line arguement # $image_name=$ARGV[0]; $img_src=$ENV{'IMG_SRC'}; $xv_dir=$ENV{'VIEWER_PATH'}; # # form the command line and pass it to the system # $command_line=join('',$xv_dir," ",$img_src,$image_name); print("$command_line\n"); system($command_line); Hope this helps, Dave S. ~ ~ -- =============================================================================== | Dave Schrader | But remember, as you stare into the abyss,| |schrader@mendel.agron.iastate.edu| so the abyss also stares into you. | | (515) 294-0421 | -Nietzsche | =============================================================================== From owner-acedb@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!demon!uknet!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: 4_0 libraries under Solaris Date: 14 Jun 1995 19:03:29 +0100 Lines: 37 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3rn89h$27a@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk The Solaris version of ACEDB 4_0 that we released was built on a machine that had X11 release 5 libraries installed on it. Solaris makes dynamic library links at run time, and so it expects the same libraries to be present at run time as at build time. The X11R5 libraries are not present on most Solaris machines, meaning that the the solaris binaries will not run. There are two ways round this if you want to run acedb 4 now: The first is to recompile yourself on your own machine from the source code, which is available in the distribution. Instructions to do this are in NOTES. You should setenv ACEDB_MACHINE to be SOLARIS_4. The second is to make symbolic links in /usr/openwin/lib to fake the missing libraries from ones that do exist. This requires root access, and is a hack, but, amazingly, appears to work fine - several people have reported doing it. A typical set of links is: ln -s libX11.so.4 libX11.so.5.0 ln -s libXaw.so.5 libXaw.so.5.0 ln -s libXext.so.0 libXext.so.5.0 ln -s libXmu.so.4 libXmu.so.5.0 ln -s libXt.so.4 libXt.so.5.0 You may need to change the names in the first column to match what you find in /usr/openwin/lib. These instructions do not touch any existing files -- they create new fake names as wanted by the precompiled xace. A third approach is to wait until we make a new release, which we hope to do in a few weeks. We will endeavour then to compile in a more standard configuration, and this will also include fixes of as many of the reported bugs as possible. Note however that run-time library mismatches appear to be a perennial problem, particularly with Solaris. Richard From owner-acedb@net.bio.net Tue Jun 13 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: announcing SampleDB release 1.0 Date: 14 Jun 1995 17:26:40 +0100 Lines: 3 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3rn2k0$qjt@mserv1.dl.ac.uk> Original-To: matthews@GREENGENES.CIT.CORNELL.EDU bravo thsi is a great initiative merci From owner-acedb@net.bio.net Thu Jun 15 23:00:00 1995 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: core dump on SGI after init Date: 16 Jun 1995 10:54:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506161755.TAA23003@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net the test.source.4_0b4a.tar.Z code does a core dump on SGI in tace after having initialized the database. after that it's working fine. Detlef ---------- The file /embnet/zdv.igd/m/dok256/aquila/ace4b4/database/ACEDB.wrm does not exist, indicating that the database is empty. Should I reinitialise the system? (y or n) !! 1 objects read with 0 errors !! 1 objects read with 0 errors Segmentation fault (core dumped) From owner-acedb@net.bio.net Sat Jun 17 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!europa.chnt.gtegsc.com!news.sprintlink.net!unix.tpe.com!usenet From: patwas@netc.com Newsgroups: bionet.software.acedb Subject: Shareware Contouring Software Date: 18 Jun 1995 07:26:47 GMT Organization: The Power Exchange, Washington DC Lines: 8 Message-ID: <3s0kfn$72m@unix.tpe.com> NNTP-Posting-Host: 199.190.110.68 X-Newsreader: AIR News 3.X (SPRY, Inc.) I am interested to find programs which are able to convert XYZ askii text data from total station surveys into contours in DXF format. If anyone knows of any Share Ware programs which are able to perform this function, I would appreciate an E-Mail at... PatWas@Netc.com Thanks! From owner-acedb@net.bio.net Mon Jun 19 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!plug.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunic!sunic.sunet.se!news.kth.se!kiev.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.general,bionet.software.acedb,bionet.microbiology,sci.med Subject: MycDB 3-8 data release Date: 20 Jun 1995 10:12:40 +0200 Organization: Biochemistry, KTH, Stockholm Lines: 144 Distribution: world Message-ID: <3s5vto$72u@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: MycDB, ACEDB, mycobacteria Xref: biosci bionet.general:15831 bionet.software.acedb:639 bionet.microbiology:2550 sci.med:83106 Stockholm & Paris June 18, 1995 The eight release of the Mycobacterium database, MycDB, is now available. MycDB is funded by the WHO and the Fondation Raoul Follereau and is maintained jointly by the Unite de Genetique Moleculaire Bacterienne at the Institut Pasteur in Paris, France and the Department of Biochemistry at the Royal Institute of Technology in Stockholm, Sweden. MycDB is available free of charge via Internet network transfer. A complete description of the procedure to retrieve and install the software and database is available through the Internet (see the end of this message for addresses). MycDB is also available through the WorldWideWeb servers at the Royal Institute of Technology (URL: http://www.biochem.kth.se/MycDB.html) and (through the good offices of the Genome Informatics Group at the National Agricultural Library) on the Agricultural Genome Information Server, AGIS, in Beltsville, Maryland, USA (WorldWideWeb URL: http://probe.nalusda.gov:8300/other/index.html or gopher URL: gopher://probe.nalusda.gov:7000/11/genome.databases/mycdb/). MycDB uses the excellent database software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg (CNRS, France). The ACEDB software allows the user to browse information by simply pointing and clicking with the workstation mouse. A variety of powerful query methods are also available. However, our experience is that most users choose the mouse interface to find the information they are interested in. As far as possible all information is connected to other information in the database. The database software presents the information in separate windows that allow many parts of the database to be viewed at one time. There are also many paths to any piece of information, allowing the user to easily navigate the connections between the various types of information. New in release 3-8: * New and edited sequences from EMBL/GenBank/DDBJ, as of May 31, 1995. Due to extensive reanalysis, annotation and merging of overlapping sequences, and the removal of the blast search data (pending new data) the number of sequences have drastically decreased (from over 4000 Sequence objects to 1832, and from 543 DNA objects to 515). However, the total number of nucleotides have increased by 171,008 (12.3%) to 1,560,886 nt. Thus, this is a considerably less redundant set of sequences from mycobacteria than in previous releases. We intend to continue this analysis and merging of sequences, and also add blast searches and coding frame predictions to the data set. There are two new subclasses, derived from the Sequence class: NucleotideSeq contains Sequence objects with attached nucleotide sequence (this replaces the earlier DNA class in the Main Window) and PeptideSeq contains protein sequences. * 112 new literature citations from MedLine, current as of May 31, 1995. The links to abstracts in the set of papers in earlier releases have been rechecked and errors removed. Of 3180 Paper objects in release 3-8, 2399 have attached abstracts. * The Antigen class has been updated, mostly from a preview of a manuscript by Jelle Thole et al. The number of antigens have increased slightly (from 202 to 249), and the number of antigens crossreferenced to sequences have almost doubled (from 49 to 97). Three new antigen codes have been assigned (in consultation with Jelle Thole). * The Locus class has been cleaned up, uninformative or erroneous names removed and crosslinking to Sequences and Antigens improved. The number of loci has consequently dropped from 373 to 312. We have tried to follow the locus naming convention used in the E.coli community. When function assignment is based on homology, the name used for the corresponding locus in E.coli has generally been used. There is a new subclass derived from the Locus class: Gene contains Loci for which sequence is known. * The number of objects in the Strain class has almost doubled (from 185 to 302) and the Strain entries in sequences have been completely reanalysed, resulting in more complete crosslinking between strains and sequences. Strains are now crossreferenced to Antibodies and Antigens. * The Colleague class has been updated with some new additions and new addresses for some colleagues. For information on earlier releases, see MycDB.3-6.Release. The database currently requires a Unix workstation running X-Windows. A variety of precompiled versions of the ACEDB database software are available through anonymous ftp. See the file MycDB.Retrieval for more info. A Macintosh version of the ACEDB software is also available, and we are working with the developers of that version to produce a complete Macintosh archive, with a preloaded database. The model changes for this release are minor, and we are therefore only distributing difference files. Thus no complete reload is necessary. The update has been split in two files to keep file sizes reasonable. The files are in compressed tar files called update.myc.3_7.tar.Z and update.myc.3_8.tar.Z. They are intended to be installed together. If you already have MycDB installed on your system, you only need these two files - put them in the same directory as the database directory, uncompress and unpack them ('zcat update.myc.3_*.tar.gz | tar xvf -') and then start MycDB, choose Add Update File from the drop-down menu in the Main Window, and click on the All Updates button. If you do not have the database installed on your system, the procedure to install the database from scratch is described in the file MycDB.Retrieval. This release (and the earlier releases 3-5 and 3-6) are intended to be used with version 3_0 of the ACEDB database manager. Unfortunately, there is currently some confusion with the binary distributions of the different versions of ACEDB: ACEDB3_0 is available from MRC in Cambridge (cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb/ace3). Other sites only have ACEDB3_7, which is a preview of ACEDB4, a greatly enhanced version of the database manager that is currently in beta test. ACEDB3_7 has some bugs that will make it crash on updating, printing and on displaying some Sequence objects. It also requires a different set of database specifications. As soon as version 4 is stable, we will make a new release of data for MycDB, but in the meantime please try to use ACEDB3_0. If you absolutely can't get version 3_0, contact Staffan. If you wish to obtain the MycDB database please contact us, via e-mail, fax, mail or telephone. If you are impatient and are already familiar with internet/ftp, all relevant information can be found at * the WWW server at the Department of Biochemistry, KTH: http://www.biochem.kth.se/MycDB.html * the ftp server at the Department of Biochemistry, KTH: ftp.biochem.kth.se (130.237.52.64) in pub/MycDB * the ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in pub/MycDB * or the mirror site at the Weizmann Institute in Israel (thanks Jaime!): bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb The file MycDB.Retrieval describes in more detail the database system requirements, network retrieval procedures for obtaining the database and methods of obtaining future updates. For more information contact Staffan Bergh or Stewart Cole. Staffan Bergh Biochemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden Email: staffan@biochem.kth.se Fax: (46 8) 24 54 52 Voice: (46 8) 790 8758 Stewart Cole Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris Cedex 15, France Email: stcole@pasteur.fr Fax: (33 1) 45.68.85.93 Voice: (33 1) 45.68.84.46 From owner-acedb@net.bio.net Mon Jun 19 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!news.sprintlink.net!news.onramp.net!convex!news.duke.edu!ratatosk.yggdrasil.com!nntp-sc.barrnet.net!nntp-hub2.barrnet.net!lamarck.sura.net!sprout.nalusda.gov!usenet From: Gail Juvik Newsgroups: bionet.software.acedb,bionet.software,bionet.genome.arabidopsis,bionet.chlamydomonas Subject: ACEDB 1995 Conference and Workshop Proceedings Date: 20 Jun 1995 20:10:46 GMT Organization: USDA-ARS-NAL Lines: 26 Message-ID: <3s7a06$nas@sprout.nalusda.gov> NNTP-Posting-Host: lars.nalusda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4m) To: genome@locus.nalusda.gov X-URL: news:bionet.software.acedb Xref: biosci bionet.software.acedb:640 bionet.software:12416 bionet.genome.arabidopsis:3450 bionet.chlamydomonas:564 The Proceedings from the 1995 ACEDB Conference and Workshop held May 15-27 is now available online at: http://probe.nalusda.gov:8000/acedocs/ace95/index.html The main goal of the 3-day Conference was information exchange. There were tutorials, oral presentations and online demonstrations. The 10-day Workshop following the conference concentrated on code development and consolidataion, database building, documentation writing, special interest group discussions and long range planning. The documents labeled "New" on the ACEDB Documentation page are from this meeting (http://probe.nalusda.gov:8000/acedocs/index.html). Numerous individuals contributed to these proceedings, particularly the folks at Lawrence Berkeley Laboratory who organized the meeting. Send your additions and/or corrections to these proceedings to gig@probe.nalusda.gov -- Gail A. Juvik USDA/ARS/National Agricultural Library Genome Informatics Group 10301 Baltimore Blvd. Tel: (301) 504-6813 Beltsville, Maryland 20705-2351 Fax: (301) 504-7473 From owner-acedb@net.bio.net Tue Jun 20 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!dog.ee.lbl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: No FAQ in June Date: 20 Jun 1995 23:31:22 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 18 Distribution: world Message-ID: <3s7loa$fg7@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov No ACEDB faq for June. Will have a new one in early July. If you need a copy of the May '95 FAQ: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html ftp://rtfm.mit.edu/usenet/news.answers/acedb-faq (hypertext and plain-text respectively). Any info to be included in the next FAQ should be emailed to acedbfaq@s27w007.pswfs.gov --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project From owner-acedb@net.bio.net Tue Jun 20 23:00:00 1995 Path: biosci!biosci!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.announce,bionet.software.acedb,bionet.microbiology,bionet.general,sci.med Subject: MycDB 3-8 data release Date: 20 Jun 1995 22:16:51 -0700 Organization: Biochemistry, KTH, Stockholm Lines: 144 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <3s4fnk$p5q@sibirien.physchem.kth.se> Reply-To: staffan@biochem.kth.se NNTP-Posting-Host: net.bio.net Keywords: MycDB, ACEDB, mycobacteria Xref: biosci bionet.announce:2214 bionet.software.acedb:642 bionet.microbiology:2555 bionet.general:15850 sci.med:83183 Stockholm & Paris June 18, 1995 The eight release of the Mycobacterium database, MycDB, is now available. MycDB is funded by the WHO and the Fondation Raoul Follereau and is maintained jointly by the Unite de Genetique Moleculaire Bacterienne at the Institut Pasteur in Paris, France and the Department of Biochemistry at the Royal Institute of Technology in Stockholm, Sweden. MycDB is available free of charge via Internet network transfer. A complete description of the procedure to retrieve and install the software and database is available through the Internet (see the end of this message for addresses). MycDB is also available through the WorldWideWeb servers at the Royal Institute of Technology (URL: http://www.biochem.kth.se/MycDB.html) and (through the good offices of the Genome Informatics Group at the National Agricultural Library) on the Agricultural Genome Information Server, AGIS, in Beltsville, Maryland, USA (WorldWideWeb URL: http://probe.nalusda.gov:8300/other/index.html or gopher URL: gopher://probe.nalusda.gov:7000/11/genome.databases/mycdb/). MycDB uses the excellent database software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg (CNRS, France). The ACEDB software allows the user to browse information by simply pointing and clicking with the workstation mouse. A variety of powerful query methods are also available. However, our experience is that most users choose the mouse interface to find the information they are interested in. As far as possible all information is connected to other information in the database. The database software presents the information in separate windows that allow many parts of the database to be viewed at one time. There are also many paths to any piece of information, allowing the user to easily navigate the connections between the various types of information. New in release 3-8: * New and edited sequences from EMBL/GenBank/DDBJ, as of May 31, 1995. Due to extensive reanalysis, annotation and merging of overlapping sequences, and the removal of the blast search data (pending new data) the number of sequences have drastically decreased (from over 4000 Sequence objects to 1832, and from 543 DNA objects to 515). However, the total number of nucleotides have increased by 171,008 (12.3%) to 1,560,886 nt. Thus, this is a considerably less redundant set of sequences from mycobacteria than in previous releases. We intend to continue this analysis and merging of sequences, and also add blast searches and coding frame predictions to the data set. There are two new subclasses, derived from the Sequence class: NucleotideSeq contains Sequence objects with attached nucleotide sequence (this replaces the earlier DNA class in the Main Window) and PeptideSeq contains protein sequences. * 112 new literature citations from MedLine, current as of May 31, 1995. The links to abstracts in the set of papers in earlier releases have been rechecked and errors removed. Of 3180 Paper objects in release 3-8, 2399 have attached abstracts. * The Antigen class has been updated, mostly from a preview of a manuscript by Jelle Thole et al. The number of antigens have increased slightly (from 202 to 249), and the number of antigens crossreferenced to sequences have almost doubled (from 49 to 97). Three new antigen codes have been assigned (in consultation with Jelle Thole). * The Locus class has been cleaned up, uninformative or erroneous names removed and crosslinking to Sequences and Antigens improved. The number of loci has consequently dropped from 373 to 312. We have tried to follow the locus naming convention used in the E.coli community. When function assignment is based on homology, the name used for the corresponding locus in E.coli has generally been used. There is a new subclass derived from the Locus class: Gene contains Loci for which sequence is known. * The number of objects in the Strain class has almost doubled (from 185 to 302) and the Strain entries in sequences have been completely reanalysed, resulting in more complete crosslinking between strains and sequences. Strains are now crossreferenced to Antibodies and Antigens. * The Colleague class has been updated with some new additions and new addresses for some colleagues. For information on earlier releases, see MycDB.3-6.Release. The database currently requires a Unix workstation running X-Windows. A variety of precompiled versions of the ACEDB database software are available through anonymous ftp. See the file MycDB.Retrieval for more info. A Macintosh version of the ACEDB software is also available, and we are working with the developers of that version to produce a complete Macintosh archive, with a preloaded database. The model changes for this release are minor, and we are therefore only distributing difference files. Thus no complete reload is necessary. The update has been split in two files to keep file sizes reasonable. The files are in compressed tar files called update.myc.3_7.tar.Z and update.myc.3_8.tar.Z. They are intended to be installed together. If you already have MycDB installed on your system, you only need these two files - put them in the same directory as the database directory, uncompress and unpack them ('zcat update.myc.3_*.tar.gz | tar xvf -') and then start MycDB, choose Add Update File from the drop-down menu in the Main Window, and click on the All Updates button. If you do not have the database installed on your system, the procedure to install the database from scratch is described in the file MycDB.Retrieval. This release (and the earlier releases 3-5 and 3-6) are intended to be used with version 3_0 of the ACEDB database manager. Unfortunately, there is currently some confusion with the binary distributions of the different versions of ACEDB: ACEDB3_0 is available from MRC in Cambridge (cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb/ace3). Other sites only have ACEDB3_7, which is a preview of ACEDB4, a greatly enhanced version of the database manager that is currently in beta test. ACEDB3_7 has some bugs that will make it crash on updating, printing and on displaying some Sequence objects. It also requires a different set of database specifications. As soon as version 4 is stable, we will make a new release of data for MycDB, but in the meantime please try to use ACEDB3_0. If you absolutely can't get version 3_0, contact Staffan. If you wish to obtain the MycDB database please contact us, via e-mail, fax, mail or telephone. If you are impatient and are already familiar with internet/ftp, all relevant information can be found at * the WWW server at the Department of Biochemistry, KTH: http://www.biochem.kth.se/MycDB.html * the ftp server at the Department of Biochemistry, KTH: ftp.biochem.kth.se (130.237.52.64) in pub/MycDB * the ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in pub/MycDB * or the mirror site at the Weizmann Institute in Israel (thanks Jaime!): bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb The file MycDB.Retrieval describes in more detail the database system requirements, network retrieval procedures for obtaining the database and methods of obtaining future updates. For more information contact Staffan Bergh or Stewart Cole. Staffan Bergh Biochemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden Email: staffan@biochem.kth.se Fax: (46 8) 24 54 52 Voice: (46 8) 790 8758 Stewart Cole Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris Cedex 15, France Email: stcole@pasteur.fr Fax: (33 1) 45.68.85.93 Voice: (33 1) 45.68.84.46 From owner-acedb@net.bio.net Wed Jun 21 23:00:00 1995 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: ACEDB main memory requirements Date: 22 Jun 1995 08:28:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506221527.RAA08554@cvx12.inet.dkfz-heidelberg.de> References: <199506211534.RAA22985@ns.DKFZ-Heidelberg.de> NNTP-Posting-Host: net.bio.net > I recall from the conference that someone said Acedb loads > the whole database into RAM when it runs. Does this means that > it actually loads all the data, or that it load just the > data model and some hash tables? If it loads the whole > database, do you have experience with running multiple > Igd sessions on 1 machine? We are wondering how our > system will be affected if we make Igd widely available and > several people start it up at once. ... > Pam Hi Pam, I open this in the acedb newsgroup, because it is relevant for more people how might also help you. It not true, the ACEDB loads the whole database into RAM when it runs. We have a 2 GB-database on a machine with 256MB RAM and when ACEDB is in full operation it takes about 100 MB of RAM. The amount of main memory ACEDB is using is controlled by a config file (wspec/cachesize.wrm). The critical problem is as you noticed correctly is having multiple sessions. There are two ways around it: 1. use client/server 2. In IGD we extract user-relevant subsets of the data in a set of small ACEDB databases which don't need much main memory. Therefore we can support several users simultaneously. Anyway, with IGD this would run on the local workstation. best wishes Detlef From owner-acedb@net.bio.net Sun Jun 25 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: ACEDB main memory requirements Date: 24 Jun 1995 15:58:42 +0100 Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3sh972$f3m@mserv1.dl.ac.uk> Original-To: D.Wolf@dkfz-heidelberg.de, bionet-news@dl.ac.uk ACEDB does NOT loads the full database in ram The amount of required memory is: size of cache 1 (configurable but at elast as big as the biggest object in the database, typically 2 or 4 Megs) size of cache 2 (typically 2 to 4 megs, however from 2-0 to 3-7 there was a wrong aasumption in the cache management which caused the cache 2 to grow larger in some cases. This is fixed in 4.0) size of the dictionaries: around 40 bytes per object, reduced to around 20 in 4.0 (however this is the theory and measurments in aquilla seem to indicate that the gain is not large, so there may be a bug in the newer system) Typically, acedb handles around 100k objs, hence this amounts to another 4Megs add to that the code and stack space and you end up with an image size between 12 and 20 Megs, a far cry from the full database size. In IGD however, we have around 1M-objs implying over 50 M of image in 3.5 hopefully closer to 30 in 4.0 If we hope to go to 10 or 100 Million objects, we will have to redesign the system at this place, and this is part of the //GD project with possibly a prototype around summer 96. If you run several session on one machine, you easilly run into problems. The non-graphic client server system works well by nozw but the graphic client still needs development work (I may work on it this summer) Jean From owner-acedb@net.bio.net Sun Jun 25 23:00:00 1995 Path: biosci!FLY2.BERKELEY.EDU!sly From: sly@FLY2.BERKELEY.EDU (Cyrus Harmon) Newsgroups: bionet.software.acedb Subject: Re> Re: ACEDB main memory requirements Date: 26 Jun 1995 11:58:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506261849.LAA13985@fly2.berkeley.edu> NNTP-Posting-Host: net.bio.net Jean says: >ACEDB does NOT loads the full database in ram >The amount of required memory is: >size of cache 1 (configurable but at elast as big as the biggest >object in the database, typically 2 or 4 Megs) >size of cache 2 (typically 2 to 4 megs, however from 2-0 to 3-7 >there was a wrong aasumption in the cache management which caused the >cache 2 to grow larger in some cases. This is fixed in 4.0) >size of the dictionaries: around 40 bytes per object, reduced to around 20 >in 4.0 (however this is the theory and measurments in aquilla seem to indicate >that the gain is not large, so there may be a bug in the newer system) >Typically, acedb handles around 100k objs, hence this amounts to another 4Megs Memory usage has long been a concern in the Macintosh version of ACeDB. Mac programs are given a set memory partition size on startup. We have found that 24 MB is usually adequate in light of what Jean says about cache1 and cache2. However, it isn't quite this simple. The lexiques get brought into the cache but are never flushed. If you have large lexiques, the size of cache2 will grow larger than the limit specifed in cachesize.wrm. I have also noticed problems when attempting to add large quantities of data in a single session. This requires memory far in excess of the cache1 and cache2 limits. The workaround I use is to save after each large .ace file. This seems to alleviate the problem somewhat. Cyrus From owner-acedb@net.bio.net Tue Jun 27 23:00:00 1995 Path: biosci!DKFZ-Heidelberg.DE!D.Wolf From: D.Wolf@DKFZ-Heidelberg.DE (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: disk leak is fixed Date: 28 Jun 1995 05:39:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 131 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506241533.RAA20179@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net Hi, I did a test: load a set of objects, delete and load again results: ace35b and the "ace4 at the end of the workshop" stabilize after 3 interations at three times the initial database size. ace950620, however, keeps constant size (see lines *.dbsize below). ace950620 requires the same amount of main memory as the ace35b. the test was run with 400 KB .ace file of Sequence data for the IGD model. Nice to see this bug fixed. best wishes Detlef ------------------------------------------------------------------ the script: load: dbinit wspec.igd t1: tace do parse igd.create.ace.gz exit d1: dbsize t2: tace do parse igd.create.ace.gz exit d2: dbsize t3: tace do parse igd.create.ace.gz exit d3: dbsize t4: tace do parse igd.create.ace.gz exit d4: dbsize credel: dbinit wspec.igd t1: tace do @igd.credel.cmd mem exit // t1 d1: dbsize t2: tace do @igd.credel.cmd mem exit d2: dbsize t3: tace do @igd.credel.cmd mem exit d3: dbsize t4: tace do @igd.credel.cmd mem exit d4: dbsize where igd.credel.cmd is: parse igd.create.ace.gz find Sequence parse igd.deltag.ace.gz find Sequence parse igd.create.ace.gz find Sequence parse igd.delobj.ace.gz where find Sequence classes ----------------- aquila 1.4 comparison -------------------------------- reference version (old): ace35b Sat Jun 24 16:49:38 MDT 1995 IRIX mbp-sgi5 5.2 02282015 IP19 mips database on local file system under test (new): atmp Sat Jun 24 17:02:41 MDT 1995 IRIX mbp-sgi5 5.2 02282015 IP19 mips ace950620 database files on local file system compiled with SGI_4_NEW label/command type old new comment/ratio ----------------------------------------------------------------------- NOTE: some lines delete by hand load.dbinit #msgs 2 6 problematic load.t1.exit real 7 8 sec, ratio 1.14 load.t1.exit cpu 3.30 3.80 sec, ratio 1.15 load.d1.dbsize KB 4995 same ratio 1.00 load.t2.exit real 4 9 sec, ratio 2.25 load.t2.exit cpu 2.80 same sec, ratio 1.00 load.d2.dbsize KB 4995 same ratio 1.00 load.t3.exit real 8 7 sec, ratio 0.88 load.t3.exit cpu 2.70 2.80 sec, ratio 1.04 load.d3.dbsize KB 4996 4995 ratio 1.00 load.t4.exit real 4 7 sec, ratio 1.75 load.t4.exit cpu 2.60 2.70 sec, ratio 1.04 load.d4.dbsize KB 4996 4995 ratio 1.00 credel.dbinit #msgs 2 6 problematic credel.t1._._.mem sz 7136 7200 ratio 1.01 credel.t1._._.mem rss 6388 6436 ratio 1.01 credel.t1.exit real 22 26 sec, ratio 1.18 credel.t1.exit cpu 8.10 9.40 sec, ratio 1.16 credel.d1.dbsize KB 4996 4995 ratio 1.00 credel.t2._._.mem sz 7104 7152 ratio 1.01 credel.t2._._.mem rss 6356 6388 ratio 1.01 credel.t2.exit real 30 26 sec, ratio 0.87 credel.t2.exit cpu 8.40 9.40 sec, ratio 1.12 credel.d2.dbsize KB 9988 4995 ratio 0.50 credel.t3._._.mem sz 7104 7152 ratio 1.01 credel.t3._._.mem rss 6368 6388 ratio 1.00 credel.t3.exit real 30 26 sec, ratio 0.87 credel.t3.exit cpu 8.20 9.00 sec, ratio 1.10 credel.d3.dbsize KB 14980 4996 ratio 0.33 credel.t4._._.mem sz 7072 7152 ratio 1.01 credel.t4._._.mem rss 6324 6388 ratio 1.01 credel.t4.exit real 21 24 sec, ratio 1.14 credel.t4.exit cpu 8.20 9.70 sec, ratio 1.18 credel.d4.dbsize KB 14981 4996 ratio 0.33 ----------------------------------------------------------------------- From owner-acedb@net.bio.net Wed Jun 28 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: sharing authorization to reinitialize a database Date: 29 Jun 1995 15:32:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506292230.AA05773@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Any user listed in passwd.wrm has write-access on the database, but not necessarily initialize-access. Deleting database/ACEDB.wrm and restarting the database may give (in ace 3-0) the error message !! FATAL ERROR 0: !! Sorry, the database seems empty. Only the person owning the $(ACEDB) directory can reinitialise it. This message isn't exactly accurate. To share initialize-access with another user, the actual requirement is to give him write-access on the file wspec/passwd.wrm. For example if the permissions are -rw-rw-r-- 1 acedb ace 836 Jun 29 17:42 passwd.wrm , all members of group 'ace' will have initialize-access. The same thing is true in ace v4_0b4, but the error message is corrected. - Dave Matthews From owner-acedb@net.bio.net Thu Jun 29 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: MISS ES HADKINS Newsgroups: bionet.software.acedb Subject: Mailing List Date: 30 Jun 1995 10:54:40 +0100 Organization: The University of Birmingham Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3t0hl0$74n@mserv1.dl.ac.uk> X-mailer: WinPMail v1.0 (R2) Original-To: acedb@dl.ac.uk I would like to subscribe to the ACEDB mailing list. Many thanks, Emma Hadkins ********************************************************************** Miss E.S.Hadkins tel: 0121 - 414 5894 Research Associate fax: 0121 - 414 5925 School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K. email: E.S.Hadkins.plb@bham.ac.uk ********************************************************************** From owner-acedb@net.bio.net Thu Jun 29 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: announcing version 2 of SampleDB Date: 30 Jun 1995 15:40:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 67 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506302238.AA08978@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net SampleDB 2.0 is now available in probe.nalusda.gov:pub/acedocs. Here's the description: - Dave :::::::::: SampleDB, version 2.0, 28 June 1995 A sample database to demonstrate features of ACEDB, especially map and sequence displays. FEATURES INCLUDED The GMAP C. elegans chromosome V and its neighbors To view, pick Map "V". There is a "guided tour" available via the online help; click the "Help" button in the main window and look at "About SampleDB..." The PMAP ctg313 and ctg893, from C. elegans chromosome V, and their neighbors To view, pick Map "V" and double-click on the yellow "Contigs" bars The Sequence Display C. elegans sequence B0272 and some of its neighbors To view, pick Sequence "B0272". The MultiMap Rice chromosome 1 vs. maize chromosomes 3 and 8 To view, examine MultiMaps "Rice 1, Maize 3,8" and "Rice 1, Maize 3,8 Anchored" The SYN map Human chromosome 21 and mouse 10 and 16 To view, pick Map 21.LBL There is a guided tour available via the online help. Improved online help SampleDB uses the new hypertexted online help system. Much of the help, including the guided tours, is only available via Mosaic. Developers and documenters are encouraged to add more features to SampleDB, by submitting - concise .ace datasets, - description of any models.wrm changes needed, and - suggested objects to look at to exercise the features. SampleDB 2.0 is distributed with a SunOS 4.x executable of xace.4.syn, 14 Jun 95, from Arun Aggarwal. All features other than the SYN map should work with xace version 4_0b4, available from ncbi.nlm.nih.gov as executables for several platforms and as source. In order to make the SYN map work, wspec/options.wrm has been slightly modified. Now when a Map object is double-clicked the SYN display is invoked; picking a Locus object invokes the GMAP. A standard C. elegans options.wrm is included for comparison or for alternate use. In addition, the standard C. elegans models.wrm (as distributed with the ACEDB v4_0b4 release) is included. The intention is to include each models.wrm used to implement each increment of features in succeeding releases of SampleDB, with a running log of the diff's at each step maintained in directory wspec/models.diffs. - Dave Matthews matthews@greengenes.cit.cornell.edu From owner-acedb@net.bio.net Fri Jun 30 23:00:00 1995 Path: biosci!rutgers!gatech!news.sprintlink.net!news.clark.net!usenet From: systems@khem.com (bob diggs) Newsgroups: bionet.software.acedb Subject: SOFTWARE: Chemical Inventory/Waste Management/Material Safety data Date: 1 Jul 1995 15:41:26 GMT Organization: khem products incorporated Lines: 20 Message-ID: <3t3qb6$80e@clarknet.clark.net> Reply-To: info@khem.com NNTP-Posting-Host: systems.clark.net Mime-Version: 1.0 X-Newsreader: WinVN 0.99.2 If you are interested in the following - Chemical Inventory Tracking Regulatory Compliance Simplified Safety Data Sheets on-line Waste Tracking Chemical Database on-line Total Integration THEN YOU SHOULD VISIT OUR WEB HOME PAGE!!! URL : http://www.khem.com/khem/home.html EMAIL: info@khem.com See you there. Khem Products, Incorporated