From owner-acedb@net.bio.net Fri Sep 01 23:00:00 1995 Path: biosci!BEANGENES.CWS.NDSU.NODAK.EDU!mcclean From: mcclean@BEANGENES.CWS.NDSU.NODAK.EDU (Phil McClean) Newsgroups: bionet.software.acedb Subject: Five line limit in the initial window display Date: 2 Sep 1995 09:12:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net When an object is selected and its window appears, if a specific piece of information contains more than five lines, then a number appears which has to be clicked to see all of the lines. Can this feature be disabled by the administrator so that all lines appear immediately? Phil McClean Dept. of Plant Sciences North Dakota State University Fargo, ND 58105 mcclean@beangenes.cws.ndsu.nodak.edu From owner-acedb@net.bio.net Sun Sep 03 23:00:00 1995 Path: biosci!nihs.go.jp!taka From: taka@nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: Re: perl version of Aceclient Date: 4 Sep 1995 03:44:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509041037.AA20144@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net Hello. Last week I send mail of my trouble with compilation of perl aceclient. But I have overcome the trouble by myself. I compiled programs not in "dynamic library loading", but in "static library loading" condition. I don't know why I failed in "dynamic loading" condition, and I think this is not the explicitl solution, but anyway the perl aceclient/aceserver works well. Maybe there is something wrong with the environment of "rld" on my machine. Thank you. Takako Igarashi National Institute of Health Sciences taka@nihs.go.jp From owner-acedb@net.bio.net Mon Sep 04 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!in1.uu.net!cis.ohio-state.edu!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!haven.umd.edu!cville-srv.wam.umd.edu!rac9.wam.umd.edu!bottino From: paul bottino Newsgroups: bionet.software.acedb Subject: computational biologist Date: Tue, 5 Sep 1995 11:15:32 -0400 Organization: University of Maryland College Park Lines: 25 Message-ID: NNTP-Posting-Host: rac9.wam.umd.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII COMPUTATIONAL BIOLOGIST- with the Genome Informatics Group at the USDA National Agricultural Libraray, Beltsville MD. Principle duties involve bringing genome information to users world-wide via the World Wide Web, Gopher, CD-ROM and other electronic means. Appointment will be Research Associate at the University of Maryland which, is the primary USDA cooperator. Specific duties include development of complex, multi-database query systems, addressing data modeling issues, development of new graphic displays for genome information, and facilitating collaboration with molecular biologists. Some travel, possibly international, will be required. Qualifications- A Ph. D. in either molecular biology or computer/information science and experience in computational biology/bioinformatics. Non-Ph. D. Candidates will be considered only if they have extensive experience in computational biology or bioinformatics. The ideal candidate would also have experience developing database management or query systems, familiarity with ACEDB or another object-oriented database management system, programming experience in C and Perl, knowledge of Unix, and experience in the development of graphic displays. For full consideration: submit resume and three letters of recommendation by September 29, 1995 to Dr. Paul J. Bottino, Department of Plant Biology, University of Maryland, College Park MD 20742 Fax 301-314-9082. From owner-acedb@net.bio.net Tue Sep 05 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Mark Blaxter Newsgroups: bionet.software.acedb Subject: Species Models for ACEDB Date: 6 Sep 1995 14:44:14 +0100 Lines: 43 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <42k8je$5ct@mserv1.dl.ac.uk> X-Sender: mbx@festival.ed.ac.uk Original-To: acedb@dl.ac.uk Has anyone written acedb model files for species taxonomy? I'm interested in being able to walk back from a species to see its relationships with everything else, and forward from higher taxa to see what species they contain. So if a paper refers to Heligmosomoides polygyrus I can find out that it is a nematode of family X rather than guessing its a horrible wasting disease of the left earlobe. I have written a set, they work, etc, but I was wondering if there was a standard set I should/could use, or if there was a standard set we could develop? In particular, a set which allowed (1) multiple taxonomies (especially at deep levels) and (2) a tree-like graphical representation. Thanks Mark Blaxter ________________________________________________ A L L C H A N G E ! Dr. Mark Blaxter has moved as of August 1st 1995 email Mark.Blaxter@ed.ac.uk Institute of Cell, Animal and Population Biology Ashworth Laboratories, King's Buildings University of Edinburgh West Mains Road EDINBURGH EH9 3JT United Kingdom Fax : (+44) 131 650 5450 phone: (+44) 131 650 6760 ________________________________________________ Dr. Mark Blaxter email Mark.Blaxter@ed.ac.uk Institute of Cell, Animal and Population Biology Ashworth Laboratories, King's Buildings University of Edinburgh, West Mains Road EDINBURGH EH9 3JT, United Kingdom phone: (+44) 131 650 6760 Fax :...650 5450 From owner-acedb@net.bio.net Thu Sep 07 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Macace 4-8 problems Date: 8 Sep 1995 10:36:53 +0100 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <42p2rl$id6@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, celegans@dl.ac.uk The original macace.4-8 distribution at NCBI contained a corrupted version of the macace.4-8C.sea.bin file, which prevented it being installed properly. I have retransferred this file to NCBI from England, and it has been checked. To complete installation of macace you should get the new copy from NCBI, and follow the original instructions. I have been told that sometimes with big self-extracting archive files they may not self-extract properly with the default memory partition set. If you single-click on the file, then "Get Info" (Apple I), you can increase the size of the memory partition. Something larger than 2096 will apparently be fine. Richard Durbin From owner-acedb@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: saving metabolic pathway diagrams Date: 11 Sep 1995 18:48:59 +0100 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <431sqb$eg3@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk David Grant asks about saving new layouts for metabolic pathways. This is easy to do. You should first get write access from the main menu first. Then display and edit the pathways (using the middle button to move items)y. As you quit an edited diagram window, it will ask if you want to save the new layout. Any for which you say yes will be saved in the databases. To make these changes permanent you must either "Save" from the main menu, or say yes when acedb asks if you want to save changes when you quit the whole program. I just checked that this works in 4_1. There is a bug fix registered for July 13 (before the 4_1 release) about saving the same thing multiple times from one invocation of acedb, but saving changed diagrams once should have worked in earlier versions. Anyway, people should be switching to 4_1. Richard From owner-acedb@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!newsxfer.itd.umich.edu!newsrelay.iastate.edu!news.iastate.edu!macgrant.agron.iastate.edu!user From: dgrant@mendel.agron.iastate.edu (David Grant) Newsgroups: bionet.software.acedb Subject: metabolic pathways Date: Mon, 11 Sep 1995 10:56:42 -0500 Organization: USDA-ARS Lines: 9 Message-ID: NNTP-Posting-Host: macgrant.agron.iastate.edu The metabolic pathways as drawn by v3.7 often need to be tweaked to make the information readable. Unfortunately we can't find a way to save these modified drawings so each time we reload the db we have to rearrange the drawings again. Does anyone know how to save the drawings (maybe in a separate file) so we can simply load them into the db when needed? Thanks, David Grant Curator, SoyBase From owner-acedb@net.bio.net Sun Sep 10 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: TableMaker queries on Text values Date: 11 Sep 1995 07:28:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509111425.AA21742@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net It looks like the Tablemaker can't query ("Condition") on the value of a field of type Text. For example: ?Image Pick_me_to_call Text Text I make a table in which column 1 is ?Image and column 2 is the first Text field (always = "xv"). In ace4-1 if I put _anything_ in the Condition field other than "*", and make it Mandatory, I get no hits. - Dave From owner-acedb@net.bio.net Mon Sep 11 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!nntp-trd.UNINETT.no!due.unit.no!nntp.uio.no!news.kth.se!sibirien.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: metabolic pathways Date: 12 Sep 1995 08:39:34 +0200 Organization: Biochemistry, KTH, Stockholm Lines: 9 Message-ID: <4339v6$vs@sibirien.physchem.kth.se> References: NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit David, (and everyone else who is fiddling with the metabolic pathways) I have written some documentation on the MetabolicPathways display and models where you'll find a description of how to save a 'tweaked' display and the technicalities of the models for the display. It's available thru the documentation server (http://probe.nalusda.gov:8300/acedocs/index.html). /staffan From owner-acedb@net.bio.net Wed Sep 13 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!torn!newshost.uwo.ca!jkiernan.anatomy.uwo.ca!jkiernan From: jkiernan@julian.uwo.ca (J. A. Kiernan) Newsgroups: bionet.software.acedb Subject: Introductory Neuroanatomy Tutorial Programme Date: Thu, 14 Sep 1995 15:40:47 GMT Organization: ITS, University of Western Ontario Lines: 50 Message-ID: NNTP-Posting-Host: jkiernan.anatomy.uwo.ca This free tutorial program may interest you if you want to learn about the human nervous system. NEUROTUT.EXE is a self-extracting archive that installs the program files. About 585 kB of hard disk space are needed, or it could be run from a 3.5" floppy. NRO Human Neuroscience Tutorial, Version 1.05 (May 1994). When installed, it provides eight introductory Neuroanatomy tutorials and (as a ninth "tutorial") over 300 revision questions that cover the whole of Human Neuroscience. The questions can also be run separately with NQI.EXE, from the DOS prompt. A color monitor is very desirable but not essential. By John A. Kiernan, Department of Anatomy, The University of Western Ontario, London, Canada. NEUROTUT is available by anonymous FTP from various medical/science FTP sites, including the following. Don't forget to type "binary" before downloading! dean.med.uth.tmc.edu MSDOS/neurotut.exe ftp.uci.edu med-ed/msdos/education/neurotut.exe ftp.monash.edu.au pub/medical/neuritut.exe (note spelling!) skynet.ul.ie pub/science/biology/neurotut.exe The program is also available from: Knowledge Transfer BBS, P.O. Box 11282, Spring, Texas 77391-1282 Sysop : Bob Wight (713) 370-5804 24hrs 14,400 N81 FAX/Voice (713) 251-7517 If you try NEUROTUT please let me know what you think of it. John A. Kiernan Department of Anatomy Univ. of Western Ontario LONDON, Canada N6A 5C1 e-mail: jkiernan@julian.uwo.ca From owner-acedb@net.bio.net Sun Sep 17 23:00:00 1995 Path: biosci!agate!news.mindlink.net!van-bc!fonorola!news.citenet.net!XR01-A20 From: MTL@AMAV.COM (AMAV Industries) Newsgroups: bionet.software.acedb Subject: Wanted: Educational Software!!! Date: Mon, 18 Sep 95 14:38:37 GMT Organization: CiteNet Telecom - Commercial Internet Service Lines: 12 Message-ID: <43k0e8$rdp@cti01.citenet.net> NNTP-Posting-Host: xr01-a20.citenet.net X-Newsreader: News Xpress Version 1.0 Beta #4 Hello, we are a leading toy distributor in Canada and are interested in distributing a line of educational software to our clients. As such, we are looking to buy the rights to various educational software products for cash or on a royalty basis. If you have anything that you think might be of interest to us, please contact us by phone: (514) 344-1234 by fax: (514) 344-1235 by e-mail: MTL@AMAV.COM (attn: Yehuda) Thank-you! From owner-acedb@net.bio.net Wed Sep 20 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: spirov@ief.spb.su (Alexandr Spirov) Newsgroups: bionet.software.acedb Subject: ACEDB for beginners, please! Date: 21 Sep 1995 18:41:07 +0100 Organization: Inst. of Evolutionary Physiology & Biochemistry, St.Petersburg Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <43s83j$50r@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Dear Colleagues: Where could I find brief description of ACEDB software usage for gene DBs? (ACEDB for beginners!). Ideally it would be FAQ or something like. Unfortunately I haven't yet possibilities for FTP & WWW. Alexander. -- * Alexander V.Spirov (PhD) +7 812 552 32 19 (phone) +7 812 552 30 12 (fax) * * Lab.Mathematical Modeling of Evolution, e-mail: spirov@ief.spb.su * * I.M.Sechenov Institute of Evolutionary Physiology and Biochemistry, * * 44 Torez Pr., 194223, St-Petersburg, Russia * From owner-acedb@net.bio.net Wed Sep 20 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: "object has > 1000 celLs, please edit the models" Date: 21 Sep 1995 13:17:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509212015.AA09726@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net When I load my .ace files into ace4_1 I get no overt error messages but log.wrm contains a sprinkling of messages like Class 30: object Text:USA has 1417 > 1000 celLs, please edit the models Class 76: object Germplasm:INIA F 66 has 1650 > 1000 celLs, please edit the models Class 62: object Map_Data:Barley, SxM has 21849 > 1000 celLs, please edit the models What is it trying to tell me? Yes, these are fairly big objects. Text "USA" does have 1417 values of Quoted_in. (I have CACHE1 and CACHE2 = 2000.) - Dave From owner-acedb@net.bio.net Thu Sep 21 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: scripts in ace Date: 22 Sep 1995 08:09:17 +0100 Lines: 6 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <43tnet$bkp@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr Sam points out that some scripts are missing in 4.1 distrib this is true efetch should be installed as equivalent to gcg fetch acedb_mailre is missing find-repeats is not distributed yet and so on From owner-acedb@net.bio.net Thu Sep 21 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: Text:USA has 1417 > 1000 celLs Date: 22 Sep 1995 04:16:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509221114.AA10738@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > the performance of acedb degrades extremelly badly when the number of > nodes in an object becomes large. Thank you Jean, it's very helpful to know this. > Text:USA could be modified to be a tag, it does not seem so crucial to > XREF back from that text to the object... Hmm, that's a neat idea. While I'm asking, is there any performance problem with having many tags available at the same point in a model? There are about 250 different country codes for example. > ... or be downgraded from ?Text to Text I don't think I ever need this auto-XREF feature of ?Text. I've been changing most of my texts from Text to ?Text partly because of bugs in Text (historical; the only current one I know of is the Tablemaker querying problem I mentioned recently) and partly because I'd thought it was stored more efficiently than ?Text. I guess I had it backwards. - Dave From owner-acedb@net.bio.net Thu Sep 21 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: Text:USA has 1417 > 1000 celLs Date: 22 Sep 1995 08:18:59 +0100 Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <43to13$bvn@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr Dave says: When I load my .ace files into ace4_1 I get no overt error messages but log.wrm contains a sprinkling of messages like Class 30: object Text:USA has 1417 > 1000 celLs, please edit the models Class 76: object Germplasm:INIA F 66 has 1650 > 1000 celLs, please edit the models Class 62: object Map_Data:Barley, SxM has 21849 > 1000 celLs, please edit the models The point is that the performance of acedb degrades extremelly badly when the number of nodes in an object becomes large. I beleive that 10^4 is already quite bad. In IGD we went much over resulting in a quasi collapse of the performances. For this reason, i introduced a message system in log.wrm issued once per class Most probably, these long lists are created by XREF Text:USA could be modified to be a tag, it does not seem so crucial to XREF back from that text to the object or be downgraded from ?Text to Text in the objects where it occurs In the case of Map_Data:Barley, i would also question the model. Generally speaking, acedb tells you that your model is counter-productive and that you may wish to modify it a bit. These warnings have nothing to do with the actual cachesize By the way, CACHE1 is now dynamic and can be started at a lower value (1000) if you have 16M or less of RAM. From owner-acedb@net.bio.net Thu Sep 21 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: counting cells Date: 22 Sep 1995 10:51:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509221749.AA11347@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net I said: > Class 62: object Map_Data:Barley, SxM has 21849 > 1000 celLs, please edit the models Jean said: > In the case of Map_Data:Barley, i would also question the model. I think I don't understand what a cell is. This Map_Data object doesn't seem to contain 20,000 of anything. (Except bytes, it's 91,000 bytes.) Here it is: // data dumped from tree display Map_Data : "Barley, SxM" Species "Hordeum vulgare L." Parent "Steptoe" Parent "Morex" Genetic Map_units "cM" Reference "TAG-86-705" Contact "Kleinhofs, Andris" Remarks "150 doubled haploid F1 progeny from a reciprocal cross. Data from the North American Barley Genome Mapping Project. 437 markers. A = Steptoe allele\; B = Morex allele\; - = missing data." Map "Hordeum-NABGMP1-1H" Map "Hordeum-NABGMP1-2H" Map "Hordeum-NABGMP1-3H" Map "Hordeum-NABGMP1-4H" Map "Hordeum-NABGMP1-5H" Map "Hordeum-NABGMP1-6H" Map "Hordeum-NABGMP1-7H" Locus "Nar1" "ABBBA ABBAB BABBB BBBAB AABAA BABBA BAABA AAABA ABABB AABBB BBAAA BBABA BABBB AABAB ABBAA ABBBB AAAAA BABAA BABAB AAAAA AAAAA AABBA BABBA ABBBA BAABB BBABB AAABB BBBBA BAAAA BABAA" Locus "Ale" " BABBA AABBA BBAAA AABBA AABAA ABAAA ABBBA ABAAA BBBBB BAAAA A---- ----A BABBA AAABB AABAA AB-AA BBBAB BBBAA AABAA AAAAB -BBAA AAAAB BABBB BAABA BAAAB BBABA ABAAA AAABB BABBA BBBAB" Locus "Dhn6" "AAABA AAABB AA-AB BBBBA BABAA ABAAA ABBAB BBBBA ABBBA BBBA- -ABAB ABABB AAABA BBBAA BAAAB ABABA AAAAA ABAAA BABBA ABABA BAABA BAABA AAABB BAAAB AAAAA BAABB AAABB BBBBA BABBB BAAAB" ... (438 more Locus values) The model is: ?Map_Data Species ?Species XREF Mapping_data Female_parent UNIQUE ?Germplasm XREF Mapping_data Male_parent UNIQUE ?Germplasm XREF Mapping_data Type Genetic Cytogenetic Chromosome_arm Physical Map_units Text Reference ?Reference XREF Mapping_data Contact ?Colleague Remarks ?Text Image ?Image XREF Map Map ?Map XREF Mapping_data Locus ?Locus XREF Data Text From owner-acedb@net.bio.net Tue Sep 26 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!usenet From: Dave Schrader Newsgroups: bionet.software.acedb Subject: acedb3_7 binarys for solaris 2.4 Date: 27 Sep 1995 14:12:14 GMT Organization: Iowa State University Lines: 9 Message-ID: <44bm3u$esu@news.iastate.edu> NNTP-Posting-Host: mendel.agron.iastate.edu 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 sun4c) X-URL: news:bionet.software.acedb Does anybody out there have the binarys for ace3_7 which are compiled under solaris 2.4 ? All I can seem to locate on the usual sources is the ace4_1 stuff which I'm not quite ready for yet. =============================================================================== | 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 Sep 26 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: "Widget vertical has zero width" crash Date: 27 Sep 1995 13:23:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509272020.AA18446@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net This problem that I reported before: > > From: matthews@greengenes.cit.cornell.edu ("Dave Matthews") > > Subject: table.menu.wrm problem in ace4-1 > > Date: 23 Aug 1995 15:40:22 -0700 > > > > Does the "Tables..." button still work in ace4-1? The wspec/table.menu.wrm > > attached below works fine in ace3-0 and 4_0b4, but in 4-1 when I click > > "Tables..." the little "Selector" window comes up just briefly and then > > ace exits with message "Error: Widget vertical has zero width and/or > > height". > > - Dave > > This problem occurs on SunOS but not on Solaris or Linux. Tricky little > devil. > - Dave , also occurs under another, more common situation. In the Table_Maker window, if you click the "Class..." box in the definition of Column 1 with the left mouse button (to get the Selector window because there are too many classes for the height of the dropdown menu), ace exits with the same error message. Again, this is for the SunOS version, no problem with Solaris or Linux. - Dave From owner-acedb@net.bio.net Tue Sep 26 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: another table.menu.wrm complaint Date: 27 Sep 1995 13:19:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509272016.AA18433@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > thanks for the report on: > Tablemaker can't query ("Condition") > i put that very high on my agenda merci! While you're in the TableMaker code, here's another problem I'm having trouble working around. The %1-substitution mechanism from the Tree window "Tables..." box (via wspec/table.menu.wrm) into the Condition of a column definition still isn't satisfactory. A long time ago (ace3-0 or before) I complained that it didn't work when the name of the current object contained multiple words, so you fixed it by substituting only the first word of the name. Thus I could find the desired objects using "%1*". E.g.: Colonne 0 Subtitle "Trait_Study" Width 0 Optional Hidden Class Class "Trait_Study" >From 0 Tag "(null)" Condition "%1*" The only problem with this was the degeneracy, that all objects beginning with that word are found as hits, not just the current object. Now under ace4_1 there's an additional problem. The "*" is being stripped off, so no hits are found at all. I wonder if it would be possible to substitute the whole object name into the Condition, enclosed in double-quotes so multiple words are allowed. - Dave From owner-acedb@net.bio.net Wed Sep 27 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!news.sprintlink.net!usenet.kornet.nm.kr!news.kreonet.re.kr!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: FAQ notes Date: 28 Sep 1995 17:44:47 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 22 Distribution: world Message-ID: <44emuf$ctu@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov I will be sending out the new version of the ACEDB FAQ in a few minutes. Thanks to Gail Juvik of the Genome Informatics Group at the National Agricultural Library for reformatting and cleaning up answer 4 (the list of ACEDB databases). Curators please check your entries for accuracy. Any errors are my fault. Drop me a note (acedbfaq@s27w007.pswfs.gov) and I'll fix them up. Remember that the best way to access the FAQ is via WWW at http://probe.nalusda.gov:8000/acedocs/acedbfaq.html. --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project From owner-acedb@net.bio.net Wed Sep 27 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!ames!lll-winken.llnl.gov!fnnews.fnal.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 28 Sep 1995 17:46:24 GMT Organization: Dendrome, A genome database for forest trees Lines: 1116 Approved: news-answers-request@MIT.Edu Message-ID: <44en1g$cud@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:728 news.answers:48057 Archive-name: acedb-faq Last-modified: 9/28/95 Version: 1.24 ACEDB FAQ ********* Curated by: Bradley K. Sherman Frequently Asked Questions about ACEDB ++++++++++++++++++++++++++++++++++++++ o Q0 : What is ACEDB? o -------------------- o Q1 : What is the current version of ACEDB? o ------------------------------------------- o Q2 : What hardware/software do I need to run ACEDB? o ---------------------------------------------------- o Q3 : Where can I get ACEDB? o ---------------------------- o Q4 : What ACEDB databases exist? o --------------------------------- o Q5 : What documentation exists for ACEDB? o ------------------------------------------ o Q6 : What other resources are available for ACEDB? o --------------------------------------------------- o Q7 : How should ACEDB be cited? o -------------------------------- o Q8 : Is ACEDB object-oriented? o ------------------------------- o Q9 : How doe one get on/off the ACEDB announcements mailing list? o ------------------------------------------------------------------ o Q10 : When and where is the next ACEDB Workshop? o ------------------------------------------------- o Q11 : Who prepared this document & where is the current version? o ----------------------------------------------------------------- Questions marked with '+' are new, those with '!' have substantially changed answers. Q0: What is ACEDB? ++++++++++++++++++ A0: +++ ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [Q4 gives contact information]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions Q1: What is the current version of ACEDB? +++++++++++++++++++++++++++++++++++++++++ A1: +++ (This answer refers to the software not the C. elegans data.) Current version is 4_1 (as of 10 August 1995). A test (beta) version of ACEDB 4.0b4 (5/95) is available. A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q9. Return to List of Questions Q2: What hardware/software do I need to run ACEDB? ++++++++++++++++++++++++++++++++++++++++++++++++++ A2: +++ The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. o Unix and X11: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series o PC 386/486/Pentium with Linux (free Unix) Jeff Bryer, jbryer@darwin.mbb.sfu.ca and Ken Clark provide a linux version of 4.1 and a complete C. elegans data set at trog.mbb.sfu.ca in /pub/acedb as bin.linux.4_1.tar.Z. o There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o Macintosh: o [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a 17" color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. o ACEDB for The NEC EWS4800 is available via anonymous ftp at ftp.nec.co.jp (192.135.93.2) in /pub/packages/acedb/ace2. Contact Tohru Sano Fundamental Research Laboratories NEC Corporation Tsukuba, 305, JAPAN, e-mail: sano@exp.cl.nec.co.jp, FAX: +81-298-56-6136, VOICE: +81-298-50-1507 (Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems SPARCstation II, and users can interact using Macintoshes and PC-clones by using X11 implementations for the personal computers and a LAN. --bks) X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions Q3: Where can I get ACEDB? ++++++++++++++++++++++++++ A3: +++ The standard ACEDB source and binaries are available in the following public access accounts (anonymous ftp sites) accessible via Internet: o lirmm.lirmm.fr in pub/acedb o cele.mrc-lmb.cam.ac.uk in pub/acedb o ncbi.nlm.nih.gov in repository/acedb o bioinformatics.weizmann.ac.il in pub/databases/acedb. MacAce is available from: o genome.lbl.gov in pub/macace o cele.mrc-lmb.cam.ac.uk in pub/acedb/macace Linux; ACEDB version 2.0 for Linux 2-10: o trog.mbb.sfu.ca /pub/acedb as bin.linux.4_1.tar.Z. ACEDB for The NEC EWS4800: o ftp.nec.co.jp in /pub/packages/acedb/ace2. Return to List of Questions Q4: What ACEDB databases exist? +++++++++++++++++++++++++++++++ A4: +++ In alphabetic order by Database name ------------------------------------ [Curators, please submit changes as new paragraphs] Database : AaeDB Species : Aedes aegypti (Mosquito) Last_update : December 1994 ACEDB_version : 3.0 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Database : AAtDB Species : Arabidopsis thaliana Current version : 3-5 Last_update : August 1995 Curator : John Morris Contact : curator@frodo.mgh.harvard.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : Macintosh version - weeds.mgh.harvard.edu in aatdb/MacAAtDB FTP : UNIX version - weeds.mgh.harvard.edu in aatdb/aatdb.3x FTP : probe.nalusda.gov in pub/aatdb Gopher : weeds.mgh.harvard.edu/ Gopher : probe.nalusda.gov:7004/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://weeds.mgh.harvard.edu/ WWW : http://probe.nalusda.gov:8300/plant/ Database : AboutDB Curator : Staffan Bergh, staffan@biochem.kth.se Subject : ACEDB itself (meta-meta-metadata) ACEDB_version: 3.0 Last_update : July 1995 WWW : http://www.biochem.kth.se/AboutDB.html Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@mrc-lmb.cam.ac.u Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Last_update : August 1995 Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ DataBase : AceMap Species : Homo sapiens Subject : Physical mapping YAC data for human chromsome X ACEDB_version : 3.0 Curator : Hugues Roest Crollius, hrc@gea.lif.icnet.uk Curator : Mark Ross, humanX@gea.lif.icnet.uk Curator : Richard Mott, rmott@gea.lif.icnet.uk Availability : beta release of the X chromosome data/models via anonymous ftp FTP : ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap Comment: Get the README file in the directory above. Contact : Genome Analysis Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, London WC2A 3PX, UK Last_update : August 1994 Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu Last_update : March 1994 ACeDB_version : 3.0 Subject: Contains 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 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. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 Last_Update : July 1995 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 1.0 Last_updated : January 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Last_update : August 1995 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Last_update : September 1995 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 Last_update : January 1995 (version 95.1) ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ 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 : EofD (Encyclopaedia of the Drosophila) Species : Drosophilidae (primarily D. melanogaster) Availability : Macintosh CD-ROM and SunOS executables via anonymous ftp Developer : Suzanna Lewis, suzi@fly2.berkeley.edu Developer : Cyrus Harmon, sly@fly2.berkeley.edu Developer : Edward Welbourne, eddy@gen.cam.ac.uk Collaborator : The FlyBase Consortium, flybase-help@morgan.harvard.edu Collaborator : The Berkeley Drosophila Genome Project, flygenome@maillink.berkeley.edu Gopher : fly.bio.indiana.edu:70+/11/Flybase WWW : http://fly2.berkeley.edu:3512/EofD.html Database : EthnobotDB (orldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Last_update : June 1995 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Last_update : May 1995 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : GrainGenes Species : Wheat, barley, oats, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 3.0 Data_version : 1.4+ Last_update : August 1995 FTP : probe.nalusda.gov in pub/graingenes Gopher : greengenes.cit.cornell.edu/ Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://wheat.pw.usda.gov/graingenes.html Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr WWW : http://moulon.inra.fr/acedb/igd.html Description : IGD (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. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : LeishDB Species : Leishmaia major, L. infantum, L. peruviana, L. donovani and others PI : Jennie Blackwell PI : Al Ivens Last_update : September 1995 ACEDB_version : 4.1 Contact : Matin Aslett FTP : ftp://parsun1.path.cam.ac.uk WWW : http://parsun1.path.cam.ac.uk/ Curator : Martin Aslett Curator : Howard Cobb 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 : MaizeDB Species : Zea mays L. ssp. mays and related species Latest_release : April 1995 Acedb_version : 3.3 Comment : MaizeDB is a periodically extracted ACeDB front end for the Maize Genome Database, MaizeDB, a SYBASE database, implemented using Genera software, developed by Stan Letovsky. Comment : Genera provides (1) up-to-the-minute form internet access to SYBASE databases, both for query (WWW and APT) and data entry (APT only); (2) database design alterations by systems administrators; (3) gopher file extraction. Comment: MaizeDB uses WWW record-to-record hard-links to 16 external databases for (1) annotated sequences: GenBank, dbEST, GenoBase, PIR, SwissProt, Prosite, ENZYME; (2) other species genome information: AAtDB(Arabidopsis), RiceGenes, GrainGenes, SaachDB (yeast), CGSC(E. coli), XLocus, RiceGenes, GrainGenes (3) germplasm: GRIN. Data : Over 100,000 records include: 6513 mapped loci (located to chromosome or better) including 1081 mapped genes and 1937 mapped probed sites (gene candidates); 2448 probes; 2460 map scores; 1551 gel patterns (Probe/Enzyme/Stock); 8777 stocks; 18,100 Variations (alleles, DNA polymorphisms, rearrangements, etc); 596 phenotypes; 317 traits; 715 gene products; 6158 bibliographic references; 2200 researchers with addresses. FTP : probe.nalusda.gov in pub/maizedb Gopher : gopher.agron.missouri.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: corncob WWW : http://www.agron.missouri.edu/top.html WWW : http://probe.nalusda.gov:8300/plant/ WWW Genera information : http://gdbdoc.gdb.org/letovsky/genera/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 : Mary Polacco, maryp@teosinte.agron.missouri.edu Assoc Curator : Pat Byrne, byrne@teosinte.agron.missouri.edu QTL data Assoc Curator : Georgia Davis, gdavis@teosinte.agron.missouri.edu Map data Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic Stock data Assoc Curator : Christiane Fauron, FAURON@GENE1.med.utah.edu Mitochondrion genome Assoc Curator : Carolyn Wetzel, cmwetzel@iastate.edu Chloroplast genome Assoc Curator : Steve Rodermel, S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome Design : Stan Letovsky, letovsky@gdb.org 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 : 11 April 1995 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Last_update : July 1995 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ DataBase : Mousedb Species : Musculus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD Last_update : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_vertion : 4.0 Last_update : June 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ 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. Curator : Staffan Bergh, staffan@biochem.kth.se Last_update : July 1995 ACEDB_version : 3.0 Data_version : 3-8 (June 18, 1995) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au Curator : Gail Juvik, gjuvik@nalusda.gov - ACEDB version ACEDB_vertion : 4.0 Last_update : September 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Last_update : June 1995 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 Last_update : September 1995 FTP : ftp.sanger.ac.uk in pub/PomBase Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Last_update : June 1995 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susah McCouch ACEDB_version : 3.0 Last_update : July 1995 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 2.0, MacAce 2.0b4 Last_update : September 1995 Data_version : 2.4.12 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB Gopher : genome-gopher.stanford.edu WWW : 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 : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Rita Schmidt, bleb@genome.stanford.edu Curator : Barbara Dunn, bdunn@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Programmer : Karen Davis, karen@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu PI : Steve Tanksley Release : ACEDB 3.0 Last_update : May 1995 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 Last_update : September 1995 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker Curator : David Grant, dgrant@mendel.agron.iastate.edu Curator : Marica Imsamde, mimsande@mendel.agron.iastate.edu Contact : Dave Schrader, schrader@mendel.agron.iastate.edu ACEDB-Version : 3.7 Last_update : August 1995 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://mendel.agron.iastate.edu:8000/main.html Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server Last_update : October 1994 FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Database : Toxo Species : Toxoplasma gondii PI : Jennie Blackwell PI : Jim Ajioka Last_update : September 1995 ACEDB_version : 4.1 Contact : Martin Aslett FTP : parsun1.path.cam.ac.uk WWW : http://parsun1.path.cam.ac.uk? Curator : Martin Aslett Curator : Howard Cobb Database : TreeGenes Species : Forest trees ACEDB_version : 3.0 Last_update : July 1995 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ Database : Trypbase Species : Trypanosoma brucei PI : Sara Malville Contact : sm160@mole.bio.cam.ac.uk Comment : Under development, feedback welcome. ACEDB_version : 4.0 Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Last_update : April 1994 FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu Last_update : September 1993 ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions Q5: What documentation exists for ACEDB? ++++++++++++++++++++++++++++++++++++++++ A5: +++ From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000 . Primary documents from the developers are: o acedb -- A C. elegans Database: I. Users' Guide. o acedb -- A C. elegans Database: II. Installation Guide. o acedb -- A C. elegans Database: III. Configuration Guide. o Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z and ftp://weeds.mgh.harvard.edu/acedb_doc . The files are in TeX (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/index.html A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html . Japanese language guides: _Japanese ACEDB Guide Ver.1.2._ _ACEDB ver.2 for NEC engineering workstation EWS4800 series_ are available in PostScript via anonymous ftp at ftp.nec.co.jp as /pub/packages/acedb/acemanjp.1_2.ps.Z . There is a Japanese language ACEDB FAQ available at http://www.cbi.or.jp/~sano/acemanjp12/index.html SampleDB, by Dave Matthews, is an ACEDB database constructed to demonstrate features of ACEDB, especially map and sequence displays. Anonymous ftp to probe.nalusda.gov:pub/acedocs/sampledb 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 Angistute.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). URL : http://genome-www.stanford.edu/docs/aatdb_man.html . 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] URL : http://probe.nalusda.gov:8000/acedocs/overview.html . 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: What other resources are available for ACEDB? +++++++++++++++++++++++++++++++++++++++++++++++++ A6: +++ Perl and WWW tools ++++++++++++++++++ > The AGIS server at the National Agricultural Library provides a tool set for integrating version 4 of ACEDB with perl and the World-Wide Web. The archive is ftp://probe.nalusda.gov/pub/tools/acelib.tar.gz For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/TextConvert . The Developers' Archive +++++++++++++++++++++++ Mike Cherry maintains an archive of tools that may be useful in curating ACEDB databases. It can be reached by anonymous ftp at URL ftp://weeds.mgh.harvard.edu/acedb_dev/ or via gopher at gopher://genome-gopher.stanford.edu:70/11/ftp If you have a contribution place it in ftp://weeds.mgh.harvard.edu/acedb_dev/incoming/ and send a message to Mike (cherry@genome.stanford.edu). The Biosci conference bionet.software.acedb +++++++++++++++++++++++++++++++++++++++++++ There is a USENET/Biosci conference titled bionet.software.acedb created expressly for discussion of ACEDB. The best way to interact with the Biosci conferences is via a newsreader like rn, trn, tin or a WWW browser. Consult your system administrator for more information. 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. o All of the articles in biosci.software.acedb are archived by Biosci at gopher://gopher.bio.net/1/ACEDB o Mike Cherry makes it possible to search past articles in biosci.software.acedb using WAIS at gopher://genome-gopher.stanford.edu:80/77/.index/acedb-biosci and at URL http://genome-www.stanford.edu/biosci_acedb.html . If your WWW browser is configured properly you may be able to read the newsgroup at news:biosci.software.acedb . And more ++++++++ The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: o http://moulon.inra.fr/acedb/acedb.html for C. elegans data o http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data o http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html A how-to manual on the Moulon server is available at http://keck.tamu.edu/cgi/staff/ace-mosaic-howto.html The Genome Computing Group, Lawrence Berkeley Laboratory, has an anonymous ftp service at machine genome.lbl.gov which contains: o flydb - LBL's Drosophila Acedb-style database o 21bdb - LBL's Human Chromosome 21 Acedb-style database o querdb - LBL's query-language extensions to Acedb o metadata - LBL's compendium of Acedb database schema variants o macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version o There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to dataabases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: o 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). o 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier Jean Thierry-Mieg et al), and the Interated Genome Database project in Heidelburg (Otto Ritter, Detlef Wolf et al). Return to List of Questions Q7: How should ACEDB be cited? ++++++++++++++++++++++++++++++ A7: +++ From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions Q8: Is ACEDB object-oriented? +++++++++++++++++++++++++++++ A8: +++ From the ACEDB User's Guide: A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions Q9: How can I get on/off the ACEDB announcements mailing list? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A9: +++ To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q6 for details] is on the mailing list. Return to List of Questions Q10: When and where is the Next ACEDB Workshop? +++++++++++++++++++++++++++++++++++++++++++++++ A10: ++++ The 1996 Workshop is not yet scheduled. If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, there are online collections: o by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; o by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; o and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions Q11:Who prepared this document & where is the current version? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A11: ++++ This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu as pub/usenet/news.answers/acedb-faq . If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html and http://s27w007.pswfs.gov/Homepage/acedbfaq.html There is a Japanese language FAQ available at http://www.cbi.or.jp/~sano/acemanjp12/index.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 Mike Cherry, John McCarthy, and Doug Bigwoody. Other contributors include: o Lisa Lorenzen o David Matthews o Edie Paul o Donn Davy o Eric De Mund o Sam Cartinhour Please cite as: Sherman,B.K., ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993,1994,1995 approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome Research Program. Return to List of Questions End of ACEDB FAQ --bks From owner-acedb@net.bio.net Sat Sep 30 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 1 Oct 1995 02:01:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 309 Sender: daemon@net.bio.net Distribution: world Message-ID: <199510010900.CAA23403@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. 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Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionaire is as follows. > > > 6. Information in English/ > > 5. Scientific and other topics/ > > 1. Finnish EMBnet BioBox/ > > 9. FAQ Files/ > > 5. Bionauts Address Database (questionaire) > IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 15-05-93 for 15 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 15-05-93, not 15-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: