From owner-acedb@net.bio.net Wed Jul 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: Renaming in acedb Date: 7 Jul 1994 23:06:18 +0100 Lines: 8 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2vhu8q$hge@mserv1.dl.ac.uk> Original-To: buia@soda.berkeley.edu You can either rename in a .ace file -R Classname Oldname Newname or using the Add/Alias/Rename tool accessible from the main window menu (for which you need Write Access). Richard From owner-acedb@net.bio.net Wed Jul 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!soda.berkeley.edu!buia From: buia@soda.berkeley.edu (Alex Bui) Newsgroups: bionet.software.acedb Subject: Renaming in acedb Date: 7 Jul 1994 17:46:03 GMT Organization: Computer Science Undergraduate Association, UC Berkeley Lines: 14 Message-ID: <2vhf0r$es9@agate.berkeley.edu> NNTP-Posting-Host: soda.berkeley.edu Hello! I'm new to this newsgroup and to AceDB, so it's quite possible that my question has an easy answer (I hope so). Looking at the code for AceDB, I haven't found an easy way to actually rename an instance of an object that's already in the database. That is, if an object has already been put into the database, is it possible to readily rename its key? Obviously, this brings up a lot of problems with regards to links in the object-oriented hierarchy and xrefs. But is there an easy way to do this rename? Any ideas would be appreciated. Thanks! Alex Bui UC Berkeley From owner-acedb@net.bio.net Wed Jul 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!gumby!wupost!medicine.wustl.edu!NewsWatcher!user From: anderson@pharmdec.wustl.edu (eric c. anderson) Newsgroups: bionet.software.acedb Subject: test Followup-To: bionet.software.acedb Date: Wed, 06 Jul 1994 10:56:58 -0500 Organization: dept. of molecular bio. and pharmacology Lines: 17 Distribution: usa Message-ID: NNTP-Posting-Host: 128.252.181.14 just a test...sorry for wasting the bandwidth -- a simple proposal for a more livable usa: let's ban all guns and personal automobiles... think about it, when was the last time you heard of a bike-by stabbing? just a suggestion eric c. anderson anderson@pharmdec.wustl.edu 314-362-3963 (work) 314-362-7058 (fax) dept. of molecular biology and pharmacology washington university school of medicine st. loser, misery 63110 From owner-acedb@net.bio.net Sun Jul 10 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!soda.berkeley.edu!buia From: buia@soda.berkeley.edu (Alex Bui) Newsgroups: bionet.software.acedb Subject: ACeDB internal code question Date: 11 Jul 1994 22:52:31 GMT Organization: Computer Science Undergraduate Association, UC Berkeley Lines: 19 Message-ID: <2vsiff$mnv@agate.berkeley.edu> NNTP-Posting-Host: soda.berkeley.edu Hello again! Thanks for all the responsees about renaming in ACeDB...I have another related question, however. I am actually working with the ACeDB code, and want to do an object rename while in the middle of processing something. To that end, I can actually output a file with the "-R : " line...but what *code* inside of the program do I call to do a parse of this file? I would assume it would be come in parse.c or bssubs.c, but I'm not sure. What I would like to do is be able to pass on a file handle or filename, and have the system parse the line. I've also tired sending the -R line directly through to parseBuffer...but I'm not sure that this is right. Does anyone have any ideas? Thanks. Alex Bui UC Berkeley From owner-acedb@net.bio.net Sun Jul 10 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!moe.ksu.ksu.edu!crcnis1.unl.edu!unlinfo.unl.edu!vwarwar From: vwarwar@unlinfo.unl.edu (vitor warwar) Newsgroups: bionet.software.acedb Subject: PAM and BLOSUM Date: 11 Jul 1994 21:21:01 GMT Organization: University of Nebraska--Lincoln Lines: 14 Message-ID: <2vsd3t$iik@crcnis1.unl.edu> NNTP-Posting-Host: unlinfo.unl.edu X-Newsreader: TIN [version 1.2 PL2] Hi: Does anyone now where I can find, in computer readble form, PAM and BLOSUM tables? Thanks, Vitor Warwar -- ______________________________________________________________________ Vitor Warwar vwarwar@unlinfo.unl.edu Department of Plant Pathology Voice (402) 472-5598 406 Plant Sciences Hall Fax (402) 472-2853 From owner-acedb@net.bio.net Sun Jul 10 23:00:00 1994 Path: biosci!sanger.ac.uk!fw From: fw@sanger.ac.uk Newsgroups: bionet.software.acedb Subject: New Software release : UNIX version of Genome Database Software Package Date: 11 Jul 1994 10:14:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 107 Sender: daemon@net.bio.net Distribution: world Message-ID: <9407111712.AA11095@sanger.ac.uk> NNTP-Posting-Host: net.bio.net Software for genome mapping by fingerprinting techniques -------------------------------------------------------- What it is ----------- A genome mapping package has been developed for reading and assembling data from clones analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. The package comprises: data entry; matching; assembly; statistical analysis; modelling. The Data is entered by a scanning and image processing system, called IMAGE. The primary emphasis in the analytical routines is on flexibility and interactive convenience, so that the operator has full knowledge of and control over the growing map, but a variety of automatic options are included. The package continually grows to meet the needs of the Caenorhabditis project. This software is the UNIX port of the CONTIG9 software package, which was running on VAX/VMS only. The Software announced here will run on a wide variety of UNIX platforms, such as SUN-Sparc, SGI-Irix . Binaries are provided for Where to find it ----------------- The package is called ContigC and is available via anonymous ftp on : ftp.sanger.ac.uk:/pub/contigc/ You'll also find directories with precompiled binaries and documentation files in HTML format (Mosaic browsable). How to use it -------------- (1) On-line documentation A documentation is available on the InterNet. You have to use Mosaic to browse the hypertext document. Mosaic is available via anonymous ftp from : ftp.ncsa.uiuc.edu:/Web/ src.doc.ic.ac.uk:/public/computing/information-systems/WWW/ncsa/ Type the following URL in the text window that comes up after pressing 'o'-key in the Mosaic Window: URL = "http://www.sanger.ac.uk/~fw/contigc.html" This document will explain exactly, what the software does and how. (2) locally installed Mosaic documents For people with a slow InterNet connection to our server there is a tarred archive of all HTML files and images, which can be installed locally. This is on : ftp.sanger.ac.uk:/pub/contigc/Doc-html/ContigC+IMAGE-HTML-doc.tar (the file to start with is "index.html") (3) documents ready to print in postscript I created three postscript files from the HTML files. They are on : ftp.sanger.ac.uk:/pub/contigc/Doc-postscript/*.ps (4) pure text files without images If neither Mosaic nor postscript programmes are available, pure text files can be viewed in any ASCII editor. They're on : ftp.sanger.ac.uk:/pub/contigc/Doc-text/*.txt How to install it ------------------ I tried to make the installation as simple as possible. A shell script reads the system configuration, calls the make files and installs the programs after a successful compilation. Type : % install to start building the software. It will then compile graphic-libraries, the image analysis software and the database programs. Note.: This is my last day at the Sanger Centre, I won't be available to answer questions or fix bugs until october, when I'll be at University. ------------------------------------------------------------ Friedemann Wobus Email: fw@sanger.ac.uk WWW: http://www.sanger.ac.uk/~fw The Sanger Centre Tel: +44 (0)223 834244 Hinxton Hall, Hinxton Fax: +44 (0)223 494919 Cambridge CB10 1RQ WWW: http://www.sanger.ac.uk From owner-acedb@net.bio.net Mon Jul 11 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!pipex!uknet!liv!tjhuang From: tjhuang@liverpool.ac.uk (Mr T.J. Huang) Subject: Help with information of Evergreen technology Message-ID: Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: uxb.liv.ac.uk Organization: The University of Liverpool X-Newsreader: TIN [version 1.2 PL2] Date: Tue, 12 Jul 1994 15:56:05 GMT Lines: 14 Dear All, Do any of you know a software company -- Evergreen Technologies, which has some software for conversion of medical images. If you have any information, please, please give me an email. Any information will be greatly appreciated. With best regards, Terrance, tjhuang@liverpool.ac.uk From owner-acedb@net.bio.net Wed Jul 13 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!agate!howland.reston.ans.net!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!olivea!uunet!newsflash.concordia.ca!CC.UMontreal.CA!megasun.BCH.UMontreal.CA!tim From: tim@megasun.BCH.UMontreal.CA (Tim Littlejohn) Subject: Re: PAM and BLOSUM Message-ID: Sender: news@cc.umontreal.ca (Administration de Cnews) Organization: Universite de Montreal References: <2vsd3t$iik@crcnis1.unl.edu> Date: Thu, 14 Jul 1994 10:40:47 GMT Lines: 30 In article <2vsd3t$iik@crcnis1.unl.edu> vwarwar@unlinfo.unl.edu (vitor warwar) writes: >Hi: > > Does anyone now where I can find, in computer readble form, >PAM and BLOSUM tables? These can be obtained at NCBI's ftp site: anonymous FTP to ncbi.nlm.nih.gov For the blosum tables, look in the directory /repository/blocks/unix/blosum For the PAM matricies, there is a program called "pam" which will generate the tables for you (get pam.c and compile). This can be found in /pub/blast/1.4d/explode/blastapp (there are also some PAM tables already generated; look in the matrix subdirectory). Tim Littlejohn -- ============================================================================== Tim Littlejohn E-mail: tim@bch.umontreal.ca Snail Mail: Departement de biochimie Phone: (514) 343-6111, x5149 Universite de Montreal Fax: (514) 343-2210 C.P. 6128, Centre-ville Montreal (Quebec), H3C 3J7 CANADA ============================================================================== From owner-acedb@net.bio.net Thu Jul 14 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!news.duke.edu!bio6.acpub.duke.edu!mps2 From: mps2@bio6.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: Surpressing a tag Date: 15 Jul 1994 13:31:20 GMT Organization: Duke University, Durham, NC, USA Lines: 13 Distribution: world Message-ID: <306338$lbf@news.duke.edu> NNTP-Posting-Host: bio6.acpub.duke.edu Is there any way to have a tag, but to surppress its appearance? For example, I have utilizzed many of the subclass features in ACE 3.0, but to do so I need a filter tag. What I would LIKE is if I can surpress this tag so the user won't see it, but still exist so that it will sort the class into its subclasses. Any ideas? Thanks, Maulin Shah mps2@acpub.duke.edu DCMB Duke University Duke Engineering '96 From owner-acedb@net.bio.net Sun Jul 17 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!convex!news.duke.edu!bio6.acpub.duke.edu!mps2 From: mps2@bio6.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: Sharp classes Date: 18 Jul 1994 13:11:30 GMT Organization: Duke University, Durham, NC, USA Lines: 20 Distribution: world Message-ID: <30dv22$b49@news.duke.edu> NNTP-Posting-Host: bio6.acpub.duke.edu I am trying to make a sharp class #date. This will appear after all my comments and most text entries where it is relevant. I have designed it as follows: ?date Date Text This is not complicated at all. Now in my Model where it is used it looks something like: Comment Text #date And finally, in my ace file it looks like: Comment "I can't figure this out!!!" Date "7/94" The problem is that when I read this into the DB, I get "Unknown tag 7/94" What am I doing wrong? Thanks for your help in advance. Maulin From owner-acedb@net.bio.net Sun Jul 17 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!convex!news.duke.edu!bio6.acpub.duke.edu!mps2 From: mps2@bio6.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: Sorry Date: 18 Jul 1994 13:16:37 GMT Organization: Duke University, Durham, NC, USA Lines: 4 Distribution: world Message-ID: <30dvbl$bd6@news.duke.edu> NNTP-Posting-Host: bio6.acpub.duke.edu Sorry people. I figured out my problem. Its a long story. In any case, please disregard the last message. Thanks. Maulin From owner-acedb@net.bio.net Tue Jul 19 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!eddy From: eddy@eddy.gen.cam.ac.uk (Edward Welbourne) Newsgroups: bionet.software.acedb Subject: Re: Window size Date: 20 Jul 1994 20:22:13 GMT Organization: FlyBase at Cambridge Lines: 16 Distribution: world Message-ID: References: <30jfrp$l9j@news.duke.edu> NNTP-Posting-Host: eddy.gen.cam.ac.uk To: mps2@bio6.acpub.duke.edu (Maulin Piyush Shah) In-reply-to: mps2@bio6.acpub.duke.edu's message of 20 Jul 1994 15:28:57 GMT In article <30jfrp$l9j@news.duke.edu> mps2@bio6.acpub.duke.edu (Maulin Piyush Shah) writes: > Is there any way I can change the default window sizes? Is it a change > in the kernel or can I do it by changing some parameters somewhere? The place for the change is in displays.wrm; see the documentation comment with which this begins. You can specify a separate window-size for each class; it's a parameter change, not a kernel change (happily). Good luck, Eddy. -- ... Few indeed are those who, travelling it, have crossed the dark and yawning Abyss of Implementation to Delivery. Many, yea, many in truth stagnate yet in the Desert of Delay, or linger ever in the ghastly limbo called Perpetual Beta. (from the LOGINATAKA) From owner-acedb@net.bio.net Tue Jul 19 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!gatech!news-feed-1.peachnet.edu!news.duke.edu!bio6.acpub.duke.edu!mps2 From: mps2@bio6.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: Its me again: Text Search Date: 20 Jul 1994 19:53:59 GMT Organization: Duke University, Durham, NC, USA Lines: 16 Distribution: world Message-ID: <30jvcn$1du@news.duke.edu> NNTP-Posting-Host: bio6.acpub.duke.edu For some reason, when I do a text search, I get into some really strange trouble. First of all, each object is shifted. For example, if my list is: ac-21 ac-22 ac-23 I get ac-22 by clicking on ac-21, ac-23 by clicking on ac-22, etc. Second, in most cases, many of the objects that are listed have absolutely nothing to do with the search. Huh? HELP!! Maulin From owner-acedb@net.bio.net Tue Jul 19 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!convex!news.duke.edu!bio6.acpub.duke.edu!mps2 From: mps2@bio6.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: Window size Date: 20 Jul 1994 15:28:57 GMT Organization: Duke University, Durham, NC, USA Lines: 4 Distribution: world Message-ID: <30jfrp$l9j@news.duke.edu> NNTP-Posting-Host: bio6.acpub.duke.edu Is there any way I can change the default window sizes? Is it a change in the kernel or can I do it by changing some parameters somewhere? Thanks. Maulin From owner-acedb@net.bio.net Wed Jul 20 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.kth.se!kiev.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: AboutDB Date: 21 Jul 1994 15:00:01 +0200 Organization: Biochemistry, KTH, Stockholm Lines: 47 Sender: staffan@biochem.kth.se Distribution: world Message-ID: <30lrgh$2b0@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 AboutDB, the ACEDB database database (deliberate doubling :-) is now on the 'web: http://kiev.physchem.kth.se/AboutDB/AboutDB.html Background and guiding ideas: AboutDB was conceived and provisionally implemented during the recently finished Ace94 workshop in St Mathieu de Treviers, outside of Montpellier, France. AboutDB collects information on all aspects of the developement and use of the database manager ACEDB, such as: people and organizations using it or implementing software for it, databases implemented in it, bug reports, projects involving the database manager, documentation, tools for the user, curator, or programmer, features within the program and tips and tricks of its use. AboutDB is implemented in ACEDB (what else) and it is aimed at people with at least some experience of ACEDB, such as programmers, curators and advanced users. The data is the same as it was July 15, when the workshop finished, and thus not really curated yet. I will try to update some of the information over the next few weeks. During this time the data and probably the models will change daily ... There is a very simple form for submitting data to the database. This will also be enhanced in the near future. If you have any comments, questions, gripes, ideas about the database, if you have data sets or corrections to data that should be in the database, or if you want to volunteer to take on some of the curation (please!), do not hesitate to contact me. /staffan Staffan Bergh Biochemistry, KTH, S-100 44 Stockholm, Sweden email: staffan@biochem.kth.se + Don't let that horse eat that violin phone: int+46 8 790 8758 + cried Chagall's mother fax: int+46 8 24 54 52 + but he kept right on painting + -- Lawrence Ferlinghetti From owner-acedb@net.bio.net Sun Jul 24 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: ACEDB curators/developers: Contribute to FAQ Date: 25 Jul 1994 17:55:05 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 39 Distribution: world Message-ID: <310u9p$op9@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov All curators and developers of ACEDB projects are encouraged to contribute a paragraph describing their work to the Frequently Asked Questions document. You do not have to have a database ready for release or even in local use. Here's a sample entry: Database : Orcdb Species : Homo troglodytus Availability : Under development Curator : Bilbo Baggins Contact : bbaggins@shire.middle-earth.com You can add any tags or data that you like. The FAQ is updated monthly, and you can resubmit a paragraph as often as you like. The next FAQ will be prepared in the first week of August. If you have multiple databases, feel free to submit a paragraph for each. Send it to: acedbfaq@s27w007.pswfs.gov (It's okay if you just reply to this message.) You can retrieve the current FAQ from net.bio.net as pub/BIOSCI/ACEDB/ACEDB.FAQ or rtfm.mit.edu as pub/usenet/news.answers/acedb-faq and other fine anonymous ftp repositories. Also available as hypermedia on the World-Wide Web as http://probe.nalusda.gov:8000/acedocs/acedbfaq.html --bks -- Bradley K. Sherman Computer Scientist Dendrome Project 510-559-6437 FAX: -6440 Institute of Forest Genetics bks@s27w007.pswfs.gov P.O. Box 245, Berkeley, CA 94701 http://s27w007.pswfs.gov/People/bks.html From owner-acedb@net.bio.net Mon Jul 25 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!uunet!solaris.cc.vt.edu!news.duke.edu!bio6.acpub.duke.edu!mps2 From: mps2@bio6.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: link missing in bsTreeBreakComment Date: 26 Jul 1994 15:19:51 GMT Organization: Duke University, Durham, NC, USA Lines: 6 Distribution: world Message-ID: <3139in$bp2@news.duke.edu> NNTP-Posting-Host: bio6.acpub.duke.edu Has any one ever had this error message when trying to make a Dump? !! FATAL ERROR 0: !! link missing in bsTreeBreakComment If so, please let me know what I am doing wrong. Thanks. From owner-acedb@net.bio.net Mon Jul 25 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re FATAL ERROR: link missing in bsTreeBreakComment Date: 26 Jul 1994 19:21:22 +0100 Lines: 21 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <313k72$etc@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk This looks like a defect in the binary database. For some reason you can not store a very long piece of text (data type Text, not class ?Text) that had to be split across multiple disk blocks. I have not seen this crash before. I just looked at the code and can't see the problem. It seems that this code can only be called when storing an edited object, if you have write access. Did you edit some objects before doing the dump? Do you get the crash if you dump without write access? Do you get the crash if you try to save without dumping? Can you produce an ace file with a minimal example that you can read into an empty database and provoked the crash? If so please send it to me and/or Jean. If you can find out which object is being saved when the crash occurs then you can create a keyset containing that object, and with write access save it in the database as a named keyset with name "DoNotDump". Any objects in that keyset will be skipped when dumping. Richard From owner-acedb@net.bio.net Wed Jul 27 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!xlink.net!news.urz.uni-heidelberg.de!ns.dkfz-heidelberg.de!news!dok421 From: dok421@mbp-sun1.dkfz-heidelberg.de (Jonathan Karges) Newsgroups: bionet.software.acedb Subject: window scrolling Date: 28 Jul 1994 16:14:38 GMT Organization: German Cancer Research Center Heidelberg Germany Lines: 11 Distribution: world Message-ID: NNTP-Posting-Host: mbp-sun1.inet.dkfz-heidelberg.de When I scroll an object in a window and then click on the update entry of the window's menu, the top of the object is displayed again. I think, for large objects it's more convenient not to change the displayed range of the object too much. Otherwise, the position to be updated has to be searched again. (Of course, I know that the original displayed range doesn't fit any more exactly because of the additional tag name displaying.) Jonathan From owner-acedb@net.bio.net Thu Jul 28 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!nntp.gmd.de!xlink.net!news.urz.uni-heidelberg.de!ns.dkfz-heidelberg.de!news!dok421 From: dok421@mbp-sun1.dkfz-heidelberg.de (Jonathan Karges) Newsgroups: bionet.software.acedb Subject: Bnew node : block overflow Date: 29 Jul 1994 11:56:27 GMT Organization: German Cancer Research Center Heidelberg Germany Lines: 24 Distribution: world Message-ID: NNTP-Posting-Host: mbp-sun1.inet.dkfz-heidelberg.de Did anybody of you ever recognize the following error message when clicking on the "save" entry of an object window (after some interactive updates of the object)? !! FATAL ERROR 0: !! Bnew node : block overflow !! FATAL ERROR 0: !! Double pinning of I think it's no problem of the cachesize. My cachesize.wrm has the following entries: CACHE1 = 8000 // Size of first cache, as used in w5/blocksubs.c CACHE2 = 2000 // Size of second cache, as used in w5/objcache.c DISK = 200 // Initial size of database on disk at creation The dump size of the specific object that dued to this behaviour is arround 20kBytes. It has about 60 references and many text-class values. After rebuilding the database from ace dumps, the problem didn't occur after repeated updates on that object. Jonathan From owner-acedb@net.bio.net Thu Jul 28 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: ACEDB '94 Highlights Date: 29 Jul 1994 22:50:30 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 50 Distribution: world Message-ID: <31c13m$pcn@overload.lbl.gov> References: <9407292033.AA09442@greengenes.cit.cornell.edu> NNTP-Posting-Host: s27w007.pswfs.gov In article <9407292033.AA09442@greengenes.cit.cornell.edu> matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") writes: > ... >I assume a lot of exciting things happened at the Montpellier workshop. And >that somebody's planning to report it to the rest of us. Hope so, we're >waiting with bated breath. > ... Just to get the ball rolling here is what I felt were the highlights: * Jean & Richard are planning on returning ACEDB to a single core distribution. * The ACEDB kernel will be a database manager and a set of display primitives (a layer on top of X11). "Approved" special purpose displays will be built on top of this kernel. Developers should avoid bypassing the kernel primitives so as to maximize portability. In this way, the two lower levels (database + display primitives) constitute ACEDB. Non-text displays are allowed to be idiosyncratic. * Otto Ritter's group announced a way to use ACEDB on top of Sybase, such that ACEDB calls result in data fetched directly from SYBASE. * Jaime Prilusky, while at the workshop, produced a demonstration mechanism for calling Mosaic from ACEDB as a help mechanism. I believe that Jean is laboring mightily to get this into the next distribution. * Sam Cartinhour, John Morris, Steffan Bergh and John McCarthy have captured the list of "magic tags". These are tags that, if included in the models.wrm file, have special meanings in the context of ACEDB displays. * Steffan Bergh created AboutDB; an ACEDB about ACEDB I am sure that I am slighting the efforts of many participants here and misrepresenting the efforts of others. My brain does not function well at the average temperature of a Montpellier summer. Others should feel free to correct me. --bks -- Bradley K. Sherman Computer Scientist Dendrome Project 510-559-6437 FAX: -6440 Institute of Forest Genetics bks@s27w007.pswfs.gov P.O. Box 245, Berkeley, CA 94701 http://s27w007.pswfs.gov/People/bks.html From owner-acedb@net.bio.net Thu Jul 28 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Tablemaker horizontal scrolling? Date: 29 Jul 1994 13:33:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9407292033.AA09442@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net I notice in ace3.1.test.source that the Tree windows have horizontal scrolling now! This is great. The Table_Maker doesn't but I sure hope it will soon, it would be a whole lot more functional. I assume a lot of exciting things happened at the Montpellier workshop. And that somebody's planning to report it to the rest of us. Hope so, we're waiting with bated breath. - Dave From owner-acedb@net.bio.net Thu Jul 28 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!news.urz.uni-heidelberg.de!ns.dkfz-heidelberg.de!news!dok421 From: dok421@mbp-sun1.dkfz-heidelberg.de (Jonathan Karges) Newsgroups: bionet.software.acedb Subject: crash after updating various objects Date: 29 Jul 1994 15:27:55 GMT Organization: German Cancer Research Center Heidelberg Germany Lines: 10 Distribution: world Message-ID: NNTP-Posting-Host: mbp-sun1.inet.dkfz-heidelberg.de When I am interactively updating several database objects in different windows and then do a save in the main menu, ACEDB sometimes crashes in case of big objects with a core dump file filling up all the user space of my machine (SUN SPARC). (size of cache1 = 8000 blocks, ace dump size of biggest object: 20kBytes) Who has any explanation ? Jonathan From owner-acedb@net.bio.net Fri Jul 29 23:00:00 1994 Path: biosci!CS.UNC.EDU!singh From: singh@CS.UNC.EDU (Raj Kumar Singh) Newsgroups: bionet.software.acedb Subject: BioSCAN Serevr Update Date: 29 Jul 1994 19:22:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <199407300222.WAA06388@polaris.cs.unc.edu> NNTP-Posting-Host: net.bio.net o _____ o _________________________________________________________ o o o ____ o o o BBBBB SSSS CCCC AA NN NN o o BB B * SS SS CC CC AAAA NNN NN o o BB BB SS CC CC AA AA NN N NN o o BBBBB i oo SSS CC AAAAAA NN NN NN o o BB BB ii o o SS CC CC AA AA NN NNN o ____ o BB BB ii o o SS SS CC CC AA AA NN NN o o BBBBB ii oo SSSS CCCC AA AA NN NN o _____ o o o UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL o _____ o Department of Computer Science o o bioscan-info@cs.unc.edu _______________________________________________________________________________ *************************** * U P D A T E -- 7/29/94 * *************************** o The BioSCAN e-mail server databases have been updated. The currently available databases are as follows: GenBank Release-83 SWISS-PROT Release-29 PIR Release-41 GenPept Release-83 o BioSCAN (Biological Sequence Comparative Analysis Node) is a computational tool designed for similarity analysis of biological sequences. Its massively parallel computer system performs rapid, rigorous, searches of biosequence databases and is compatible with popular software packages such as BLAST and FASTA. To receive current set of instructions on using the BioSCAN e-mail server, send an e-mail to the address "bioscan@cs.unc.edu". Put the word "HELP"or "help" on a line by itself in the body of the message. A tutorial ("tutor.txt") can be retrieved via anonymous FTP to "ftp.cs.unc.edu" from "/pub/bioscan" directory. Please send your questions and comments to "bioscan-info@cs.unc.edu". o Searches: bioscan@cs.unc.edu, User support: bioscan-info@cs.unc.edu o This research was supported in part by NSF under grant MIP-9024585. ======================================================================= Raj K. Singh singh@cs.unc.edu +1 (919) 962-1744 From owner-acedb@net.bio.net Fri Jul 29 23:00:00 1994 Path: biosci!agate!ames!decwrl!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!gpu!asimmond From: asimmond@gpu.srv.ualberta.ca (Andrew Simmonds) Newsgroups: bionet.software.acedb Subject: Help installing ace2 on LINUX Date: 30 Jul 1994 02:59:30 GMT Organization: University of Alberta Lines: 16 Message-ID: <31cfmi$dq6@quartz.ucs.ualberta.ca> NNTP-Posting-Host: gpu.srv.ualberta.ca X-Newsreader: TIN [version 1.2 PL2] Is there anyone willing to supply a neophyte UNIX person, having limited experience, with a idiot walk through to install ace2 on a LINUX based computer. The documentation and FAQ talk of a binary available for LINUX but I have yet been able to find one. I have tried to compile from the source but have had a world of trouble... (it took me two hours to get the source file uncompressed). Any help at all would be appreciated. Andrew ______________________________________________________________________________ Andrew Simmonds - Department of Genetics - University of Alberta CANADA ASIMMOND@GPU.SRV.UALBERTA.CA G216 Biological Sciences Centre Edmonton, Alberta, CANADA T6G 2E9 ****************************************************************************** "Does steel wool come from magnetic sheep?" ****************************************************************************** From owner-acedb@net.bio.net Sat Jul 30 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: code 3.3 Date: 30 Jul 1994 17:50:48 +0100 Lines: 37 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <31e0d8$g2r@mserv1.dl.ac.uk> Original-To: ace94@nsfnet-relay.ac.uk i am making available on ncbi a code release code.3.3.tar.Z it incorporates help in mosaic datetypes printer control multidiscs Gels vmap improved multimap(mieg) pmap as usual gmap (as altenative display in ace2) and lots of other goodies you can compile it by having in the wmake/MACHINE_DEF either -DACEDB2 or -DACEDB3 there is a known bug on dec alpha: intron/exon widget of genes does not work it incorporates some of the new code control of Erik not the multi map of LBL or Arun's display the tags file is still needed but this will go off in next release the file disptypes.wrm is completelly changed and no longer read at run time which eliminates loads of problems This code is intended for developpers or datbase curators It also has dna assembly algotrithms and shows the ABI trace files this is done via some modules off Staden's and Dear's ted system all gathered in directory wstaden: this file are temporary please do not use them individually I will, in a few weeks make a real release with binaries any bug you find will help me but i won t answer my mail for a couple of weeks Jean From owner-acedb@net.bio.net Sat Jul 30 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: ace wizardry Date: 31 Jul 1994 14:28:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9407312128.AA10298@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net On Fri Jul 29 18:53:24 1994 Bradley K. Sherman said: > * Sam Cartinhour, John Morris, Steffan Bergh and John McCarthy > have captured the list of "magic tags". These are tags that, > if included in the models.wrm file, have special meanings in > the context of ACEDB displays. Great! On Tue Jul 26 14:40:29 1994 Richard Durbin said: > If you can find out which object is being saved when the crash occurs > then you can create a keyset containing that object, and with write > access save it in the database as a named keyset with name > "DoNotDump". Any objects in that keyset will be skipped when dumping. !!? Magic keyset names? Are there any others? How about environment variables, is anybody making a list of these? - Dave From owner-acedb@net.bio.net Sun Jul 31 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!news.kth.se!kiev.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: ace wizardry Followup-To: poster Date: 1 Aug 1994 07:37:27 +0200 Organization: Biochemistry, KTH, Stockholm Lines: 30 Sender: staffan@biochem.kth.se Distribution: world Message-ID: <31i1mn$kqm@kiev.physchem.kth.se> References: <9407312128.AA10298@greengenes.cit.cornell.edu> NNTP-Posting-Host: kiev.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article <9407312128.AA10298@greengenes.cit.cornell.edu>matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") writes: >On Fri Jul 29 18:53:24 1994 Bradley K. Sherman said: <...> >> have captured the list of "magic tags". These are tags that, <...> >!!? Magic keyset names? Are there any others? DoNotDump and searchedClasses are the only ones as far as I know ... >How about environment variables, is anybody making a list of these? The suggestions are duly noted, as ideas for AboutDB classes -- other things we've thought about are: displays, menu items and buttons. Anyone have more suggestions? /staffan Staffan Bergh Biochemistry, KTH, S-100 44 Stockholm, Sweden AboutDB is at URL: "http://kiev.physchem.kth.se/AboutDB.html" MycDB is at URL: "http://kiev.physchem.kth.se/MycDB.html" email: staffan@biochem.kth.se + Don't let that horse eat that violin phone: int+46 8 790 8758 + cried Chagall's mother fax: int+46 8 24 54 52 + but he kept right on painting + -- Lawrence Ferlinghetti From owner-acedb@net.bio.net Sun Jul 31 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: kristoff (David Kristofferson) Newsgroups: bionet.software.acedb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 1 Aug 1994 02:00:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 322 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408010900.CAA05410@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. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. 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WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). Finally, the BIOSCI archive files are accessible by anonymous FTP to net.bio.net [134.172.2.69] in the directory pub/BIOSCI. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS, waismail, and gopher access. If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. 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 questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->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 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 CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs 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 MOLECULAR-EVOLUTION bionet.molbio.evolution 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 STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast 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: From owner-acedb@net.bio.net Sun Jul 31 23:00:00 1994 Path: biosci!agate!doc.ic.ac.uk!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: LINUX binary Date: 1 Aug 1994 16:09:48 +0100 Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <31j37s$3sh@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk There is no LINUX binary currently at the ACEDB ftp sites, contrary to the documentation, which referred to an earlier version 1 binary. I have recently obtained a linux machine, and compiled a Linux version myself. As we will be using this for demos I plan to keep it running and up to date. Unfortunately the current code, when compiled, seems to give arbitrary crashes that I do not understand, so I am not keen to release it just now. I hope to release it soon, and will announce this to the newsgroup. Richard