From owner-acedb@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!feed1.news.erols.com!news1.erols.com!uunet!in1.uu.net!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!usenet From: feichtin@alf.biochem.mpg.de (Richard Feichtinger) Newsgroups: bionet.celegans,bionet.software.acedb Subject: macace update again Date: 3 Oct 1996 10:14:13 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 66 Sender: -Not-Authenticated-[2621] Message-ID: <5303ll$5ks9@sat.ipp-garching.mpg.de> NNTP-Posting-Host: macwurm.biochem.mpg.de X-Posted-From: InterNews 1.0.8@macwurm.biochem.mpg.de Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.celegans:1082 bionet.software.acedb:992 jdhardin@facstaff.wisc.edu (Jeff Hardin) wrote: >Hi Richard- > >Sorry to bother you, but we have tried (repeatedly) to download your Macace >datasets including updates through WS1.4-20. Unfortunately, the transfer >was extremely slow (approximately 50 bytes/sec!!), and eventually the >connection to your server was terminated each time. So, as an alternative, >are their any special steps to adding the Unix data updates to Macace? I >noticed that they're just text files, so once the tarZ files are >decompressed, they ought to work. Is there some place I can look for more >information? > >Many thanks! > >Jeff Sometimes I think of the transatlantik internet connection like in the years of telegraphy before seacables when you could morse a message within seconds to the coast, ship the written message across the sea and telegraph it again on the other continent. The first one who gets the update in the states please put it on a server there. P.S. Today, Oct. 3rd, is a holiday in Germany, there is a realistic chance to get macace.WS1.4-20.sea.bin within 24 hours. ftp://ftp.biochem.mpg.de/share/Schnabel A short instruction of updating macace: Get the new unix updates on your local unix machine (see news ACEDB data updates for C.elegans for details). If you have installed a unix acedb already the update files are in $ACEDB/rawdata. To do it by hand: uncompress update.WS1.4-*.tar.Z #short: uncompress *.Z tar -xvf *.tar #to see what's in the files: tar -tf *.tar #you can combine those steps with: zcat *.tar.Z | tar -xf - the updates are in /rawdata. In case there are new wspec files they are in /wspec (none this time). Take a Macintosh ftp program (e.g. fetch) and get them to your Mac. From the sanger center you can download update.WS1.4-17 to 20 directly with fetch on your local mac (e.g. folder acedb:rawdata) ftp://ftp.sanger.ac.uk/pub/acedb/celegans/rawdata add the suffix .ace to each file in acedb:rawdata Have your mac about 60M of RAM (use virtual memory if necessary) start acedb with 55M or so, get write access (password acedb) and select Read .ace files from the acedb menu in the main window click Open ace file, choose the first update file in the file parser and click Read all. This may take a long time for some updates, especially if you had to turn virtual memory on. If it doesn't work that way I'm also helpless. Good luck, Richard Feichtinger feichtin@alf.biochem.mpg.de From owner-acedb@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: re: acedb query language proposals Date: 5 Oct 1996 15:30:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <9610052229.AA00317@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > From BIOSCI-REQUEST@net.bio.net Fri Sep 20 14:07:01 1996 > To: acedb@net.bio.net > From: > Subject: acedb query language proposals The proposed new query language sounds great. I have an important user- submitted query I can't do with the existing language, "find all Loci within x units of Locus A on any Map", for lack of the num_op (arithmetic) functionality included in the proposal. So I'm really looking forward to it. A few suggestions: 1. The "right_of" relation Jean mentioned, e.g. the relation between c and d in FOO f tag a b tag c d is crucial. Maybe it could be given its own operation name? 2. Should there be an escape prefix like \ for the wildcard characters * and ?, as well as for ( and ) and any other syntax-reserved characters? Currently (well, ace4_3c), using "" to protect such characters in my queries is not working. 3. > 3) possible member specific operations on tree classes? e.g. things to > test interval overlap/containment for maps and sequences. Perhaps we might > even want interval objects? Any furtherance of this would be good. Actually we need a graphical interface to select and compare (multimap) subsections of Maps. 4. Should there be a flag to request case-dependent searches? Both in text and in classes that are defined as -CaseSensitive. 5. Will the old syntax still be available? Or some query client with similar syntax? I can learn to write the new syntax but I'd hate to have to tell my users they have to learn it. 6. I hope the new version will sort lists correctly even if they're very long, instead of piecewise like the current Tablemaker. - Dave From owner-acedb@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!KAA.CRBM.CNRS-MOP.FR!mieg From: mieg@KAA.CRBM.CNRS-MOP.FR (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: (none) Date: 7 Oct 1996 01:47:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 65 Sender: daemon@net.bio.net Distribution: world Message-ID: <9610061001.AA21289@kaa> NNTP-Posting-Host: net.bio.net in ace.4.3, escaping anything does work, but, in what may be rather crytic, we have a double notation: acedb>Find Paper [cgc* will find [cgc-173] that is: acedb>Find Paper xxx takes xxx verbatim, without any attemmpt to interpret special char like [] () + - etc this is equivalent to acedb>Query Find Paper IS "[cgc*" where the "" protects [ from beeing interpreted (actually IS is optional) however: acedb>Query Find Paper IS [cgc* -> unbalance [ error ******** Here is the table to perform the operation: "find all Loci within x units of Locus A on any Map", //////////////////////////////////////////////////////// //////////////////////////////////////////////////////// see below: //////////////////////////////////////////////////////// //////////////////////////////////////////////////////// 4. Should there be a flag to request case-dependent searches? Both in text and in classes that are defined as -CaseSensitive. i suggest that case dependant seqrches only work for casesensitive class in which case we should allow =~ or something like that to mathc reg-exp, including among other case-non-sensitive 5 The old syntax will continue to be available 6: i am responsible and very sorry for the piece sorting of very long tables i have actually fixed that, i did not realized it went into 4-3 actually, i was not aware of the bug before it was reproted by Ladeana, and i then fixed it immediatly PLEASE: DO NOT FORGET to report such bugs, the correct way is not to wait for some eventual complete revamp to talk about such things but to complain ASAP this is not a failure of the old syntax, but a plain IMPLEMENTATION bug and there is not the slightest doubdt that even a new syntax will be plagued at the beginning with implementation bugs. All system have bugs, including Mac-OS, c - compilers, UNIX, and yes acedb beats them all by the density of implementation bugs, but we know about them we are very willing to fix them. From owner-acedb@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: (none) Date: 7 Oct 1996 08:03:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <9610071501.AA01768@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Hi Jean, thanks for the help. > acedb>Query Find Paper IS "[cgc*" > > where the "" protects [ from beeing interpreted But there is no way to protect * from being interpreted? Anyway thanks for this tip. I was trying acedb>Query Find Paper IS "[cgc"* , which seems more logical to me, but returns all the Papers in the database. > Here is the table to perform the operation: > "find all Loci > within x units of Locus A on any Map", > > //////////////////////////////////////////////////////// > //////////////////////////////////////////////////////// > see below: Help! No table definition was included in your mail. Please send! - Dave From owner-acedb@net.bio.net Wed Oct 09 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!newsstand.cit.cornell.edu!news.acsu.buffalo.edu!news.atl.bellsouth.net!newsrelay.iastate.edu!news.iastate.edu!macgrant.agron.iastate.edu!user From: dgrant@iastate.edu (David Grant) Newsgroups: bionet.celegans,bionet.software.acedb Subject: Re: macace update again Date: Thu, 10 Oct 1996 15:16:55 -0500 Organization: USDA-ARS and Iowa State University Lines: 45 Message-ID: References: <5303ll$5ks9@sat.ipp-garching.mpg.de> NNTP-Posting-Host: macgrant.agron.iastate.edu Xref: biosci bionet.celegans:1093 bionet.software.acedb:996 > >are their any special steps to adding the Unix data updates to Macace? I > >noticed that they're just text files, so once the tarZ files are > >decompressed, they ought to work. Is there some place I can look for more > >information? > > > A short instruction of updating macace: > > Get the new unix updates on your local unix machine (see news > ACEDB data updates for C.elegans for details). If you have installed > a unix acedb already the update files are in $ACEDB/rawdata. > To do it by hand: > > uncompress update.WS1.4-*.tar.Z #short: uncompress *.Z > tar -xvf *.tar #to see what's in the files: tar -tf *.tar > #you can combine those steps with: zcat *.tar.Z | tar -xf - > > the updates are in /rawdata. In case there are new wspec files they are > in > /wspec (none this time). > > Take a Macintosh ftp program (e.g. fetch) and get them to your Mac. > From the sanger center you can download update.WS1.4-17 to 20 directly > with fetch on your local mac (e.g. folder acedb:rawdata) > ftp://ftp.sanger.ac.uk/pub/acedb/celegans/rawdata > > add the suffix .ace to each file in acedb:rawdata > > Have your mac about 60M of RAM (use virtual memory if necessary) > start acedb with 55M or so, get write access (password acedb) > and select Read .ace files from the acedb menu in the main window > click Open ace file, choose the first update file in the file parser > and click Read all. This may take a long time for some updates, > especially if you had to turn virtual memory on. > This will work ONLY AFTER you convert the UNIX line endings to Mac ones. There are many free programs to do this. If you don't have one, let me know and I'll put one on my FTP server. It is possible to eliminate a step by getting the tar.z files directly to your Mac and using a Mac program to un-Z and un-tar them. StuffIt Expander w/ DropStuff will do this quite nicely. David Grant dgrant@iastate.edu USDA-ARS and Iowa State University From owner-acedb@net.bio.net Sun Oct 13 23:00:00 1996 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: life beyond xv? Date: 13 Oct 1996 18:00:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <9610140100.AA11402@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Is there anything better than xv to call as a gif/jpg displayer from ACEDB? It would be nice to have a viewer that can show big images in a scrolling window instead of shrinking them to illegibility. - Dave From owner-acedb@net.bio.net Wed Oct 16 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news-peer.gsl.net!news.gsl.net!news.uoregon.edu!waikato!celebrian.otago.ac.nz!usenet From: Krishna Patel Newsgroups: bionet.software.acedb Subject: Dumping the ACEDB model Date: Thu, 17 Oct 1996 15:09:01 +1300 Organization: MBU, Dept of Biochemistry, Otago University, NZ Lines: 3 Message-ID: <3265953D.41C6@pandora.otago.ac.nz> NNTP-Posting-Host: pandora.otago.ac.nz Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V4.0 alpha) Can anyone please advise how to dump the ACEDB Model as either ascii text or an .ace file. Can this be done? Or is there a "Model file' hidden somewhere? From owner-acedb@net.bio.net Thu Oct 17 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!news.uoregon.edu!waikato!celebrian.otago.ac.nz!usenet From: Krishna Patel Newsgroups: bionet.software.acedb Subject: ER diagram for ACEDB or similar Date: Fri, 18 Oct 1996 15:03:58 +1300 Organization: MBU, Dept of Biochemistry, Otago University, NZ Lines: 13 Message-ID: <3266E58E.41C6@pandora.otago.ac.nz> NNTP-Posting-Host: pandora.otago.ac.nz Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V4.0 alpha) Thanks to all those who answered my novice question yesterday. Cheers! The ftp sites and FAQs make no mention of any entity/relationship diagrams for ACEDB or similar. I would find one really useful in helping to get me up to speed on ACEDB. If necessary I'll construct one myself, but I don't like re-inventing the wheel... :-) Has someone constructed an ER Diagram of ACEDB? Is such an ERD available somewhere? If so could someone please let me know. Thx. From owner-acedb@net.bio.net Thu Oct 17 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: aceserver solaris Date: 18 Oct 1996 14:36:59 +0100 Lines: 239 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <54815r$rdm@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk this is a solaris bug, htey have several versions of rpcgen, some of them bugged i do have a binary aceserver for solaris i ll add it to ncbi, but i hope it does not depend on the excat solaris machine the problem is: the rpc self generated code wrpc/rpcace_svc.c forks AFTERR establishing the pipe the rest of this message contained a correct file: wrpc/rpcace_svc.c to be substituted inside wrpc directory after rpcgen has run: make aceserver: this will call rpcgen and cretae the faulty rpcace_svc.c cp the fixed rpcace_svc.c: cp rpcace_svc.c.ok rpcace_svc.c touch rpcace_svc.c to garantee that mkake will not overwrite it make aceserver verify that make recompiles the new rpcace_svc.c and relinks and that after that rpcace_svc.c is still the fixed one ! If the server still does not work, let me know here is rpcace_svc.c.ok FOR SOLARIS machines ONLY /* * Please do not edit this file. * It was generated using rpcgen. */ #include "rpcace.h" #include #include /* getenv, exit */ #include #include #include #include #include #include /* rlimit */ #include #ifdef DEBUG #define RPC_SVC_FG #endif #define _RPCSVC_CLOSEDOWN 120 static int _rpcpmstart; /* Started by a port monitor ? */ /* States a server can be in wrt request */ #define _IDLE 0 #define _SERVED 1 #define _SERVING 2 static int _rpcsvcstate = _IDLE; /* Set when a request is serviced */ static void _msgout(msg) char *msg; { #ifdef RPC_SVC_FG if (_rpcpmstart) syslog(LOG_ERR, msg); else (void) fprintf(stderr, "%s\n", msg); #else syslog(LOG_ERR, msg); #endif } static void closedown(sig) int sig; { if (_rpcsvcstate == _IDLE) { extern fd_set svc_fdset; static int size; int i, openfd; struct t_info tinfo; if (!t_getinfo(0, &tinfo) && (tinfo.servtype == T_CLTS)) exit(0); if (size == 0) { struct rlimit rl; rl.rlim_max = 0; getrlimit(RLIMIT_NOFILE, &rl); if ((size = rl.rlim_max) == 0) { return; } } for (i = 0, openfd = 0; i < size && openfd < 2; i++) if (FD_ISSET(i, &svc_fdset)) openfd++; if (openfd <= 1) exit(0); } if (_rpcsvcstate == _SERVED) _rpcsvcstate = _IDLE; (void) signal(SIGALRM, (void(*)()) closedown); (void) alarm(_RPCSVC_CLOSEDOWN/2); } static void rpc_ace_1(rqstp, transp) struct svc_req *rqstp; register SVCXPRT *transp; { union { ace_data ace_server_1_arg; } argument; char *result; bool_t (*xdr_argument)(), (*xdr_result)(); char *(*local)(); _rpcsvcstate = _SERVING; switch (rqstp->rq_proc) { case NULLPROC: (void) svc_sendreply(transp, xdr_void, (char *)NULL); _rpcsvcstate = _SERVED; return; case ACE_SERVER: xdr_argument = xdr_ace_data; xdr_result = xdr_ace_reponse; local = (char *(*)()) ace_server_1; break; default: svcerr_noproc(transp); _rpcsvcstate = _SERVED; return; } (void) memset((char *)&argument, 0, sizeof (argument)); if (!svc_getargs(transp, xdr_argument, &argument)) { svcerr_decode(transp); _rpcsvcstate = _SERVED; return; } result = (*local)(&argument, rqstp); if (result != NULL && !svc_sendreply(transp, xdr_result, result)) { svcerr_systemerr(transp); } if (!svc_freeargs(transp, xdr_argument, &argument)) { _msgout("unable to free arguments"); exit(1); } _rpcsvcstate = _SERVED; return; } main() { pid_t pid; int i; char mname[FMNAMESZ + 1]; if (!ioctl(0, I_LOOK, mname) && (!strcmp(mname, "sockmod") || !strcmp(mname, "timod"))) { char *netid; struct netconfig *nconf = NULL; SVCXPRT *transp; int pmclose; _rpcpmstart = 1; openlog("rpcace", LOG_PID, LOG_DAEMON); if ((netid = getenv("NLSPROVIDER")) == NULL) { /* started from inetd */ pmclose = 1; } else { if ((nconf = getnetconfigent(netid)) == NULL) _msgout("cannot get transport info"); pmclose = (t_getstate(0) != T_DATAXFER); } if (strcmp(mname, "sockmod") == 0) { if (ioctl(0, I_POP, 0) || ioctl(0, I_PUSH, "timod")) { _msgout("could not get the right module"); exit(1); } } if ((transp = svc_tli_create(0, nconf, NULL, 0, 0)) == NULL) { _msgout("cannot create server handle"); exit(1); } if (nconf) freenetconfigent(nconf); if (!svc_reg(transp, RPC_ACE, RPC_ACE_VERS, rpc_ace_1, 0)) { _msgout("unable to register (RPC_ACE, RPC_ACE_VERS)."); exit(1); } if (pmclose) { (void) signal(SIGALRM, (void(*)()) closedown); (void) alarm(_RPCSVC_CLOSEDOWN/2); } svc_run(); exit(1); /* NOTREACHED */ } else { #ifndef RPC_SVC_FG int size; struct rlimit rl; pid = fork(); if (pid < 0) { perror("cannot fork"); exit(1); } if (pid) exit(0); rl.rlim_max = 0; getrlimit(RLIMIT_NOFILE, &rl); if ((size = rl.rlim_max) == 0) exit(1); for (i = 0; i < size; i++) (void) close(i); i = open("/dev/console", 2); (void) dup2(i, 1); (void) dup2(i, 2); setsid(); openlog("rpcace", LOG_PID, LOG_DAEMON); #endif } if (!svc_create(rpc_ace_1, RPC_ACE, RPC_ACE_VERS, "netpath")) { _msgout("unable to create (RPC_ACE, RPC_ACE_VERS) for netpath."); exit(1); } svc_run(); _msgout("svc_run returned"); exit(1); /* NOTREACHED */ } From owner-acedb@net.bio.net Thu Oct 17 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!newsfeed.ed.ac.uk!news From: "Stewart W. Morris" Newsgroups: bionet.software.acedb Subject: Re: life beyond xv? Date: Fri, 18 Oct 1996 14:15:35 +0100 Organization: MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK Lines: 11 Message-ID: <326782F6.167EB0E7@hgu.mrc.ac.uk> References: <9610140100.AA11402@greengenes.cit.cornell.edu> NNTP-Posting-Host: tomatin.hgu.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 4.1.3 sun4m) To: Dave Matthews Dave Matthews wrote: > > Is there anything better than xv to call as a gif/jpg displayer from ACEDB? > It would be nice to have a viewer that can show big images in a scrolling > window instead of shrinking them to illegibility. I use the ImageMagick package which allows scrolling within windows, a "moving magnifying glass" feature plus a host of other goodies. Use archie to find your nearest ftp site. - Stewart From owner-acedb@net.bio.net Thu Oct 17 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: jattwood@hgmp.mrc.ac.uk (Mr J. Attwood) Newsgroups: bionet.software.acedb Subject: Aceserver problems with Solaris 2.5.1 Date: 18 Oct 1996 13:21:25 +0100 Lines: 36 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <547so5$mi3@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Hi, Has anyone got the 4.3 aceserver to work under Solaris 2.5.1? I can get it to work in standalone mode but have hit major problems when trying to start it through inetd. There are obvious discrepancies between the installation instructions and Solaris 2.5.1 (no portmap, for example) so I'm wondering if the existing code won't run. Our entries in system files are as follows (not the same server as I'm posting this from):- /etc/rpc:- scw9db 20000114 rpc.acedbd /etc/services:- scw9db 20000114/tcp rpc.acedbd /etc/inetd.conf:- 20000114/1 stream rpc/tcp wait aceserv /usr/local/bin/rpc.acedbd rpc.acedbd /share1/packages/acedb/scw9db 20000114 600:600:0 It works perfectly in standalone mode but when I run aceclient and point it at port 20000114 we get a stalled copy of rpc.acedbd which is immediately replaced when it dies after 10 minutes, so that there is always a server process in existence. The client eventually reports that it cannot establish a connection and gives up. Every 10 or 20 minutes syslog reports:- svc_tp_create: Could not register prog 20000114 vers 1 on tcp and we have to reboot to get rid of the constantly restarted server process. We've tried entries in NIS versions of services and rpc, without the slightest effect, and have run out of ideas. Suggestions on what to try, or how to debug the situation, much appreciated. Thanks in advance, John Attwood (j.attwood@hgmp.mrc.ac.uk). From owner-acedb@net.bio.net Thu Oct 17 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: xv problem hanging xace Date: 18 Oct 1996 12:42:29 +0100 Lines: 7 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <547qf5$k7b@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk the script should have a & after the xv command to detach xv from teh calling process other wise at stop, xv returns probably an exit(1) which exits acedb or something like thsi From owner-acedb@net.bio.net Thu Oct 17 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!cssun.mathcs.emory.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: xv problem Date: 18 Oct 1996 09:28:37 GMT Organization: University of Georgia, Athens Lines: 25 Message-ID: <547ik5$bku@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi: I compiled acedb 4.3i (Solaris 2.5, gcc 2.7.2, no obvious compile problems). I have a model using "Pick_me_to_call", and the data for that model include a line "Pick_me_to_call xv filename". I have two questions: 1) xv works, but it seems as though ACEDB has exec'd it; that is, no other acedb activity is possible while the image is displaying, and more importantly acedb exits without messages after xv quits (quitting from xv's menu). 2) I tried "Pick_me_to_call scriptname arg", where "scriptname" is the name of a script in the "wscripts" directory, and the shell from which I invoked acedb reports that "scriptname" wasn't found, ie. acedb had not looked in the "wscripts" directory to find the script. I also saw this happen under earler 4_3 releases of acedb. Am I missing something? Thanks! -- Paul Brunk, former ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Thu Oct 17 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: er diagram Date: 18 Oct 1996 09:13:27 +0100 Lines: 21 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <547e77$6at@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk As I understand it, the file models.wrm in acedb is the functional equivalent, for an object oriented database, of the ER diagram of a relational db There is a difference, because objects are defined intrinsically, by their unique key, rather than virtually by content as in a relational db In addition, in the particular case of acedb, the unique key is expoartable as the string doublet (className:objectName) I beleive therefore that a classic ER diagram does not correctly describe the content of an OO database. Although it may be valuable for people used to this approach, it should always be considered as an approximation. Pleasae correct me if I am mistaken. Jean From owner-acedb@net.bio.net Thu Oct 17 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!newsfeed.internetmci.com!newshub.csu.net!newsserver.sdsc.edu!news.cerf.net!news From: "Eric E. Snyder" Newsgroups: bionet.software.acedb Subject: Re: ER diagram for ACEDB or similar Date: Thu, 17 Oct 1996 20:03:04 -0700 Organization: Sequana Therapeutics, Inc. Lines: 31 Message-ID: <3266F368.7818@sequana.com> References: <3266E58E.41C6@pandora.otago.ac.nz> NNTP-Posting-Host: 198.207.137.6 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b7Gold (X11; I; SunOS 5.5.1 sun4u) To: Krishna Patel Krishna Patel wrote: > > Thanks to all those who answered my novice question yesterday. Cheers! > > The ftp sites and FAQs make no mention of any entity/relationship > diagrams for ACEDB or similar. > > Has someone constructed an ER Diagram of ACEDB? Is such an ERD > available somewhere? If so could someone please let me know. I'll take a crack at this. Hopefully I understand the question correctly.... Although the usual ACEDB distribution contains a models.wrm which defines a "schema" for the database, it is really just a starting point. It can be changed easily; many variations exist. There are several versions available from the Sanger Centre web site which support different projects and databases. In other words, the ER diagram is totally dependent on the models used in the database. It would be interesting if there were a tool analogous to SilverRun for Sybase that would generate such a diagram, give a definition in the form of a models.wrm file. I haven't seen such a tool however. Maybe someone would like to write one-- I would use it! Eric E. Snyder, PhD Associate Director of Genome Analysis Sequana Therapeutics, Inc. 11099 North Torrey Pines Road, Suite 160 La Jolla, CA 92037, USA N 32 54'32" W 117 14'26" (619) 646-8279; (619) 452-6653 fax; eesnyder@sequana.com http://beagle.colorado.edu/~eesnyder From owner-acedb@net.bio.net Sun Oct 20 23:00:00 1996 Path: biosci!GDB.ORG!beth From: beth@GDB.ORG (Beth Gatewood) Newsgroups: bionet.software.acedb Subject: help in loading the c. elegans data Date: 21 Oct 1996 06:57:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610211357.JAA04239@corndog.gdb.org> NNTP-Posting-Host: net.bio.net Hi- I have installed ACEDB 4.3 (solaris version) on my Sun station (running SunOs 5.5). I obtained update files update.WSI.4.1-4.20 and placed these into the rawdata directory. Upon attempting to add all update files, an error message appears that update 4.1 is not found. Should I be loading 4.1 files or do I need to edit something? Thank you in advance for any help- Beth Gatewood From owner-acedb@net.bio.net Mon Oct 21 23:00:00 1996 From: "Spenser Barlow" Subject: Watson and Crick in 96 High School Fund Raiser Newsgroups: bionet.software.acedb,dna.chat,dna.support Message-ID: <01bbc052$2d8bab80$263040ce@sbarlow> X-Newsreader: Microsoft Internet News 4.70.1155 NNTP-Posting-Host: 206.64.48.38 Date: 22 Oct 96 07:55:40 GMT Lines: 222 Path: biosci!rutgers!uwm.edu!nntp.primenet.com!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!in1.uu.net!news.accessone.com!news.localaccess.com! ---WATSON & CRICK in '96--- Note: This is an advertisement for a HILARIOUS and MOCKING T-shirt. The cost is $15, and we have approximately 75 T-shirts left. SO ORDER SOON! The money is being raised to fund a high-school biotechnology class in Centralia, WA, so this is a worthwhile cause. If you are interested read on. If you are not interested, read on - this ad is quite funny. In case you don't trust us to send you a T-shirt after we receive your money, we welcome you to call us at (360) 736-2146 or E-mail us at docdna@localaccess.com. If that still does not satisfy your fears, I have no idea what you can do and, therefore, you should probably not order from us. ATTENTION: All Molecular Biologists w/money, Geneticists w/money, Biochemists w/money, Microbiologists w/money, Biologists w/money, Science Teachers w/money, Teachers w/money, Biology Students w/money, Students w/money, General Public interested in Genetics w/money, General Public w/money, Dogs of the above people w/money, Goldfish of the above people w/money, Small Furry Animals named Ralph w/money, Small Furry Animals not named Ralph w/money, etc. I think you get the picture. We do not care who you are - just that you have money. In otherwords, we want your money. Now, a logical and sane human being might say NO to sending money to complete strangers. However, we know most BIOLOGISTS and CHEMISTS are NOT SANE. Still, just so you don't look like a fool when your friends ask you why you are sending off $15 dollars to people you don't know, we WILL send you a stylish t-shirt so you can gloat in those doubting Thomas' faces. The Shirt features a blue and red field separated by a white double-helix. On the top red field Watson is emblazoned and on the bottom blue field Crick is labeled. A white "96" is positioned on the right side of the double-helix which stops the helix from reaching the far right side of the T-shirt. See .jpg file attachment. HOW TO ORDER: To order, send a SASE w/check or cash to the order of $18.00 ($15 + $3 shipping) to: Henri Weeks 919 W. Reynolds Ave. Centralia, WA 98531 Option #2: We can ship the shirt COD (check or money order). Write, call, or e-mail us to initiate shipping. All checks must be made out to Henri Weeks. You should receive your order just as soon as the US Mail service or UPS can get it to you. Thank-you for you time. By sbarlow@localaccess.com begin 600 W&C96.jpg M_]C_X `02D9)1@`!`0$!+ $L``#_VP!#``$!`0$!`0$!`0$!`0$!`0$!`0$! M`0$!`0$!`0$!`0$!`0$!`0("`0$"`0$!`@("`@("`@("`0("`@("`@("`@+_ MVP!#`0$!`0$!`0$!`0$"`0$!`@("`@("`@("`@("`@("`@("`@("`@("`@(" M`@("`@("`@("`@("`@("`@("`@("`@+_P `1" `X`$L#`2(``A$!`Q$!_\0` M'P```04!`0$!`0$```````````$"`P0%!@<("0H+_\0`M1 ``@$#`P($`P4% M! 0```%]`0(#``01!1(A,4$&$U%A!R)Q%#*!D:$((T*QP152T? D,V)R@@D* M%A<8&1HE)B7J#A(6&AXB)BI*3E)66EYB9FJ*CI*6FIZBIJK*SM+6VM[BYNL+#Q,7& MQ\C)RM+3U-76U]C9VN'BX^3EYN?HZ>KQ\O/T]?;W^/GZ_\0`'P$``P$!`0$! M`0$!`0````````$"`P0%!@<("0H+_\0`M1$``@$"! 0#! <%! 0``0)W``$" M`Q$$!2$Q!A)!40=A<1,B,H$(%$*1H;'!"2,S4O 58G+1"A8D-.$E\1<8&1HF M)R@I*C4V-S@Y.D-$149'2$E*4U155E=865IC9&5F9VAI:G-T=79W>'EZ@H.$ MA8:'B(F*DI.4E9:7F)F:HJ.DI::GJ*FJLK.TM;:WN+FZPL/$Q<;'R,G*TM/4 MU=;7V-G:XN/DY>;GZ.GJ\O/T]?;W^/GZ_]H`# ,!``(1`Q$`/P#8\.+X8\7? 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M%8-$WBWP;K9!#.#GB23[[=S\"_VI/A7\'-.LO%>L_L=_!_XK_M+?#^W@;X _ MM%>*O%GCW2A\+M8T^*]7POXN\8_!;2+P^%_CEXO\,2:A/<>$K_6X+:?2+B*T M%\^KV^GZ;;VOQQ=75W?7-S?7UY=WU]>W$]W>WU[-=7=Y>W=S*\US=W=U-,SW M-U+.[O)([,[N[,Y+$FOR_P"C1]'7Q1ROQ.S+#^,O#6'H>'7@5P[B>!."*RQ, M,1//2Y74IU8TY3K4:SC%2A4C"L364J$/A!XZT32-5UF^MO WB+XC/;FT\$^(;?1 M_&/C/1XY=3$5J]KU7 M2-)\`?#;]G[XF>#OC'X;T721?$^)/&OQ9^*?A.^NO#VA:>UBD5MHNDV&HW>I MW4^HOJ&HG2[*P\O4/CB7[]O_`-=Y/_9ZW-<_Y#VI?[EC_P"DPK^O^#?!J'AS MQ#Q76X,XKQ.4<(\;9YBN)\9D[PV%JQI9MBZE"681P.,E%5<-EN98B"Q6,P4J M=:I&O4Q"P>*PE*LZ4>*=7VTH49Q5TE24E_(J3FFT[IRBFXJ5TK)-IM'[\_\` M!>?XN_!GXSV?_!/2\^#'QF^$_P`6X?A+^R!X5^"WQ#C^'/CSP_XGN?"WCWPU M%ILFH:??V&FW`F_LUE,JPWT<)LY&MI(UE20(C?H!XB_;]_9S_9TTO_@WG^)U MC\:?A=\29?V+O!_C+X9B9](CM58/'O#9<54TO98>E6S'#\6Y7G>3YA1Q$XQ<:7LL'G^.6 M'G0C&2JQP]2HIJG.%46/FW[>,%&6*E3O9NT7"TDU?>[@D[WNFUI?3]ZO^"FW M[-W[)/A3]LG7/CU^S]^W%^SO\8_"_P"TU^T%HGQ-\ ?#WX?>*8=5U7X:6WCW MQ=%XP^)&I_'#Q;<72:+\-?!^F:E?72:3]HU";5;^+4(FN-,L+>QN[A_Z"_VF M_P#@H%^Q3^U[^T+^VY^Q9\:/VHO@)>_L1_M&?LJ_#KQ=\&_CG:>-O!L^E?"C M]HSP%JDFB30-)$5NYO$L^J2^'-7BCG667[+X%2&(_8;Z<1?P+W/^OC_[`ND_ M^F^&LJ+_`(]5_P"NL7_HUJ\;B?Z&F7\<9/X9X?BSQ4SG.,_\*,KK9=DV7$QJ3E%N3B^523B[MMQE[25TFDK1LE9W^F?''QB^.WA;X('\$?#[Q-I>H_"?QEXNM=0!A\:#5M MXF^(6F>=;PWFCMJV[]?*;..G7\!T"GJ/\`>;_T Original-To: acedb@dl.ac.uk Thanks to all who replied on this. Jean Thierry-Mieg sent me a replacement for rpcace_svc.c as many Solaris rpcgen programs produce buggy code, and this seems to work perfectly once it was compiled and linked into the aceserver binary. It seems that the version generated by rpcgen establishes the pipe before forking, and this was what was causing it to restart whenever it timed out and died. The fixed version responds to client requests and dies as it should after 10 minutes. Next step the Perl aceclient.... John. From owner-acedb@net.bio.net Tue Oct 29 22:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!news.sprintlink.net!news-peer.sprintlink.net!newsfeed.internetmci.com!mr.net!newshub.tc.umn.edu!fu-berlin.de!cs.tu-berlin.de!uni-erlangen.de!lrz-muenchen.de!ipp-garching.mpg.de!usenet From: feichtin@alf.biochem.mpg.de (Richard Feichtinger) Newsgroups: bionet.celegans,bionet.software.acedb Subject: Re: macace update again Date: 28 Oct 1996 18:04:25 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 16 Sender: -Not-Authenticated-[2621] Message-ID: <552sj9$5jbe@sat.ipp-garching.mpg.de> References: <5303ll$5ks9@sat.ipp-garching.mpg.de> NNTP-Posting-Host: macwurm.biochem.mpg.de X-Posted-From: InterNews 1.0.8@macwurm.biochem.mpg.de Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.celegans:1127 bionet.software.acedb:1011 Please note that I changed the site for the macace update macace.WS1.4-20.sea.bin to ftp.biochem.mpg.de/mac/acedb There are obviously also updates available on the well known and unchanged servers ncbi.nlm.nih.gov/repository/acedb/macace and ftp.sanger.ac.uk/pub/acedb/macace Richard Feichtinger feichtin@alf.biochem.mpg.de From owner-acedb@net.bio.net Thu Oct 31 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Nov 1996 02:00:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199611011000.CAA01584@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net