From owner-acedb@net.bio.net Mon Mar 04 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!ra.nrl.navy.mil!news.math.psu.edu!psuvax1!uwm.edu!chi-news.cic.net!nntp.coast.net!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.informatik.uni-stuttgart.de!news From: baumann@habakuk.informatik.uni-stuttgart.de (Joachim Baumann) Newsgroups: bionet.software.acedb Subject: TextConvert Version 1.3 Date: 05 Mar 1996 15:31:10 +0100 Organization: IPVR, University of Stuttgart, Germany Lines: 40 Sender: baumann@habakuk.informatik.uni-stuttgart.de Message-ID: NNTP-Posting-Host: habakuk.informatik.uni-stuttgart.de X-Newsreader: Gnus v5.1 Hi all, it's more or less a year since the last release of TextConvert (version 1.2). A few minor bugs are removed, and functionality for manipulating the splitting strategy has been added. Here is the overview: TextConvert is a program that takes as input a description file in a format that resembles the format of AWK-scripts, reads a data stream and produces another data stream according to patterns and attached code, so called actions, in the description file. The patterns can be formed according to Perl's regular expressions, and the actions are formulated as Perl source code enriched with additional commands to ease the conversion of text-based data. The additional commands support the ACEDB [ACEDB] format. The current version can be ftp'ed from ftp://ftp.informatik.uni-stuttgart.de/pub/DART/TextConvert/ The name of the archive is textconvert-1.3.tar.gz I also placed the HTML version of the documentation into the same directory: ftp://ftp.informatik.uni-stuttgart.de/pub/DART/TextConvert/TextConvert.html One remark to the maintainer of the FAQ. In the FAQ the wrong address for the ftp-server is given. Could you please be so friendly to change this? Happy Converting, Joachim ------------------------------------------------------------------------------- Snail: Joachim Baumann, | Room: 2.172 Universitaet Stuttgart, IPVR, | Phone: (+49 | 0 ) 711/7816-218 Breitwiesenstr. 20-22, | Fax: (+49 | 0 ) 711/7816-424 70565 Stuttgart, Germany | EMail: joachim.baumann@informatik.uni-stuttgart.de(.sol_3.milky-way.universe) PGP: finger baumann@orgel.informatik.uni-stuttgart.de From owner-acedb@net.bio.net Sat Mar 09 22:00:00 1996 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: purified seg-fault data Date: 9 Mar 1996 16:08:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: <9603100004.AA12933@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Hi Richard, Jean, I'm having trouble with segmentation faults while loading ace4_1 from rawdata/.ace files. This has been going on for a few weeks now, ever since I set up a copy of the database on a Solaris machine that I reinitialize and reload every night via tace. Since it always fails on only one of my 115 rawdata files I thought it might be some error in the file, so I've been trying to isolate the problem. Now that I've purified it I think my file is innocent, but maybe some of the observations I've made would be helpful to you. The problem file ("p.ace") is about 90 kbytes. The crash always occurs at the same point in p.ace, unless I've made changes in other files that are loaded prior to it. Here is the record that crashes it under one set of conditions: Locus : "alpha-Amy-D2" Chromosome 7D Chromosome_arm 7DL I.e. if I delete everything in the file after this point (about 60% of it), it still crashes. If I remove this whole record there is no crash, and in addition the entire p.ace can then be loaded in the next tace session with no crash. Removing just one or both of the data values, Chromosome 7D Chromosome_arm 7DL gives an intermediate result: there is no immediate crash but loading the whole p.ace in the next session crashes. The Locus object "alpha-Amy-D2" does not already exist in the database at the time this is loaded. Both tags, Chromosome and Chromosome_arm are ?Text. I notice that if I query "find text 7d" I get an error ">?Text should be followed by at least 3 characters". Could this be part of the problem? In the completely loaded database there are 233 "7D"s and 88 "7DL"s. No error is reported by tace in log.wrm. tace's exit $status is always -2147483637. The problem seems to be the same on two different Solaris machines. I just tested under SunOS and got a seg-fault in a different file instead. A weirdness: After I've loaded all 115 files (with p.ace duly crashing), I can then load it with no problem. But if I try to load it immediately after it has crashed it only crashes again. ... Hmm, maybe my file wasn't so innocent after all. I just changed those two tags from ?Text to Text and reinitialized. No crash!! So should I change all my ?Texts to Texts? - Dave From owner-acedb@net.bio.net Sun Mar 10 22:00:00 1996 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: purified seg-fault data Date: 11 Mar 1996 08:23:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <9603111619.AA15361@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > Please import from ncbi repository/acedb/ace4.3.test > and try agin Yes, that fixes my problem. After changing my model back from Text to ?Text, tace 4.3 loads everything without crashing. Thanks! - Dave From owner-acedb@net.bio.net Sun Mar 10 22:00:00 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: Re: purified seg-fault data Date: 11 Mar 1996 04:10:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9603111205.AA14763@alpha.crbm.cnrs-mop.fr> NNTP-Posting-Host: net.bio.net I beleive you may be encountering a bug that we fixed very recently ?Text is an object, the n.th one creates and expansion of the table which provoked a dangling pointer in very rare occasions Please import from ncbi repository/acedb/ace4.3.test and try agin i can provide the binary if needed From owner-acedb@net.bio.net Sun Mar 10 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!ra.nrl.navy.mil!news.math.psu.edu!chi-news.cic.net!news.uiowa.edu!news.physics.uiowa.edu!newsrelay.iastate.edu!news.iastate.edu!macgrant.agron.iastate.edu!user From: dgrant@iastate.edu (David Grant) Newsgroups: bionet.software.acedb Subject: displaying images in MacACE solved Date: 11 Mar 1996 16:25:38 GMT Organization: Iowa State University Lines: 110 Message-ID: NNTP-Posting-Host: macgrant.agron.iastate.edu Colleagues, this was originally posted a few days ago but at least one site did not get it - I'm reposting in case it was missing at other sites also DG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A while back I posted a message asking how to get MacACE to display images the way the UNIX versions of ACeDB would. No one had an answer then but after some poking around I have found a method that works. The biggest problem I had was that although the images distributed with MacACeDB 4-1b1 are labeled as JPEGs, they are actually PICTs. Only PICTs will work with MacACE. I discovered this for myself but later found that the images distributed with MacAAtDB_3-6 are correctly labeled as PICT. The PICT images must be in a folder named 'pictures' in the same folder as MacACE, and the database and wspec folders. This is in contrast to our UNIX ACeDB where the GIF files were stored in a folder named 'externalFiles'. I altered our models.wrm and options.wrm to change 'Image' to 'Picture' to match MacACeDB. Later I found that 'Image' is used in MacAAtDB so the exact name is apparently not important. The 'Picture' line in my options.wrm was lifted verbatum from the MacACeDB file. The equivalent line in MacAAtDB is somewhat different though I don't know the significance of the differences. All of our *.ace files that used the tag 'Image' were modified to use 'Picture'. I left in the 'Pick_me_to_call' line although I am fairly certain it is not needed. The following shows the before and after versions of my *.wrm files. original SoyBase UNIX version in options.wrm _VImage -H in displays.wrm _DDtImage -g TEXT_FULL_SCROLL -t "Image" -width .6 -height .4 -help Image in models.wrm ?Image Probe ?Probe XREF Image Locus ?Locus XREF Image Pathology ?Pathology XREF Image Gene ?Gene XREF Image Pick_me_to_call UNIQUE Text Text ... ... ... Last_update UNIQUE Text ?Gene Name Gene_class UNIQUE ?Gene_Class XREF Gene Correct_name ?Gene XREF Other_name Other_name ?Gene XREF Other_name Image ?Image XREF Gene ... ... ... Last_update UNIQUE Text Macintosh SoyBase version in options.wrm _VImage -H _VPicture -H -D DtImage (this line added) in displays.wrm (unchanged from UNIX original) _DDtImage -g TEXT_FULL_SCROLL -t "Image" -width .6 -height .4 -help Image in models.wrm (all instances of 'Image' in the other classes also changed to 'Picture') ?Picture Probe ?Probe XREF Picture Locus ?Locus XREF Picture Pathology ?Pathology XREF Picture Gene ?Gene XREF Picture Pick_me_to_call UNIQUE Text Text ... ... ... Last_update UNIQUE Text ?Gene Name Gene_class UNIQUE ?Gene_Class XREF Gene Correct_name ?Gene XREF Other_name Other_name ?Gene XREF Other_name Picture ?Picture XREF Gene ... ... ... Last_update UNIQUE Text I make no claims to being a MacACE expert and it is possible that some of the changes I made are unneeded. I would be glad to hear from anyone who understands ACeDB better than I as to what the changes I made are doing and which, if any, should be reversed or modified. -- David Grant dgrant@iastate.edu (515) 294-1205 From owner-acedb@net.bio.net Mon Mar 11 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: 4.3test Date: 11 Mar 1996 12:09:45 -0000 Lines: 3 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4i1569$3ue@mserv1.dl.ac.uk> Original-To: leon@eatworms.swmed.edu would you be kind enough to import and try ncbi acedb/ace4.3test the loading of aliases should be MUCH faster and all teh usual stuff From owner-acedb@net.bio.net Mon Mar 11 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: 4.3 Date: 11 Mar 1996 12:10:16 -0000 Lines: 3 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4i1578$3vc@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk correct address is ftp://ncbi.nlm.nih.gov/repository/acedb/ace4.3.test source code is there and some binaries i can make more binaries if you need them From owner-acedb@net.bio.net Mon Mar 11 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Mark Blaxter Newsgroups: bionet.software.acedb Subject: Parasite Genome Computer Scientist Position - First Advertisement Date: 12 Mar 1996 14:24:42 -0000 Lines: 43 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4i41fa$h2n@mserv1.dl.ac.uk> X-Sender: mbx@festival.ed.ac.uk Original-To: acedb@dl.ac.uk the University of Edinburgh in collaboration with the University of Cambridge and the European Bioinformatics Institute ____________________________________________________________________ The Parasite Genome Initiatives Database Computer/Bioinformatics Scientist ____________________________________________________________________ Global collaborative initiatives are under way to study five of the major human parasites (causing leishmaniasis, sleeping sickness, Chagas' disease, filariasis and schistosomaiasis) at the genome level. Physical mapping, cDNA sequencing and genome sequencing projects are well advanced. We are seeking a motivated computer/bioinformatics scientist to construct and maintain central genome databases for all five projects, and to design www/internet interfaces to allow worldwide online access to them. Applicants should have experience in some or all of the following: PERL, biological sequence data analysis, WWW site management & ACEDB. The appointee will be based at the European Bioinformatics Institute (EBI) at the Wellcome Trust Genome Campus, Hinxton, near Cambridge, UK (a site which the EBI shares with the Sanger Centre and the Medical Research Council's Genome Project Resource Centre). There may be opportunities for travel to other non-UK Parasite Genome labs. The position, funded by the World Health Organisation initially for one year, is available immediately at a salary level of up to =A317,466 (RA1A grade point 5, AD grade point 2) depending on age and status. The position will remain open until a suitable applicant is found, but we would like to appoint as soon as is possible. ___________________________________________________________________ Please phone or email Mark Blaxter to ask for more information NOW. = =20 +44 131 650 6760 Mark.Blaxter@ed.ac.uk =20 Mark Blaxter, ICAPB, Ashworth Labs, King's Buildings, University of Edinburgh, Scotland EH9 3JT=20 __________________________________________________________________ From owner-acedb@net.bio.net Sun Mar 17 22:00:00 1996 Path: biosci!agate!howland.reston.ans.net!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 Mar 1996 14:10:07 GMT Organization: University of Georgia, Athens Lines: 14 Message-ID: <4ijqrv$2dt@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi folks: I've had this problem under release 4.2 and 4.3, no modifications to distributed source code. If an object has a tag "Pick_me_to_call xv filename", xv will be invoked, but when the user quits xv, the whole xace quits with a core dump. Solaris 2.4, gcc 2.7. -- Paul Brunk, former ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Tue Mar 19 22:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news From: pd@mole.bio.cam.ac.uk (Phil Davey) Newsgroups: bionet.software.acedb Subject: How to view .ace file? Date: 20 Mar 1996 15:02:01 GMT Organization: University of Cambridge, England Lines: 15 Message-ID: <4ip6l9$1fj@lyra.csx.cam.ac.uk> Reply-To: pd@mole.bio.cam.ac.uk NNTP-Posting-Host: nab.path.cam.ac.uk Hello, I have installed acedb 4.1 on a Solaris machine and it works ok, in that I can view the human X chromosome map, following the instructions that came with it. The problem is, I have a .ace file (only) which I want to look at. I've tried following the instructions as for the X map, but it didn't work. It wants a model file as well, which I haven't got. So is there any way to view a .ace file by itself? Thanks for any help, Phil [E-mail pd@mole.bio.cam.ac.uk] From owner-acedb@net.bio.net Thu Mar 21 22:00:00 1996 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: fixed: extra, empty tags in acedumps Date: 21 Mar 1996 16:02:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <9603212359.AA17865@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net On Thu Nov 2 13:58:08 1995 I said: > I'm seeing some unwanted extra stuff in my acedumps, apparently related to > the timestamping. For example, the empty tags Authority and Data_source in > this record: > > // data dumped from tree display > > Probe : "AC1" > General_remark "Repeat sequences (TG)18" > General_remark "Product size 157 in Geneva PI505819" > Authority "Blake, Tom" > Authority > Authority "Sorrells, Mark E." > Data_source "Blake, Tom" "95.08.24" > Data_source > Data_source "Sorrells, Mark E." "95.09.13" This is fixed in ace4_3c. Grazie! A warning though, that being fixed causes kind of a mess in acediff updates from the old to the new, which come out like this: Probe : "AC1" -D Authority -D Data_source - Dave From owner-acedb@net.bio.net Thu Mar 21 22:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!jussieu.fr!univ-lille1.fr!cict.fr!news From: CORNILLOT Newsgroups: bionet.software.acedb Subject: Problem with class ?Grid Date: 22 Mar 1996 15:44:28 GMT Lines: 6 Message-ID: <4iuhss$g20@news.cict.fr> NNTP-Posting-Host: biohp.insa-tlse.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; HP-UX A.09.01 9000/715) X-URL: news:bionet.software.acedb I'm working on ACEDB 4.1 and I'm trying to use objects of the class ?Grid. But I obtain the message "Textbounds called on invalid graph type 2" I don't understand... where is my mistake? E_mail: cornillo@biohp.insa-tlse.fr From owner-acedb@net.bio.net Thu Mar 21 22:00:00 1996 Path: biosci!rutgers!gatech!europa.chnt.gtegsc.com!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!sgigate.sgi.com!nntp.coast.net!fu-berlin.de!rag2.rz-berlin.mpg.DE!leser From: Ulf Leser Newsgroups: bionet.software.acedb Subject: Re: How to view .ace file? Date: Fri, 22 Mar 1996 18:05:37 +0100 Organization: MPI: "Molekulare Genetik", Berlin, Dahlem Lines: 37 Message-ID: <3152DDE1.167E@mpimg-berlin-dahlem.mpg.de> References: <4ip6l9$1fj@lyra.csx.cam.ac.uk> NNTP-Posting-Host: rag2.rz-berlin.mpg.de (141.14.130.102) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-User: leser X-Access: 16 25 816 X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.0 alpha) Phil Davey wrote: > > Hello, > > I have installed acedb 4.1 on a Solaris machine and it works ok, in that I can > view the human X chromosome map, following the instructions that came with it. > > The problem is, I have a .ace file (only) which I want to look at. > I've tried following the instructions as for the X map, but it didn't work. > It wants a model file as well, which I haven't got. > > So is there any way to view a .ace file by itself? > > Thanks for any help, > Phil > [E-mail pd@mole.bio.cam.ac.uk] Hello Davey, I assume that you are speaking of the dataset that is provided by the MPI fuer Molekulare Genetik in Berlin, because I saw you on our registration-list. Well, I'm one of the guys managing it. So, in principle a .ace-file is a plain-text-file, so you can look it it with any arbitrary text-viewer or editor like more,less,cat (UNIS), type,word (DOS) etc. You'll see all the INFORMATION it contains in a quite raw format. Reading it into your ACEDB-database might be much more difficult. To do that, that actual data-structure of your database and the model the .ace-file is based on MUST match. If they don't, it can be a nightmare of work. I wrote a small perl-program which analyses a .ace-file and prints out something like they model that was used to create it - it's not perfect, but I could send it to you if you want. Hope it helps, Ulf From owner-acedb@net.bio.net Tue Mar 26 22:00:00 1996 Path: biosci!biosci!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb,bionet.microbiology Subject: MycDB 4-12 Date: 26 Mar 1996 19:58:06 -0800 Organization: Biochemistry, KTH, Stockholm Lines: 120 Sender: daemon@net.bio.net Distribution: world Message-ID: <4j940o$d51@sibirien.physchem.kth.se> NNTP-Posting-Host: net.bio.net Summary: New release Keywords: mycobacteria, ACEDB Xref: biosci bionet.software.acedb:873 bionet.microbiology:5472 MycDB 4-12 Stockholm & Paris March 26, 1996 The 12th release of the Mycobacterium database, MycDB, is now available. MycDB is funded by the WHO and the Fondation Raoul Follereau and is maintained jointly by the Unite de Genetique Moleculaire Bacterienne at the Institut Pasteur in Paris, France and the Department of Biochemistry at The Royal Institute of Technology in Stockholm, Sweden. MycDB is available free of charge via Internet network transfer. A complete description of the procedure to retrieve and install the software and database is available through the Internet. MycDB is also available through the WorldWideWeb servers at the Royal Institute of Technology (URL: http://www.biochem.kth.se/MycDB.html) and (through the good offices of the Genome Informatics Group at the National Agricultural Library) on the Agricultural Genome Information Server, AGIS, in Beltsville, Maryland, USA (WorldWideWeb - URL: http://probe.nalusda.gov:8300/other/index.html or gopher - URL: gopher://probe.nalusda.gov:7000/11/genome.databases/mycdb/). Be aware that it may take some time for the update to reach NAL. MycDB uses the excellent database software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg (CNRS, France). The ACEDB software allows the user to browse information by simply pointing and clicking with the workstation mouse. A variety of powerful query methods are also available. However, our experience is that most users choose the mouse interface to find the information they are interested in. As far as possible all information is connected to other information in the database. The database software presents the information in separate windows that allow many parts of the database to be viewed at one time. There are also many paths to any piece of information, allowing the user to easily navigate the connections between the various types of information. This release comes as three files, thus the jump in release numbers. New in release 4-12: * Support for ace3 is discontinued as of this release. If you are absolutely unable to upgrade to ace4, contact Staffan. * The DraI/AsnI map of M. tuberculosis H37Rv. from Wolfgang Phillip and Stewart Cole, is now included. Locus positions will follow in a later release. * Annotation of the M. leprae cosmid sequences is somewhat more developed. All cosmid sequences now have the blastx matches against SwissProt included. These data are used for assigning function to orfs. The cosmids B26, B27, B32, B50, B650, B912, B937, B983, B1133, B1229 and BL308 have had their annotation updated. Two cosmid sequences have been added, B1770 and B1846. * The number of sequences have increased due to the breaking out of the peptide sequence data into separate objects (in general called 'xxx_pepXX', where xxx is the nucleotide sequence it is derived from and XX is a counter). These as yet contain very little data, often only the accession number for the NCBI gene index database and/or the DDBJ/EMBL/GenBank PID accession numbers. The breaking out of these is in preparation for a major model change, the implementation of a Protein class with its own display. * The amount of sequence data is now: 9971 Sequence objects, of which 769 contain nucleotide sequences (DNA objects). Of these, 212 come from the M. tuberculosis/M. bovis cluster (total 366,773 nt), 55 from M. leprae (total 1,678,065 nt) and 43 from M. smegmatis (63,711 nt). Total amount of sequence is 2,528,147 nt, an increase of 12.9% since last release. The coverage of EMBL/GenBank is current up to March 17. There are 2194 Peptide sequences, of which slightly more than half are from mycobacteria (the rest are blastx hits from SwissProt). * There are 238 new Papers from MedLine, current up to March 8. * The webserver has gone through a complete overhaul and now has clickable images and a greatly improved query interface. (This was actually done in January, but no announcement has been made). * We now have a mirror site for the files at the University of British Columbia, thanks to Yossef Av-Gay. For information on earlier releases, see the file MycDB.4-9.Release.txt at the ftp sites. The database currently requires a Unix workstation running X-Windows or a Macintosh. A variety of precompiled versions of the ACEDB database software are available through anonymous ftp. See the file MycDB.Retrieval for more info. If you have any questions, problems or comments please contact us, via e-mail, fax, mail or telephone. If you are impatient and are already familiar with internet/ftp, all relevant information can be found at * the WWW server at the Department of Biochemistry, KTH: http://www.biochem.kth.se/MycDB.html * the ftp server at the Department of Biochemistry, KTH: ftp.biochem.kth.se (130.237.52.64) in pub/MycDB * the ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in pub/MycDB * the mirror site at the Weizmann Institute in Israel (thanks Jaime!): bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb * or the mirror site at the Microbiology Dept., University of British Columbia in Canada (thanks Yossef!): cod.microbiology.ubc.ca (137.82.165.101) in pub/MycDB The file MycDB.Retrieval.txt describes in more detail the database system requirements, network retrieval procedures for obtaining the database and methods of obtaining future updates. For more information contact Staffan Bergh or Stewart Cole. Staffan Bergh Biochemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden Email: staffan@biochem.kth.se Fax: (46 8) 24 54 52 Voice: (46 8) 790 9230 Stewart Cole Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris Cedex 15, France Email: stcole@pasteur.fr Fax: (33 1) 45.68.85.93 Voice: (33 1) 45.68.84.46 From owner-acedb@net.bio.net Thu Mar 28 22:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!in1.uu.net!fu-berlin.de!rag2.rz-berlin.mpg.DE!leser From: Ulf Leser Newsgroups: bionet.software.acedb Subject: Annoucement: A X-chromosome YAC ACeDB-database Date: Fri, 29 Mar 1996 18:29:10 +0100 Organization: MPI: "Molekulare Genetik", Berlin, Dahlem Lines: 51 Message-ID: <315C1DE6.41C6@mpimg-berlin-dahlem.mpg.de> NNTP-Posting-Host: rag2.rz-berlin.mpg.de (141.14.130.102) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-User: leser X-Access: 16 25 816 X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.0 alpha) Max-Planck-Institut fuer Molekulare Genetik ANNOUNCEMENT An X chromosome YAC map - IXDB release 1.0 - The X chromosome YAC map constructed at the ICRF Genome Analysis lab (London) and later at the Max-Planck-Institut fr Molekulare Genetik (Berlin) is now available. Approximately 125 Mb are covered (80 %) in 25 contigs, and include 906 YAC clones. The data is stored and graphically displayed in an acedb database (version 4.0) named IXDB release 1.0. To facilitate the integration and comparison with other maps from the X chromosome community, we have kept the same scale and banding pattern as for the consensus map constructed at the last X chromosome workshop. To access the data, simply connect to http://www.mpimg-berlin-dahlem.mpg.de/~xteam using a World Wide Web browser. Follow the instructions to first install the acedb program on your local computer, and then download the X chromosome data from our server. The database contains results from about 2000 hybridisations, 972 gel fingerprints of Alu-PCR products and 172 FISH mapping experiments. We strongly encourage you to also download the X chromosome subset of the Integrated Genome Database (IGD), fully compatible with our dataset. This will enable you to merge the experimental YAC mapping data with information from GDB, OMIM, EMBL, RLDB, and other genome related databases in a single step. Dept. H. Lehrach Max-Planck-Institut fr Molekulare Genetik Ihnestrasse 73 14195 Berlin Germany _____________________________________________________________________ Hugues Roest Crollius Tel: +49 30 8413 1612 Abt. Lehrach FAX: +49 30 8413 1380 Max-Planck-Institut fur Molekulare Genetik Ihnestrasse 73 14195 Berlin Germany e-mail: roest@mpimg-berlin-dahlem.mpg.de _____________________________________________________________________ From owner-acedb@net.bio.net Sat Mar 30 22:00:00 1996 Path: biosci!dkfz-heidelberg.de!O.Ritter From: O.Ritter@dkfz-heidelberg.de (Otto Ritter) Newsgroups: bionet.software.acedb Subject: ace'96 meeting not at DKFZ Date: 30 Mar 1996 17:25:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <199603310119.DAA22734@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net Dear colleagues and friends, We discussed several possibilities with Richard and Jean and the conclusion is that DKFZ will not organise the ace'96 meeting. Best regards, Otto Ritter DKFZ Heidelberg From owner-acedb@net.bio.net Sun Mar 31 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 1 Apr 1996 02:21:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 149 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604011000.CAA13215@net.bio.net> NNTP-Posting-Host: net.bio.net I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We have three sponsors to date with a couple more pending. The process is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we hope to have new and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. 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. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Statistics are for the four week period from 22 Jan. - 18 Feb. 1996 and usage continues to grow. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5000 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 600 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. ----------------------------------------------------------------------