From owner-acedb@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!nihs.nihs.go.jp!taka From: taka@nihs.nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: give me informations Date: 2 Sep 1994 03:40:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409021038.AA19006@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net I have two quetions. I will be happy if anyone give me any information about my questions. 1. I am working on producing new database using the ACEDB program. It includes the data of cell signalling molecules and their mutual interactions. Then, I would like to know if anyone has already made any kind of database like this , for example metabolic reactions etc . I would like to contact them if possible. 2. I got source files of ACEDB , and I noticed that there was fetch program in wscripts directory. Can I use fetch through ACEDB ? If so, I wish to use that facility. Thank you very much for your attention to this mail. Takako Igarashi National Institute of Health Sciences taka@nihs.nihs.go.jp From owner-acedb@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!uunet!Germany.EU.net!nntp.gmd.de!dearn! barilvm!vms.huji.ac.il!wisipc.weizmann.ac.il!inherit4.weizmann.ac.il! lsprilus Newsgroups: bionet.software.acedb Subject: compiling ace 3.3 Message-ID: <1994Sep3.191947.18774@wisipc.weizmann.ac.il> From: Jaime Prilusky Date: Sat, 3 Sep 1994 19:19:47 GMT Sender: news@wisipc.weizmann.ac.il (News User) Organization: Weizmann Institute of Science X-Xxmessage-Id: X-Xxdate: Sat, 3 Sep 1994 19:17:11 GMT X-Newsreader: Nuntius Version 1.2 Lines: 17 Hi, I am still with problems compiling version 3.3. I keep getting the following link error message: ld: Undefined symbol _XtStrings _XtShellStrings As far as I know, I am using the correct X11R5 libraries. Are those routines needed ? Is there a way to make the link without asking for those routines? Thanks in advance, Dr Jaime Prilusky, Head Bioinformatics Unit ! LSPRILUS@WEIZMANN.WEIZMANN.AC.IL Weizmann Institute of Science ! fax: 972-8-344113 76100 Rehovot - Israel ! tel: 972-8-343456 From owner-acedb@net.bio.net Sun Sep 04 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!psgrain!quagga.ru.ac.za!ucthpx!medix.mmi.uct.ac.za!root From: root@medix.mmi.uct.ac.za (root) Newsgroups: bionet.software.acedb Subject: Linux and AceDB Date: 5 Sep 1994 14:30:03 GMT Organization: University of Cape Town Lines: 59 Message-ID: <34fa1d$jcp@ucthpx.uct.ac.za> NNTP-Posting-Host: 137.158.133.97 X-Newsreader: TIN [version 1.2 PL2] In article <344o6p$aj5@kiev.physchem.kth.se> you wrote: : Hi : can anyone help with this? I don't have any experience with Linux : at all, and I don't think we have any users currently using Linux. : You can email me and I'll pass it on. : TIA /staffan (staffan@biochem.kth.se) : =================================== : Dear Staffan, : I, Tanmay Banerjee, would like your help in installing : MycDB software running under Linux on PC-386. I am working with Dr. Indira : Ghosh, who spoke to you regarding MycDB software on her last visit to : Stockholm. Here are certain points on which I would like your comments: : : 1. We have not been able to get a Xwindow working with colour. We ran the : 2. Can you tell us how to use tvga9000 instead of VGAmono? : 3. Can you provide us the name & e-mail of a person, who is using MycDB on : PC-386 under Linux ? : Hi I'm trying to get AceDb to work on LINUX (on a 386). Thanks to some help from Richard Durbin, I have been able (so-far) to get it partially working. To get the source to compile for version 3_0, there are two functions in w4/session.c that have to be commented out - the error messages will tell you where :). For source 3_3, there are 2 lines that have to be moved out of a commented section in w7/fmapcontrol.c (as far as I remember), but again the errors will say where. Also for acedb3.3 a script file in wscripts/Mosaic must be edited to point to your copy of Mosaic. The software works well in that I can follow various links through the database. The problem I am having is that as soon as I choose a DNA sequence related link, AceDB crashes with a 'floating exception' error??? If I run the text version of AceDB, when I 'model DNA' it says to the effect that cannot show model {strange characters and garbage}. Hopefully Richard will be able to help again ... As far as the problems Tanmay is having, they are probably better suited to comp.os.linux.help. I struggled a bit to get the setup correct, but the samples that came with Slackware 2.0 proved useful. For my Xconfig file, RGBPath points to /usr/X386/lib/X11/rgb and rgb is NOT a directory, but in /usr/X386/lib/X11 there is a file rgb.txt. The answer to question 2, also lies in setting up Xconfig correctly. Are you using a generic SVGA library? Its a bit of a fiddle to get the mode set up... I went through various options and samples as documented in the files in /usr/X11/etc. To answer question 3, you can contact me (Brendan Babb) at the following locations: bbabb@medmicro.uct.ac.za root@medix.mmi.uct.ac.za Hopefully we'll get AceDB working properly on LINUX soon :) Cheers Brendan From owner-acedb@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!agate!gmrubin5.berkeley.edu!user From: sly@fly2.berkeley.edu (Cyrus Harmon) Newsgroups: bionet.software.acedb Subject: Re: compiling ace 3.3 Date: Wed, 07 Sep 1994 10:47:47 -0700 Organization: UC Berkeley Lines: 20 Distribution: bionet Message-ID: References: <34k5nd$oeo@mserv1.dl.ac.uk> NNTP-Posting-Host: gmrubin5.berkeley.edu > ld: Undefined symbol > _XtStrings > _XtShellStrings > > As far as I know, I am using the correct X11R5 libraries. > Are those routines needed ? > > Dr Jaime Prilusky, Head I too have encountered this same problem. I fixed it, though, and can't remember exactly what I did. My hunch is that you are not actually using the correct X11R5 libraries. Make sure that your $PATH is set up to look at the right libraries first. Even if you have the right in your path, if the old ones show up first, they will be used. If this doesn't solve the problem, make sure you are using a good version of make. -Cyrus Harmon sly@fly2.berkeley.edu From owner-acedb@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!CS.Arizona.EDU!uunet!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: compiling ace 3.3 Date: 7 Sep 1994 11:47:09 +0100 Lines: 23 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34k5nd$oeo@mserv1.dl.ac.uk> Original-To: lsprilus@weizmann.weizmann.ac.il i don t have a clue about this problem Prilusky cannot link ace.3.3 becasue he gets: ld: Undefined symbol _XtStrings _XtShellStrings As far as I know, I am using the correct X11R5 libraries. Are those routines needed ? Is there a way to make the link without asking for those routines? Thanks in advance, Dr Jaime Prilusky, Head Bioinformatics Unit ! LSPRILUS@WEIZMANN.WEIZMANN.AC.IL Weizmann Institute of Science ! fax: 972-8-344113 76100 Rehovot - Israel ! tel: 972-8-343456 i don t suppose this is related to 3.3 in particular way hints welcom jean From owner-acedb@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!dog.ee.lbl.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 7 Sep 1994 20:45:02 GMT Organization: Dendrome, A genome database for forest trees Lines: 1099 Approved: news-answers-request@MIT.Edu Message-ID: <34l8oe$rld@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.pswfs.gov Summary: Frequently Asked Questions about finding and getting started with the database system ACEDB. ACEDB is used to collect information regarding the molecular biology of the genome. Xref: biosci bionet.software.acedb:403 news.answers:22755 Archive-name: acedb-faq Last-modified: 9/7/94 Version: 1.14 ---------------------------------------------------------------------- Common Questions, with Answers, about ACEDB. Q0: What is ACEDB? Q1: What is the current version of ACEDB? Q2: What hardware/software do I need to run ACEDB? Q3: Where can I get ACEDB? Q4: !What ACEDB databases exist? Q5: What written documentation exists for ACEDB? Q6: Where can I find further information about ACEDB? Q7: How should ACEDB be cited? Q8: Is ACEDB object-oriented? Q9: What's all this about Gopher|WAIS|ftp|WWW|URL ... Q10: How can I get on/off the ACEDB announcements mailing list? Q11: When and where is the next ACEDB Workshop? Q411: Who prepared this document & where is the current version? Questions marked with + are new, those with ! have substantially changed answers. ---------------------------------------------------------------------- Q0: What is ACEDB? A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [see Q4]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the European integrated Genome Project. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage -missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions ---------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: [This answer refers to the software not the C. elegans data.] Currently there are two threads of the ACEDB kernel: the 2.x series which represents the C. elegans project under the tutelage of Richard Durbin, and the 3.x series from Jean Thierry-Mieg. However, the differences in the code are slight and the two authors committed to a single kernel at the ACEDB workshop in July, 1994. The most recent release is an experimental version 3.3 which is available from the repositories. A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q10. Return to List of Questions ---------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: Unix and X11: Sun/SunOS 4.x Sun/Solaris DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series PC 386/486 with Linux (free Unix) [note from Jeff Bryer, jbryer@darwin.mbb.sfu.ca] I just installed up Linux yesterday and today spent the many hours to compile in the C. elegans data for ACEDB v2.0 So to save other people the trouble of doing the same the entire package ACEDB for Linux 2-10 is available on trog.mbb.sfu.ca in /pub/acedb as linux.2_10.tar.Z The data was compiled in on a 486DX-33 with 16MBs of RAM running Linux 1.1.18 (Slackware 2.0.0 distribution) and a 32MB swap device (and it chugged away for a couple hours chewing up all 16MBs and half the swap space). File size is about 73MBs uncompressed, 26MBs compressed. This is based on the ACEDB v2.0 port for Linux that Ken Clark (ken@darwin.mbb.sfu.ca) did. There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu MSDOS/Windows/NT: A port to NT is rumored to be in the works. Macintosh: [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a decent color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. To retrieve the software see Q3. For cost savings, a combination of a high-end Intel platform with Linux appears very attractive. [Though the port does not seem robust, yet --bks] Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems SPARCstation II, and users can interact using Macintoshes and PC-clones by using X11 implementations for the personal computers and a LAN. X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions ---------------------------------------------------------------------- Q3: Where can I get ACEDB? A3: All the files are available in the following public access accounts (anonymous ftp sites) accessible via Internet: lirmm.lirmm.fr (193.49.104.10) in pub/acedb cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb (version 1-10 is available in repository/aatdb) bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb. MacAce is available from: genome.lbl.gov (131.243.224.80) in pub/macace cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb/macace Linux; ACEDB version 2.0 for Linux 2-10: trog.mbb.sfu.ca /pub/acedb as linux.2_10.tar.Z A typical session would be: ftp ncbi.nlm.nih.gov login: anonymous password: your email address cd repository/acedb/ace3 binary ls get README_3 get NOTES get INSTALL get bin.sparc.3.0.tar.Z quit Return to List of Questions ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alphabetic order by Database name. Curators, submit changes as new paragraphs.--bks] Database : AAnDB-1.0 Species : Aspergillus nidulans PI : Leland Ellis Last_update : February 1994 ACEDB_version : 3.0 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : AAtDB Species : Arabidopsis thaliana Current version : 3-3 Last_update : June 1994 Curator : John Morris Contact : curator@frodo.mgh.harvard.edu Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x Availability : Macintosh version in /aatdb/MacAAtDB directory URL : gopher://weeds.mgh.harvard.edu/ URL : http://weeds.mgh.harvard.edu:80/index.html Database : ABtDB-1.0 Species : Bovine, Bos taurus ACEDB_version : 3.0 extended PI : Leland Ellis Last_update : February 1994 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : AboutDB Curator : Staffan Bergh PI : Staffan Bergh Subject : ACEDB itself (Is this meta-meta-metadata) ACEDB 3.0 Contact : staffan@biochem.kth.se URL http://kiev.physchem.kth.se/AboutDB.html Database : ACeDB Species : Caenorhabditis elegans Current version: 2-10 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@mrc-lmb.cam.ac.uk Contact : mieg@kaa.crbm.cnrs-mop.fr Last_update : May 1994 DataBase : AceMap Species : Homo sapiens (Mus musculus under development) Focus : Physical mapping of human chromsome X and 21 ACEDB_version : 3.0 Curator : Hugues Roest Crollius PI : Hans Lehrach Availability : beta release of the X chr. data/models by anonymous ftp to ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap. Get the README file in the directory above. Contact : hrc@gea.lif.icnet.uk (Hugues Roest Crollius) ICRF, Lincoln's Inn Fields London, UK. Last_update : August 94 Database : ace11 Species : Homo sapiens Focus : Physical mapping of chromosome 11 Availability : under development Curator : Benedict Arnold PI : Peter Little Contact : Benedict Arnold Dept. Biochemistry, Imperial College, London, SW7 2AZ b.arnold@ic.ac.uk Database : AGsDB A Genus species Database Species : Aspergillus nidulans Species : Neurospora crassa Species : cow w/ human anchor loci Species : cotton (demo) Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast PI : Leland Ellis Curator : Leland Ellis Last_update : March 1994 ACeDB_version : 3.0 (beta still), with extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe) yeast); interacting loci via defined Interactions for each locus Models : as of 3.13.94 Data : as of 3.13.94 Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux (ducoux@moulon.inra.fr). URL : http://keck.tamu.edu/ibt.html Contact : leland@straylight.tamu.edu Database : ChlamyDB Species : Chlamydomonas PI : Elizabeth Harris Contact : mps2@acpub.duke.edu Curator : Maulin P. Shah Availability : Under development (Est. Sept. 94) Last_update : 30 Sept. 1993 Database : CottonDB Species : Gossypium hirsutum (cotton) PI : Russell J. Kohel USDA-ARS Southern Crops Research Laboratory Route 5, Box 805, College Station, Texas 77845 Curator : Gerard R. Lazo Curator : Sridhar Madhavan Last_update : July, 1994 ACEDB_version : 3.0 Contact : rjk0339@zeus.tamu.edu (Russell Kohel) Contact : lazo@genome.tamu.edu (Gerard Lazo) Availability : still under construction Phone : 409-260-9311 Fax : 409-260-9333 Database : CSNDB Focus : Cell Signalling Molecules and Interactions Contact : Takako Igarashi National Insitute of Health Sciences Division of Chem-Bio Informatics Setagaya-ku, Tokyo, Japan 158 taka@nihs.go.jp Database : EcoDB Species : E. coli PI : Staffan Bergh Contact : staffan@biochem.kth.se Availability : Still under construction Last_update : Aug. 1994 Database : FlyBace Species : Drosophila melanogaster Availability : gopher or gopher+ ftp.bio.indiana.edu Availability : ACeDB-style interface to SyBase server due by end of 1994 Curator : Edward Welbourne Contact : eddy@gen.cam.ac.uk Contact : flybase@morgan.harvard.edu PI : William Gelbart PI : Michael Ashburner PI : Thomas Kaufman PI : Kathy Matthews PI : John Merriam [Curator_note : This is part of FlyBase project, hope to clear up my conceptual problems with Flybase vs. FlyBace in the next FAQ. --bks] Database : FlyBase [Curator_note : See FlyBace --bks] Database : Flydb Species : Drosophila melanogaster Curator : Suzanna Lewis Contact : suzi@fly2.berkeley.edu Database : GrainGenes Species : Wheat, barley, oats, relatives Availability : Anonymous ftp from probe.nalusda.gov:pub/grains Availability : Gopher greengenes.cit.cornell.edu port 70 Availability : Gopher probe.nalusda.gov port 7002 Curator : David E. Matthews PI : Olin D. Anderson Contact : matthews@greengenes.cit.cornell.edu Contact : oandersn@wheat.usda.gov URL : gopher://greengenes.cit.cornell.edu/1/ Data_version : 1.3 Released : 12 Jan 1994 Based_on : acedb.1-10 Availability : See following WWW URL URL : http://probe.nalusda.gov:8000/acedbs/acedbs/graingenes/index.html Last_update : Feb. 1994 Database : human.c17 Species : Homo sapiens Availability : the database is under development Contact : lsprilus@weizmann.weizmann.ac.il Focus : mapping & sequencing of Human Chromosome 17 Based_on: acedb.3-0 Last_update : Jan. 1994 Database : IGD - the Integrated Genomic Database Species : Homo sapiens (later mouse and other mammalian species) Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter [ o.ritter@dkfz-heidelberg.de ] Curator : tba Description : IGD - the Integrated Genomic Database - aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie_paule Lefranc Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr Database : Maize Species : Zea mays L. ssp. mays Focus : Maize genome Acedb_version : 1.9 FTP : probe.nalusda.gov, pub directory; anonymous ftp Comment : Maize is an acedb front end for the Maize Genome Database, MaizeDB, a SYBASE database. Comment : MaizeDB is updated daily and has WWW connectivity to external databases: GenBank (loci, alleles and probes), SwissProt (gene products) and the E. coli Stock Center (loci). Data : Major data categories: 4522 mapped loci (located to chromosome or better) including 684 mapped genes and 1423 mapped probed sites (gene candidates); 982 probes; 1850 map scores; 1533 gel patterns (Probe/Enzyme/Stock); 4231 stocks; 5105 Variations (alleles, DNA polymorphisms, rearrangements, etc); 465 phenotypes; 223 traits; 547 gene products; 5314 bibliographic references; 1979 persons with addresses. Gopher : host = teosinte.agron.missouri.edu, port = 70 Telnet : telnet teosinte.agron.missouri.edu login as guest, use password 'corncob' HTTP : http://teosinte.agron.missouri/top.html HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant Genome Database Comment : Genera is a software toolkit for creating and extracting data from Sybase databases; used to create MaizeDB and Worldwide Web connectivity. HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu Curator : Pat Byrne byrne@teosinte.agron.missouri.edu Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu Curator : Mary Polacco maryp@teosinte.agron.missouri.edu Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Curator : Christiane Fauron FAURON@GENE1.med.utah.edu Curator : Carolyn Wetzel cmwetzel@iastate.edu Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU Design : Stan Letovsky letovsky-stan@CS.YALE.EDU Design : Mary Berlyn mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 25 April 1994 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. PI : Staffan Bergh PI : Stewart Cole PI : Doug Smith Curator : Staffan Bergh Contact : staffan@biochem.kth.se Last_update : Apr. 1994 WWW : http://kiev.physchem.kth.se/MycDB.html WWW : http://kiev.physchem.kth.se/MycDB.html ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb Database : PomBase Curator : Sean Walsh Curator : Marie-Adele Rajendream PI : Bart Barrell Species : Schizosaccharomyces pombe Contact : svw@sanger.ac.uk Contact : barrell@sanger.ac.uk Comment : Not yet available for distribution Database : RiceGenes Species : Rice (O. sativa) Availability : Anonymous ftp from probe.nalusda.gov:pub/rice Availability : Gopher nightshade.cit.cornell.edu port 70 Availability : Gopher probe.nalusda.gov port 7007 Curator : Edie Paul PI : Susah McCouch Contact : epaul@nightshade.cit.cornell.edu Release : ACEDB 1-10 Last_update : May 1994 Database : SacchDB Species : Saccharomyces cerevisiae Focus : Budding Yeast Genome Acedb_version : 2.0, MacAce FTP : genome-ftp.stanford.edu, not available yet. Comment : The database is in beta test by a small number of yeast labs. The WWW-ACEDB gateway version is currently available, see HTTP below. The Gopher server contains only the Olson restriction map information and views of the resulting Clone (Physical) Map. Data : Olson/Riles Physical Map, Mortimer Genetic Maps and Information, Sequences from GenBank, Gene/Clone associations using the Wash Univ. prime clone filters. Gopher : host = genome-gopher.stanford.edu, port = 70 HTTP : URL http://genome-www.stanford.edu Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Fred Dietrich, dietrich@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Systems : Dan Mosedale, mosedale@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Last_update : 9 August 1994 Database : SolGenes Coverage: Solanaceae - tomato, potato, pepper Availability : Anonymous ftp from probe.nalusda.gov:pub/solgenes Availability : Gopher nightshade.cit.cornell.edu port 71 Availability : Gopher probe.nalusda.gov port 7006 Curator : Edie Paul PI : Steve Tanksley Contact : epaul@nightshade.cit.cornell.edu Release : ACEDB 3.0 Last_update : May 1994 Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz USDA-ARS Dept. of Soil & Crop Sciences Texas A&M University College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 E_mail : schertz@tamvm1.tamu.edu Curator : Najeeb U. Siddiqui Southern Crop Improvement Facility Crop Biotechnology Center Texas A&M University College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 E_mail : nus6389@tamsun.tamu.edu Last_update : July 1994 ACEDB_version : 3.0 Availability : Under Development Database : SoyBase Species : Soybeans Curator : Lisa Lorenzen PI : Randy Shoemaker Contact : lorenzen@mendel.agron.iastate.edu Phone : 515-294-0421 Fax : 515-294-2299 Last_update : Sept. 1993 Database : Sybace Species : Homo sapiens Creator : Detlef Wolf Comment : Custom software --ACEDB front-end to SYBASE data Contact : D.Wolf@dfkz-heidelberg.de See_also : IGD Database : TreeGenes Species : Forest trees Availability : alpha, contact curator ACEDB_version : 1-10 Curator : Bradley K. Sherman PI : David B. Neale Contact : Dendrome@s27w007.pswfs.gov Contact : bks@s27w007.pswfs.gov Contact : dbn@s27w007.pswfs.gov Last_update : March 1994 URL : gopher://s27w007.pswfs.gov/ URL : http://s27w007.pswfs.gov/ URL : ftp://probe.nalusda.gov/pub/trees Database : 21Bdb Species : Homo sapiens Focus : STS content mapping & sequencing of Human Chromosome 21 Availability : by request, via ftp, world-wide-web Based_on : acedb.1-10 plus moulon server URL : ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z URL : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy Contact : DFDavy@lbl.gov Contact : aggarwal@genome.lbl.gov Focus : STS content mapping & sequencing of Human Chromosome 21 PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng Last_update : Apr. 1994 Database : 22ace Species : Homo sapiens Curator : Ian Dunham Focus : Physical mapping of chromosome 22 PI : Ian Dunham Contact : Ian Dunham Sanger Centre Hinxton Hall, Cambs. UK. id1@sanger.ac.uk Database : VoxPop Species : Populus spp. Availability : contact curator Curator : Carl G. Riches PI : Reinhard F. Stettler Contact : cgr@poplar1.cfr.washington.edu Contact : STETTLER@coyote.cfr.washington.edu Last_update : Sept. 1993 Database : Xace Species : Homo sapiens Curator : Gareth Maslen Focus : Physical mapping of chromosome X PI : David Bentley Contact : Gareth Maslen Sanger Centre Hinxton Hall, Cambs. UK. glm@sanger.ac.uk Database : ? Species : Homo sapiens Focus : Physical mapping of human chromosome 6. Curator : Ioannis Ragoussis Availability : Unknown Contact : Guy's hospital Database : ? PI : Scott Chasalow Species : Potato Contact : Scottish Crop Institute, Dundee Last_update : Sept. 1993 Database : ? PI : George Murphy PI : David Flanders Species : Arabidopsis thaliana Contact : John Innes Center, Norwich, England Last_update : Sept. 1993 Database : ? Species : Homo Sapiens Focus : Physical and linkage mapping of chromosome 8 Availability : Curator : Stephen Wood PI : Stephen Wood Contact : Stephen Wood Dept. Medical Genetics University of B. C. Vancouver, B. C. Canada swood@unixg.ubc.cq Return to List of Questions ---------------------------------------------------------------------- Q5: What written documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000. Primary documents from the developers are: acedb -- A C. elegans Database: I. Users' Guide. acedb -- A C. elegans Database: II. Installation Guide. acedb -- A C. elegans Database: III. Configuration Guide. Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z And ftp://weeds.mgh.harvard.edu/acedb_doc The files are in tex and postscript. [I have had some difficulty printing these. Jean Thierry-Mieg suggests latex xxxx.tex, dvi2ps xxxx.dvi > xxxx.ps, lpr xxxx.ps.] You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angisturte.ps and angistute.hqx available by anonymous ftp at ncbi.hih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Return to List of Questions ---------------------------------------------------------------------- Q6: Where can I find further information about ACEDB? A6: There is a Usenet/Biosci conference titled bionet.software.acedb. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. Mike Cherry has set up an ACEDB Developer's archive. For anonymous ftp use the hostname weeds.mgh.harvard.edu and look in the acedb_dev directory. If you wish to contribute you can put files in the incoming directory. Send a message to Mike (cherry@genome.stanford.edu) that you have put something in that directory then Mike will move it out for general access. For gopher you can connect to weeds.mgh.harvard.edu (132.183.190.21) and ... --> N. FTP Archives for Molecular Biology/ then --> M. ACEDB Developer's archive/ [N and M are integers which are subject to change.] The bionet.software. acedb.conference is archived and can be searched using WAIS. Here is a Gopher-style link to the WAIS archive. (This is also courtesy of Mike Cherry.): # Type=7 Name=ACEDB BioSci Electronic Conference Path=7/.index/acedb-biosci Host=genome-gopher.stanford.edu Port=70 The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: http://moulon.inra.fr/acedb/acedb.html for C. elegans data http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html http://moulon.inra.fr/acedb_conf.html (en francais) The Genome Computing Group, Lawrence Berkeley Laboratory has an anonymous ftp service at machine genome.lbl.gov (131.243.224.80) which contains: flydb - LBL's Drosophila Acedb-style database 21bdb - LBL's Human Chromosome 21 Acedb-style database querdb - LBL's query-language extensions to Acedb metadata - LBL's compendium of Acedb database schema variants macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to dataabases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier Jean Thierry-Mieg et al), and the Interated Genome Database project in Heidelburg (Otto Ritter, Detlef Wolf et al). Return to List of Questions ---------------------------------------------------------------------- Q7: How should ACEDB be cited? A7: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit, available by Anonymous FTP from ... Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions ---------------------------------------------------------------------- Q8: Is ACEDB object-oriented? A8: From the ACEDB User's Guide. A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions ---------------------------------------------------------------------- Q9: What's all this about Gopher/WAIS/ftp/WWW ... A9: These terms all refer to Internet protocols. An excellent introduction to the Internet is: _The Whole Internet User's Guide & Catalog_, by Ed Krol, O'Reilly & Associates, 1992. Or ask your system administrator to provide you with a gopher client or mosaic client and begin navigating on your own. URL is a Universal Resource Locator on the World-Wide Web (WWW). There are many free Internet browsers available that allow you to use an Internet connection and a URL to access services. Mosaic may be the most popular and it is available for Mac, PC or Unix via anonymous ftp from ftp.ncsa.uiuc.edu. Return to List of Questions ---------------------------------------------------------------------- Q10: How can I get on/off the ACEDB announcements mailing list? A10: To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb is on the mailing list. Return to List of Questions ---------------------------------------------------------------------- Q11: When and where is the Next ACEDB Workshop? In planning, California 1995. If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers taken by Mike Cherry with the camera on an SGI workstation, the URL is: http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html. John Morris has provided some more at URL: http://weeds.mgh.harvard.edu/ace94/ace94.image.html. Return to List of Questions ---------------------------------------------------------------------- Q411:Who prepared this document & where is the current version? [Note to international readers: 411 is the phone number for information in the USA. --bks] This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. Answer 3 demonstrates a sample FTP session. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html http://s27w007.pswfs.gov/Homepage/acedbfaq.html Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov Major contributions in getting this FAQ off the ground were made by John McCarthy and Mike Cherry. Other contributors include: Lisa Lorenzen David Matthews Edie Paul Donn Davy Eric De Mund Sam Cartinhour Please cite as: Sherman, Bradley K. (1994) "ACEDB Genome Database FAQ." Usenet news.answers. Available via Universal Resource Locators ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq and http://probe.nalusda.gov:8000/acedocs/acedbfaq.html. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome Research Program. --bks Return to List of Questions ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!gatech!cs.utk.edu!stc06.CTD.ORNL.GOV!druid!ptv From: ptv@druid.epm.ornl.gov (Sergey Petrov) Newsgroups: bionet.software.acedb Subject: more fun compiling ace 3.3 Date: 7 Sep 1994 19:54:27 GMT Organization: Oak Ridge National Lab/CESAR Lines: 32 Distribution: world Message-ID: <34l5pj$r7c@stc06.CTD.ORNL.GOV> References: Reply-To: ptv@druid.epm.ornl.gov NNTP-Posting-Host: druid.epm.ornl.gov In article 0709941047470001@gmrubin5.berkeley.edu, sly@fly2.berkeley.edu (Cyrus Harmon) writes: >> ld: Undefined symbol >> _XtStrings >> _XtShellStrings >> >> As far as I know, I am using the correct X11R5 libraries. >> Are those routines needed ? >> >> Dr Jaime Prilusky, Head > >I too have encountered this same problem. I fixed it, though, and can't remember >exactly what I did. My hunch is that you are not actually using the correct >X11R5 libraries. Make sure that your $PATH is set up to look at the right >libraries >first. Even if you have the right in your path, if the old ones show up >first, they >will be used. If this doesn't solve the problem, make sure you are using a good >version of make. > >-Cyrus Harmon >sly@fly2.berkeley.edu I have a *better* problem: ld: Undefined symbol ___main as a result of an attempt to compile acedb. Does anybody know what does it mean? Sergey Petrov From owner-acedb@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!emory!cs.utk.edu!stc06.CTD.ORNL.GOV!druid!ptv From: ptv@druid.epm.ornl.gov (Sergey Petrov) Newsgroups: bionet.software.acedb Subject: Re: more fun compiling ace 3.3 Date: 7 Sep 1994 22:56:35 GMT Organization: Oak Ridge National Lab/CESAR Lines: 13 Distribution: world Message-ID: <34lgf3$etd@stc06.CTD.ORNL.GOV> References: <34l5pj$r7c@stc06.CTD.ORNL.GOV> Reply-To: ptv@druid.epm.ornl.gov NNTP-Posting-Host: druid.epm.ornl.gov I solved the problem with 'Undefined.. ___main' just by loading a fresh version 3.3 (I believe, I solved it). Now, with the new version: 1. 'mktime': I needed to replace it by 'timelocal' 2. declaration of 'ctime' : conflict with 'time.h' 3. : ld: Undefined symbol _fMapTraceDestroy _fMapShowVirtualMultiTrace Sergey Petrov From owner-acedb@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!EU.net!news.kreonet.re.kr!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: ACEDB Genome Database Software FAQ Date: 7 Sep 1994 21:32:29 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 22 Message-ID: <34lbhd$s2j@overload.lbl.gov> References: <34l8oe$rld@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov The answer to question 4 in the ACEDB FAQ which lists the manifold and multiplex ACEDB databases, is intended to be self-policing. If you don't like the paragraph that describes your ACEDB, please send me a better one. I cannot speak for Staffan Berg, but I'm sure that he'd like to hear from you about AboutDB. We will try to keep the FAQ and AboutDB in sync, but ... The FAQ (and its curator) are getting too fat. We are going on a diet this month. I will be doing some editing of the October version to try to get it back under 50K bytes. --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 Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!uunet!psinntp!barilvm!vms.huji.ac.il!wisipc.weizmann.ac.il!inherit4.weizmann.ac.il! lsprilus Newsgroups: bionet.software.acedb Subject: solved: compiling ace 3.3 Message-ID: <1994Sep7.174127.5259@wisipc.weizmann.ac.il> From: Jaime Prilusky Date: Wed, 7 Sep 1994 17:41:27 GMT Sender: news@wisipc.weizmann.ac.il (News User) References: <1994Sep3.191947.18774@wisipc.weizmann.ac.il> Organization: Weizmann Institute of Science X-Xxmessage-Id: X-Xxdate: Wed, 7 Sep 1994 17:40:03 GMT X-Newsreader: Nuntius Version 1.2 Lines: 13 > I don t have a clue about this problem > ld: Undefined symbol > _XtStrings > _XtShellStrings Thank you to all of you that tried to find a solution to our compiling problem. I finally succeed in compiling ace 3.3 by taking a fresh X11R5 library. Dr Jaime Prilusky, Head Bioinformatics Unit ! LSPRILUS@WEIZMANN.WEIZMANN.AC.IL Weizmann Institute of Science ! fax: 972-8-344113 76100 Rehovot - Israel ! tel: 972-8-343456 From owner-acedb@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!sdd.hp.com!spool.mu.edu!howland.reston.ans.net!gatech!cs.utk.edu!stc06.CTD.ORNL.GOV!druid!ptv From: ptv@druid.epm.ornl.gov (Sergey Petrov) Newsgroups: bionet.software.acedb Subject: Re: more fun compiling ace 3.3 Date: 8 Sep 1994 18:10:08 GMT Organization: Oak Ridge National Lab/CESAR Lines: 18 Distribution: world Message-ID: <34nk20$juu@stc06.CTD.ORNL.GOV> References: <34lgf3$etd@stc06.CTD.ORNL.GOV> Reply-To: ptv@druid.epm.ornl.gov NNTP-Posting-Host: druid.epm.ornl.gov I'm sorry to mention to the community the trivial problem: > ld: Undefined symbol > _fMapTraceDestroy > _fMapShowVirtualMultiTrace > It is easy to avoid just commenting out these two functions in 'fmapcontrol.c' and 'fmap.h'. They both have zero c code. I found no other problems in ACEDB3.3 compiling Thank you for help, Sergey Petrov From owner-acedb@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: database on NFS Date: 9 Sep 1994 07:33:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409091433.AA17252@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net Hi, did you also experience this: if the database directory is on an NFS-mounted file system and the NFS-server machine has high load than the ACEDB process goes into an eternal disk wait. This was between SunOS -- SunOS, SunOS -- DEC alpha, SunOS -- (some mainframe NFS server) moral: run the ACEDB process on a CPU local to the database disk. From owner-acedb@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: tags numbers gone Date: 9 Sep 1994 16:38:57 +0100 Lines: 4 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34pvih$oea@mserv1.dl.ac.uk> Original-To: net@cnusc.fr i just finished a version where tags and class hard nubers and completelly gone it is now under test, i will sip it around soon From owner-acedb@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!cs.utk.edu!stc06.CTD.ORNL.GOV!druid!ptv From: ptv@druid.epm.ornl.gov (Sergey Petrov) Newsgroups: bionet.software.acedb Subject: crush Date: 12 Sep 1994 14:57:42 GMT Organization: Oak Ridge National Lab/CESAR Lines: 10 Distribution: world Message-ID: <351q96$6j5@stc06.CTD.ORNL.GOV> Reply-To: ptv@druid.epm.ornl.gov NNTP-Posting-Host: druid.epm.ornl.gov Keywords: gmapdisplay.c I tried to use c21 data with 3.3 ACEDB. Any attempt to view a map crashes the system. Fault address: (413) look->lastTrueSeg = arrayMax(look->segs) ; in 'gmapdisp.c.' I'll appreciate any hints. Sergey Petrov From owner-acedb@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: lock Date: 12 Sep 1994 08:04:17 +0100 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <350uhh$etr@mserv1.dl.ac.uk> Original-To: net@cnusc.fr the suggestion of henry: to remove the lock can be done now via NO_LOCK sorry NOLOCK as a one line entry in passwd.wrm but this seems dangerous in onther ways since without locks you may screw the system in multiple environmenet removing the lock is not, i think, a good solution but a good way to test. jean From owner-acedb@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: database on NFS Date: 12 Sep 1994 03:30:11 GMT Organization: University of California, Berkeley Lines: 29 Distribution: world Message-ID: References: <199409091433.AA17252@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: D.Wolf@dkfz-heidelberg.de's message of 9 Sep 1994 07:33:20 -0700 In article <199409091433.AA17252@cvx12.inet.dkfz-heidelberg.de> D.Wolf@dkfz-heidelberg.de (Detlef Wolf) writes: >Hi, >did you also experience this: >if the database directory is on an NFS-mounted file system >and the NFS-server machine has high load than the ACEDB process >goes into an eternal disk wait. >This was between SunOS -- SunOS, >SunOS -- DEC alpha, SunOS -- (some mainframe NFS server) >moral: run the ACEDB process on a CPU local to the database disk. This is doubtlessly my fault. Try it again without TRUST_LOCKD defined (if this constant is still in the 3.3 make, otherwise make the switch from the F_SETLK fcntl manually), and see if it doesn't crap out. If that clears it up (at some loss of distributed performance), then the code will need to be reworked to distrust the remote lockd daemon. I neglected to test for high loading against the vendors supplied daemon, but I'm not with the project anymore, and so can only wish you'll the best of luck here. -- Henry J. Cobb hcobb@fly2.berkeley.edu All items Copyright (c) 1994, by their respective authors, permission is granted to redistribute as long as proper credit is given. From owner-acedb@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!xmission!u.cc.utah.edu!not-for-mail From: kr5205@u.cc.utah.edu (Kerry Rowe) Newsgroups: bionet.software.acedb Subject: general questions about acedb Date: 13 Sep 1994 11:05:42 -0600 Organization: University of Utah Computer Center, Salt Lake City, Ut. Lines: 35 Distribution: bionet Message-ID: <354m56$fi4@u.cc.utah.edu> References: <350uhh$etr@mserv1.dl.ac.uk> NNTP-Posting-Host: u.cc.utah.edu I have several general questions about ACEDB. The answers may be in the FAQ; if someone could mail the FAQ to me, that would probably suffice. Please do not respond directly to this mail id, as I am "borrowing" it. Please either post a follow up to the news group or mail me at bayer@darwin.med.utah.edu. We would like to set up a lab database system for human sequences, STSs, markers, etc. We would like to track experimental procedures, capture resulting data, and display/manipulate data and information. 1. From the little I've studied ACEDB, it appears that ACEDB would not be appropriate as a general lab system (for capturing data) because the data entry capabilities/procedures are more "batch" oriented. However, ACEDB does appear to be very useful for displaying data and information once the data has been generated. Is this an appropriate evaluation? 2. Is there an ACEDB facility available that allows "interactive" data entry, and/or data editing? 3. Would it be feasible and/or appropriate to set up both UNIX and Mac versions of the ACEDB application and have them be able to read the same data files? Or would separate copies need to be placed on each platform? 4. Since we would like to use ACEDB with human data, which of the available databases would be the best to use as a template? Thanks in advance. Steve Bayer Myriad Genetics SLC, Utah 801-584-3642 bayer@darwin.med.utah.edu From owner-acedb@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!rutgers!netnews.upenn.edu!dsinc!spool.mu.edu!howland.reston.ans.net!EU.net!news.kreonet.re.kr!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: general questions about acedb Date: 13 Sep 1994 21:16:03 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 19 Distribution: bionet Message-ID: <3554qj$2rn@overload.lbl.gov> References: <350uhh$etr@mserv1.dl.ac.uk> <354m56$fi4@u.cc.utah.edu> NNTP-Posting-Host: s27w007.pswfs.gov In article <354m56$fi4@u.cc.utah.edu> kr5205@u.cc.utah.edu (Kerry Rowe) writes: >I have several general questions about ACEDB. The answers may be in the >FAQ; if someone could mail the FAQ to me, that would probably suffice. I have mailed a copy of the FAQ. Your assessment seems fair though there are many features of ACEDB that are not immediately apparent. The question of whether ACEDB is appropriate as a Laboratory Information Management System remains open. It is hard to beat its performance/price ratio. --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 Tue Sep 13 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!quagga.ru.ac.za!ucthpx!uctvax.uct.ac.za!bbbbre01 From: bbbbre01@uctvax.uct.ac.za (Brendan Babb) Newsgroups: bionet.software.acedb Subject: MycDB/Linux response please Date: 14 Sep 94 10:01:08 +0200 Organization: University of Cape Town Lines: 16 Message-ID: <1994Sep14.100108.1@uctvax.uct.ac.za> NNTP-Posting-Host: uctvax.uct.ac.za Hi I am trying to run the mycobacterial database using acedb on a linux system. The problem is that whenever I try to access sequence information, acedb crashes with a 'floating exception' error. The problem appears to be related to opening a features window. Please, if anyone has been using acedb software successfully on linux, let me know, especially if you're using the mycobacterial database. Thanks Brendan (bbabb@medmicro.uct.ac.za) From owner-acedb@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!nihs.nihs.go.jp!taka From: taka@nihs.nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: macace privilege Date: 14 Sep 1994 03:20:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409141019.AA17715@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net I installed a macace. But I have one trouble with it. I want to have a privilege of "write access", but I cannot. I added my name to passwd.wrm file, but that had no effect. Could anyone tell me how I should do ? Thank you for your attention of this mail. Takako Igarashi National Institute of Health Sciences taka@nihs.nihs.go.jp From owner-acedb@net.bio.net Thu Sep 15 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!swrinde!cs.utexas.edu!convex!news.duke.edu!chlamy.botany.duke.edu!user From: chlamy@acpub.duke.edu (Elizabeth Harris) Newsgroups: bionet.software.acedb Subject: collapsing lists in 3.0 Followup-To: bionet.software.acedb Date: 16 Sep 1994 17:14:15 GMT Organization: Duke University Lines: 8 Distribution: world Message-ID: NNTP-Posting-Host: chlamy.botany.duke.edu How can I make displays default to show long lists in a collapsed rather than expanded format when the window first comes up? I can collapse them on the screen with no problem, but I'd like that to be the default condition. It's a particular problem in the Allele class where there may be 30 or more strains in my collection with a given allele. Elizabeth Harris chlamy@acpub.duke.edu From owner-acedb@net.bio.net Sat Sep 17 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!rutgers!princeton!molyworm.princeton.edu!yuan From: Jeffrey Yuan Subject: Re: macace privilege Message-ID: <1994Sep16.202421.15263@Princeton.EDU> X-Xxmessage-Id: Originator: news@nimaster X-Xxdate: Fri, 16 Sep 94 14:44:52 GMT Sender: news@Princeton.EDU (USENET News System) Nntp-Posting-Host: molyworm.princeton.edu Organization: Princeton University X-Useragent: Nuntius v1.1.1d20 References: <9409141019.AA17715@nihs.nihs.go.jp> Date: Fri, 16 Sep 1994 20:24:21 GMT Lines: 22 Subject: macace privilege From: Takako Igarashi, taka@nihs.nihs.go.jp Date: 14 Sep 1994 03:20:41 -0700 In article <9409141019.AA17715@nihs.nihs.go.jp> Takako Igarashi, taka@nihs.nihs.go.jp writes: > >I installed a macace. But I have one trouble with it. >I want to have a privilege of "write access", but I >cannot. I added my name to passwd.wrm file, but that >had no effect. >Could anyone tell me how I should do ? > >Thank you for your attention of this mail. > >Takako Igarashi >National Institute of Health Sciences >taka@nihs.nihs.go.jp Try typing ACEDB. It should work now. Jeffrey Yuan yuan@phoenix.princeton.edu From owner-acedb@net.bio.net Mon Sep 19 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!u.cc.utah.edu!not-for-mail From: kr5205@u.cc.utah.edu (Kerry Rowe) Newsgroups: bionet.software.acedb Subject: human chromosome 13 Date: 20 Sep 1994 09:46:18 -0600 Organization: University of Utah Computer Center, Salt Lake City, Ut. Lines: 10 Message-ID: <35n04a$8gg@u.cc.utah.edu> NNTP-Posting-Host: u.cc.utah.edu Is anyone using ACEDB for human chromosome 13? We're just getting started with ACEDB and if you're open to helping us get started by sharing data or models, please respond to the following email address: bayer@darwin.med.utah.edu Thanks bayer From owner-acedb@net.bio.net Tue Sep 20 23:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!charlie.lif.icnet.uk!hrc From: hrc@gea.lif.icnet.uk (Hugues Roest Crollius) Newsgroups: bionet.software.acedb Subject: Re: GelPatterns and Contig editor Date: 21 Sep 1994 20:00:06 +0100 Organization: Imperial Cancer Research Fund Lines: 13 Sender: hrc@news.lif.icnet.uk Distribution: world Message-ID: <35pvrm$cku@gea.lif.icnet.uk> References: <35pma6$9h8@gea.lif.icnet.uk> NNTP-Posting-Host: gea.lif.icnet.uk OK, I think I found the solution to the Fingerprinting display : Clicking on the tag Gel in the text window of a YAC, Clone... fires the display with the lanes etc. Still I would be interested to know how to use the Contig Editor (if it is implemented), and the display for ABI sequencer traces. Thanks in advance for any help. Hugues Roest Crollius From owner-acedb@net.bio.net Tue Sep 20 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!doc.ic.ac.uk!charlie.lif.icnet.uk!hrc From: hrc@gea.lif.icnet.uk (Hugues Roest Crollius) Newsgroups: bionet.software.acedb Subject: GelPatterns and Contig editor Date: 21 Sep 1994 17:17:10 +0100 Organization: Imperial Cancer Research Fund Lines: 28 Sender: hrc@news.lif.icnet.uk Distribution: world Message-ID: <35pma6$9h8@gea.lif.icnet.uk> NNTP-Posting-Host: gea.lif.icnet.uk Hi, I have been trying to use the Fingerprint tool and the Contig Editor in acedb.3-3 but without much success. Could anybody familiar with these features point me in the right direction ? I have parsed some data following the model : ?YAC Gel ?Probe #Lane // Magic tag2 construct ?Lane UNIQUE Bands UNIQUE Float REPEAT Band_Lengths UNIQUE Float REPEAT Band Float Text But I only get Text displays. How does one actually get the lanes on the screen ? Thanks, Hugues Roest Crollius Genome Analysis Lab, ICRF, London UK From owner-acedb@net.bio.net Tue Sep 20 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: GelPatterns and Contig editor Date: 21 Sep 1994 23:14:33 +0100 Lines: 8 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <35qb89$36g@mserv1.dl.ac.uk> Original-To: hrc@gea.icnet.uk Contig Editor is not really implemented yet i think ABI sequencer traces. is in axce3, make abi, you need SCF_FILE to point to a filename for SCF format in directory setenv SCF_DATA SCF_FILE is a tag in ?Sequence From owner-acedb@net.bio.net Wed Sep 21 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Upgrade 2-10 to 2-11 crashes Message-ID: <1994Sep22.062118.23157@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Date: Thu, 22 Sep 1994 06:21:18 GMT Lines: 16 I get a 'memory allocation failure' if I try to upgrade 2-10 to 2-11 on a Sun running SunOS 4.1.2 with ACeDB, 2.0. The Hardware has 94Mb RAM and lots of disk. 'unlimit' didn't help. Surprisingly, the error message appears after having read in 46% of the data, and tells that it cannot allocate 8 MB memory. Any ideas? Regards Reinhard -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-acedb@net.bio.net Thu Sep 22 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swrinde!emory!cs.utk.edu!stc06.CTD.ORNL.GOV!druid!ptv From: ptv@druid.epm.ornl.gov (Sergey Petrov) Newsgroups: bionet.software.acedb Subject: overlap&highlight Date: 23 Sep 1994 15:48:32 GMT Organization: Oak Ridge National Lab/CESAR Lines: 11 Distribution: world Message-ID: <35utcg$b0q@stc06.CTD.ORNL.GOV> Reply-To: ptv@druid.epm.ornl.gov NNTP-Posting-Host: druid.epm.ornl.gov In ASCEDB 3.3 vmap viewer the length of highlighted aligned fragments (e.g. chromosome bands) is wrong if fragments overlap. When map is drawn, the every next fragment is displayed on the top of previous one. So, highlighted fragment is partly covered and is not seen. To fix it i modifyed vMapReColor in vmapdisp.c: white (transparent) fragments are drawn in another cycle before all others. I wonder if the solution is sound and if a better one exists. Sergey Petrov From owner-acedb@net.bio.net Fri Sep 23 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!uunet!seas.smu.edu!news.uta.edu!wbar.uta.edu!patrick From: patrick@wbar.uta.edu (Patrick Phillips) Subject: Sequence searches Message-ID: <1994Sep21.201515.28342@news.uta.edu> Sender: news@news.uta.edu (USENET News System) Nntp-Posting-Host: wbar.uta.edu Organization: /usr/local/lib/news/organization Date: Wed, 21 Sep 1994 20:15:15 GMT Lines: 31 I'm interested in searching the C. elegans database for specific short DNA sequences (I'm looking for RAPD priming sites). The DNA analysis window with the Genome_Seq keyset provides the ideal method, except that one is limited to only three 10-mers because of the finite length of text input bar. This seems like a serious user interface limitation (i.e., the text bar does not scroll, but just stops at about 40 characters). I would like to do many searches simultaneously, so this is a problem. I've tried to figure out the Query equivalent to the DNA analysis window, but I'm afraid that even after three years of dabbling with it, I still don't fully understand how the query syntax works. Trying something simple like find Sequence DNA=*tgcggctgag* doesn't find anything, so I must be barking up the wrong tree. It obviously must be possible to do this, so could someone out there tell me what I'm doing wrong? It is truly amazing to be able to do searches like this on over 6 Megabases on my own computer. I thank everyone who has contributed to this tremendous resource. Patrick Phillips Biology Department University of Texas at Arlington patrick@wbar.uta.edu (817) 273-2409 From owner-acedb@net.bio.net Fri Sep 23 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!cs.utk.edu!stc06.CTD.ORNL.GOV!druid!ptv From: ptv@druid.epm.ornl.gov (Sergey Petrov) Newsgroups: bionet.software.acedb Subject: physical map Date: 24 Sep 1994 15:02:39 GMT Organization: Oak Ridge National Lab/CESAR Lines: 9 Distribution: world Message-ID: <361f2f$1hl@stc06.CTD.ORNL.GOV> Reply-To: ptv@druid.epm.ornl.gov NNTP-Posting-Host: druid.epm.ornl.gov How to 'switch on' display of (horisontal ?) physical map consisisting of clones and contigs? My attempts to modify 'options.wrm' and set pMap to PMAP failed. I'll appreciate any hints. S.Petrov From owner-acedb@net.bio.net Fri Sep 23 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: Sequence searches Date: 24 Sep 1994 07:52:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409241452.AA08226@cvx12.inet.dkfz-heidelberg.de> References: <1994Sep21.201515.28342@news.uta.edu> NNTP-Posting-Host: net.bio.net > find Sequence DNA=*tgcggctgag* > doesn't find anything, so I must be barking up the wrong tree. this looks for a sequence whose _name_ contains tgcggctgag, so your assumption is right. Perhaps in future ACEDB could treat the DNA class like LongText and search DNA, too, when clicking on the "Long Search" button in the main window. For the time being you can e.g. click on class DNA in the main window, then in the main KeySet choose "Ace dump" from the menu, then use emacs or whatever unix tool on the resulting .ace file. regards Detlef From owner-acedb@net.bio.net Fri Sep 23 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: find Sequence DNA=*tgcggctgag* Date: 24 Sep 1994 17:52:55 +0100 Lines: 5 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <361lh7$n2j@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr selelct all sequences do DNA form main menu serch *tgcggctgag* even with error rate From owner-acedb@net.bio.net Fri Sep 23 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: Sequence searches Date: 24 Sep 1994 17:49:59 +0100 Lines: 7 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <361lbn$n0v@mserv1.dl.ac.uk> Original-To: patrick@wbar.uta.edu find Sequence DNA=*tgcggctgag* does not work one muist invke the DNA analyser, which is not part of the query angugae it should, i ll remember that, but it is not you must do it from the analysis button of the sequence window or the DNA menu entry of the main window From owner-acedb@net.bio.net Fri Sep 23 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: Sequence searches Date: 24 Sep 1994 18:12:35 +0100 Lines: 27 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <361mm3$o3p@mserv1.dl.ac.uk> Original-To: patrick@wbar.uta.edu You can do what you want, in a slightly complex way. The query window is no use to you, as others have said. You must create objects in the "Restriction" class, which normally has restriction sites. It is best to make a file of them, and read them in. To see what the file should look like, use "Ace dump" on a set of restriction site objects from the Main KeySet window. You should give the new objects names that do not just contain ACGT -- though not strictly necessary it will help avoid confusion. Now if get write access from the main menu, and read your file in from the "Read .ace files" window, also accessed via the main menu. Next you want to make a keyset of all your motifs, preferably by them having a shared name element, e.g. RAP1, RAP2 etc., so you can give a template RAP* in the main window, and get the list you want in the Main KeySet window. The pink "Selected KeySet" box should be on in the window containing your keyset of motifs. If not, then click something in the window. Finally, you can now use the "Motif KeySet" button in the DNA_Analysis window, and when you do a search it will search with all the patterns in your keyset, which is what you wanted, I think. Although this sounds complicated it allows you to seach with any set of patterns, and store the patterns with names for future use. The "Max mismatch" button should still work to allow mismatches. Richard From owner-acedb@net.bio.net Sat Sep 24 23:00:00 1994 Path: biosci!FLY2.BERKELEY.EDU!suzi From: suzi@FLY2.BERKELEY.EDU (Suzanna Lewis) Newsgroups: bionet.software.acedb Subject: Re: Sequence searches Date: 24 Sep 1994 18:28:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409250126.SAA21503@fly2.berkeley.edu> NNTP-Posting-Host: net.bio.net Hi everyone, These are just some thoughts on the new Attach button found in the standard tree display. I'm hoping to get some feedback on this, because while I see some real potential in this feature its not all the way there yet. The first reaction of everyone I've spoken with so far (including myself), is what the h--- is that for?... and why is it sitting on top of the data? (all right, its just 4 people, but still) The next reaction (after poking and prodding a bit) is oh, it joins/collects data from some related object and makes it a part this view, thats kinda cool. This is shortly followed by, hey where did it go???, you mean it only sticks around for as long as the window is open? I expected it to still be there when another object of that type was opened up...darn, that's no good. It would have been simpler to just double-click to to get to the related data.... But still, there is this potential. This is a way of creating personal views of the data, by joining bits from related objects. This could be quite powerful, if (and only if) the views could be made persistent in some way. The closest analog is with table maker (which is also a way of composing a views). I realize the 2 are implemented in very different ways, but at least in table maker (once you've brute forced it to get what you want) the view can be saved and recovered again. Maybe Attach has this, and this capability is already there? In that case the problem is----yet another hidden feature! If persistance is not yet implemented, would it be worthwhile to do so? While I'm on the subject of views, it would be very nice to be able to use table-maker to create custom .ace files. I realize this is somewhat a perversion of what .ace files have been used for (database dumps and reloads). But, I find myself using them more and more to pass data to outside programs. Most of the time its only a limited set of tags values that are of interest and it would be handy if I could define this set using table maker and then produce output that was in .ace format, even if (strictly speaking) it wasn't .ace data. So: 1. Does anyone else have any opinions on the Attach feature? 2. Does anyone else ever use customized .ace format files? -Suzanna From owner-acedb@net.bio.net Sun Sep 25 23:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: attach @query Date: 26 Sep 1994 10:53:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409261749.AA19655@cvx12.inet.dkfz-heidelberg.de> References: <199409250126.SAA21503@fly2.berkeley.edu> NNTP-Posting-Host: net.bio.net > 1. Does anyone else have any opinions on the Attach feature? ... > the views could > be made persistent in some way. in models.wrm you can say ?Locus ?Citation XREF Locus @"generic_properties # summary" i.e. attach the query in the model. Hope I didn't misunderstand the long message. Is this what you want? Greetings Detlef From owner-acedb@net.bio.net Sun Sep 25 23:00:00 1994 Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!not-for-mail From: DEVOS (Tel ) Newsgroups: bionet.software.acedb Subject: Position available Date: 26 Sep 1994 16:04:11 +0100 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <366ntb$997@mserv1.dl.ac.uk> Sensitivity: Company-Confidential Original-To: acedb@dl.ac.uk (Receipt Notification Requested) (Non Receipt Notification Requested) A position is available immediately at the Cereals Research Department of the John Innes Centre to develop an ACeDB-based database for Pearl Millet. The succesful candidate will also be responsible for data input. Candidates are required to have good computer knowledge and experience with ACeDB-database systems is a benefit. The position runs for 6 months with a starting date not later than 1st November, and is at the research assistant level, although a higher level may be negotiated. If you are interested, please e-mail your C.V. together with the names and addresses of two referees to Devos@BBSRC.AC.UK, or mail them to Dr. K.M. Devos, John Innes Centre, Norwich Research Park, Colney, Norwich, U.K. From owner-acedb@net.bio.net Mon Sep 26 23:00:00 1994 Path: biosci!POP.PSU.EDU!zimmer From: zimmer@POP.PSU.EDU (Mike Zimmerman) Newsgroups: bionet.software.acedb Subject: Using ACeDB for other applications Date: 27 Sep 1994 06:32:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello, I am just now becoming acquainted with ACeDB, and I'd be interested to know if many people are using it for other (non-genome-related) database management applications. (I've seen the "AboutACeDB" database page, of course.) We are looking at using it to create an automated library catalog which could be linked to Postscript documents and geographic information system information, for instance. The object-oriented design of ACeDB and the PS-to-GIF and clickable map capabilities of the ACeDB-to-WWW gateway would be marvelous for that kind of application. The software presents all kinds of possibilities which aren't available with conventional relational database library systems, and I'd appreciate hearing about other people's "alternative" uses. Thanks, Michael Zimmerman ============================================================================== Michael Zimmerman Population Research Institute Library zimmer@pop.psu.edu The Pennsylvania State University From owner-acedb@net.bio.net Mon Sep 26 23:00:00 1994 Path: biosci!VECTOR.NALUSDA.GOV!scartinh From: scartinh@VECTOR.NALUSDA.GOV (Sam Cartinhour) Newsgroups: bionet.software.acedb Subject: attach @query Date: 27 Sep 1994 04:18:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409271113.AA11376@vector.nalusda.gov> NNTP-Posting-Host: net.bio.net >> the views could >> be made persistent in some way. > >if the view is defined in the moel file it becomes persistent it would be nice if ordinary users could make a view persistent by applying it to a keyset or by saving its "definition" so it could be loaded and applied at another time. This would encourage users to develop complex customized views. I think Jean mentioned applying attach to keysets at the workshop? sam From owner-acedb@net.bio.net Mon Sep 26 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: attach @query Date: 27 Sep 1994 12:02:04 +0100 Lines: 8 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <368u3c$bj@mserv1.dl.ac.uk> Original-To: D.Wolf@dkfz-heidelberg.de .... > the views could > be made persistent in some way. if the view is defined in the moel file it becomes persistent just have the attach close in some new fake class and make that class visible From owner-acedb@net.bio.net Mon Sep 26 23:00:00 1994 Path: biosci!FLY2.BERKELEY.EDU!suzi From: suzi@FLY2.BERKELEY.EDU (Suzanna Lewis) Newsgroups: bionet.software.acedb Subject: Re: attach @query Date: 27 Sep 1994 12:04:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409271901.MAA00450@fly2.berkeley.edu> NNTP-Posting-Host: net.bio.net Detlef explained.. > in models.wrm you can say > > ?Locus ?Citation XREF Locus @"generic_properties # summary" > > i.e. attach the query in the model. Thank you, Detlef, this may come in handy. The problem with this method however is that the binding occurs at the model design stage, not at runtime. similarly Jean says.. > if the view is defined in the model file it becomes persistent > > just have the attach close in some new fake class > and make that class visible I'm not quite sure what you mean Jean when you say "close in some new fake class". I can't see anything in the menus that hints of anything like this. Could you explain this further. The issue is that the "Attach" button (as now coded) is transitory. Like Sam C. said... > it would be nice if ordinary users could make a view persistent by > applying it to a keyset or by saving its "definition" so it could be > loaded and applied at another time. This would encourage users to > develop complex customized views. I think Jean mentioned applying > attach to keysets at the workshop? > I don't see anything new on the menu that allows Attach to work on a keyset. I'm I missing something here, and this would be a very handy feature. Finally if one does a ace dump of the tree display after performing an Attach the results do Not include the attached tags and values. There is no way to obtain the .ace form of what you see in the display. This is not what an ordinary user expects. They would expect the two to match. Oops one more thing. Multiple attaches don't work. I give up, I'm disabling Attach. -S From owner-acedb@net.bio.net Tue Sep 27 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: attach Date: 28 Sep 1994 10:51:15 +0100 Lines: 36 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <36beaj$hbe@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr richard says: I've never used attach either, though I too think it has something good about it. Maybe one wants to be able to create a View object, which specifies how to decorate a simple object. It would need pairs of queries -- the first to specify where to attach things, and the second what to attach. Then you could use a view on a single tree display, or a keyset, and maybe dump via a view. In fact if you ONLY dumped the parts that were specified, then you would have your limited .ace dumper. Maybe there is a real idea here. Maybe it could just be a file with pairs of queries. but this is indeed how attach was created and used we needed for the igd project (otto and myself) to do view dumps so we created additional classes where all fields are derived via attachments these classes are visible whereas the real ones are hidden then you use acedb the attach owrks then on objetcs, keystes and dumps you can even parse what you dumped, but these fields are ignored but then you make a second acedb with the same models as the views but with direct fields and you read the dumps from the other system now consider the server client model the server can dump the (dynamically constructed) views as ace files which are then read as direct ace files by the client teh only missing link is thta only the super user can create these views since they are part of the modelsx file now remember that i have a running version without clss/tags files where it is necessary to read a model file, so we now have the tools for what you need from my experience of a couple of months, i think that attach is the most powerful addition to the ace semantics since we introduced constructed types. jean From owner-acedb@net.bio.net Tue Sep 27 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!uknet!strath-cs!st-and!usenet From: jm6@dcs.st-and.ac.uk (John Michalopoulos) Newsgroups: bionet.software,bionet.software.acedb Subject: Visualisation of Postscript files in Macs? Date: 28 Sep 1994 22:52:50 GMT Organization: University of St Andrews Lines: 15 Distribution: world Message-ID: <36cs42$jko@calvin.st-and.ac.uk> Reply-To: jm6@dcs.st-and.ac.uk NNTP-Posting-Host: irv1.st-andrews.ac.uk Xref: biosci bionet.software:9467 bionet.software.acedb:439 Hello, I can make some PostScript files, using GCG in Sun machines. I would be grateful, if you could recommend any particular programme that I can use to view these .ps files in a Macintosh. Thank you in advance, John Michalopoulos University of St Andrews, Scotland, Britain From owner-acedb@net.bio.net Tue Sep 27 23:00:00 1994 Path: biosci!bcm!news.msfc.nasa.gov!europa.eng.gtefsd.com!howland.reston.ans.net!swrinde!sgiblab!sgigate.sgi.com!olivea!charnel.ecst.csuchico.edu!xmission!u.cc.utah.edu!not-for-mail From: kr5205@u.cc.utah.edu (Kerry Rowe) Newsgroups: bionet.software.acedb Subject: ACEDB 3.3 Date: 28 Sep 1994 09:26:54 -0600 Organization: University of Utah Computer Center, Salt Lake City, Ut. Lines: 13 Message-ID: <36c1vu$608@u.cc.utah.edu> NNTP-Posting-Host: u.cc.utah.edu Is there a site where I can retrieve the binary for 3.3? I don't have the X libraries set up yet and can only id the source files on the ftp sites. Please do not respond to this account; please respond to the newsgroup or to the following address: bayer@darwin.med.utah.edu Thanks in advance. Steve Bayer Myriad Genetics From owner-acedb@net.bio.net Wed Sep 28 23:00:00 1994 Newsgroups: bionet.software,bionet.software.acedb Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Subject: Re: Visualisation of Postscript files in Macs? Message-ID: Sender: news@demon.co.uk (Usenet Administration) Nntp-Posting-Host: visigoth.demon.co.uk Organization: Unlikely... References: <36cs42$jko@calvin.st-and.ac.uk> Date: Thu, 29 Sep 1994 07:44:32 GMT Lines: 21 Xref: biosci bionet.software:9471 bionet.software.acedb:440 In article <36cs42$jko@calvin.st-and.ac.uk>, jm6@dcs.st-and.ac.uk wrote: > Hello, > > I can make some PostScript files, using GCG in Sun machines. I would be grateful, if > you could recommend any particular programme that I can use to view these .ps files in a > Macintosh. You need to get GhostScript, an FSF program. You can ftp it from src.doc.ac.ic.uk in directory /0-Most-Packages/mac/sumex/Graphic/Utility as mac-ghostscript-252b3.hqx. It is approx 2.3 Mb (this includes fonts, but there is a copy without fonts, which is called mac-ghostscript-252b3-no-fonts.hqx which is only 712 Kb. -- James Petts ----------- DO NOT READ THIS .sig UNDER PENALTY OF LAW! FUTILE CODE SECTION 4 SUBSECTION A.1.7 From owner-acedb@net.bio.net Thu Sep 29 23:00:00 1994 Path: biosci!FLY2.BERKELEY.EDU!suzi From: suzi@FLY2.BERKELEY.EDU (Suzanna Lewis) Newsgroups: bionet.software.acedb Subject: Re: attach Date: 29 Sep 1994 22:50:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409300547.WAA15132@fly2.berkeley.edu> NNTP-Posting-Host: net.bio.net Dear Jean, There is a contradiction here. You say that: > > but this is indeed how attach was created and used > But this isn't how it works from a user's point of view! Why does the "Attach" button appear at all, if the supporting models are not available? The very fact that the button is available on the screen suggests that it ought to do something. But what you seem to be saying is that it only works if the models are appropriately set up. > the attach owrks then on objetcs, keystes and dumps I can see a button for an object, but where are the user hooks for keysets and dumps? I can't see anything on menus or buttons that seems to apply. > you can even parse what you dumped, but these fields are ignored I tried dumping a tree object after doing an attach and none of the attach data was present in the dump. If you can't dump it what does parsing matter? My impression is that we are using the same terms to describe two completely (vastly?, no) different tools. We both say "Attach" but don't mean the same thing at all. I would be interested in hearing from Otto, because I'm not sure I have correctly interpreted what you have written. The tool that Richard described sounds more like what I was thinking of. It would act in a way similar to the query editor or table maker interface. That is, anyone could use it, no special privileges, models, or anything required. Secondly, the view definition could be saved (made persistent) so users could recall a particular view of the data on demand. its not the same thing at all, but something new I guess -s From owner-acedb@net.bio.net Thu Sep 29 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!sdd.hp.com!col.hp.com!csn!yuma!purdue!mozo.cc.purdue.edu!darwin2.bio.purdue.edu!user From: flip@bogie2.bio.purdue.edu (Phillip D. Russell) Newsgroups: bionet.software,bionet.software.acedb Subject: Mac Printing (Was Visualisation of Postscript files in Macs?) Date: Fri, 30 Sep 1994 12:53:22 -0600 Organization: Purdue University Lines: 23 Distribution: world Message-ID: References: <36cs42$jko@calvin.st-and.ac.uk> <36hd6l$ehm@lyra.csx.cam.ac.uk> NNTP-Posting-Host: darwin2.bio.purdue.edu Xref: biosci bionet.software:9487 bionet.software.acedb:443 In article <36hd6l$ehm@lyra.csx.cam.ac.uk>, bjd12@cus.cam.ac.uk (Ben Davis) wrote: > While we're talking mac printing software, save-a-tree is good > for big text files. Lets you print 4 pages on one sheet of paper, so if > you've got a database search you want to read over a coffee, you can. Very > civilised. I guess you don't have the laserwriter 8 extention. You can print multiple pages on one sheet from any program. The laserwriter 8 extention should be at all FTP site with Mac shareware. Flip -- __@ Phillip "Flip" Russell | Purdue University __@ _ -_,_-\<,_flip@bogie2.bio.purdue.edu | West Lafayette, IN _ -\<,_ (_)-----/-(_) The important things... (_)-/-(_) My bikes and my Macintosh From owner-acedb@net.bio.net Thu Sep 29 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!lyra.csx.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.software,bionet.software.acedb Subject: Re: Visualisation of Postscript files in Macs? Date: 30 Sep 1994 16:08:53 GMT Organization: University of Cambridge, England Lines: 36 Distribution: world Message-ID: <36hd6l$ehm@lyra.csx.cam.ac.uk> References: <36cs42$jko@calvin.st-and.ac.uk> NNTP-Posting-Host: grus.cus.cam.ac.uk X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:9484 bionet.software.acedb:442 Rajan Nair (rnair@umich.edu) wrote: : > I can make some PostScript files, using GCG in Sun machines. I would be grateful, if : > you could recommend any particular programme that I can use to view these .ps files in a : > Macintosh. : I don't know of an easy way to look at the postscript file on the monitor. : But if you just want to print it, you could open the file with Microsoft : Word, select the entire contents, and change format from normal to : Postscript. In Word 5.0 and higher you do do this by holding down the shift : key, clicking the mouse on the "normal" style on the left of the top : ribbon, and dragging down to the postscript option. This operation will : change your font to Chicago. Now you can print the file on any Postscript : printer. There's quite a few very good shareware programs for printing ps files directly from the mac. MacLPR is the one we use - just drop the ps or ascii text icon onto it, and it prints - fast, easy to use (it sorts out whether its ps or ascii itself). There's a couple others whose names I've forgotten, but if anyone's depserate, I can dig them out. While we're talking mac printing software, save-a-tree is good for big text files. Lets you print 4 pages on one sheet of paper, so if you've got a database search you want to read over a coffee, you can. Very civilised. Ben -- ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-acedb@net.bio.net Fri Sep 30 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swiss.ans.net!solaris.cc.vt.edu!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.software,bionet.software.acedb Subject: Re: Visualisation of Postscript files in Macs? Followup-To: bionet.software Date: 1 Oct 1994 12:56:44 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 28 Distribution: world Message-ID: <36jmacINN119a@sat.ipp-garching.mpg.de> References: <36hd6l$ehm@lyra.csx.cam.ac.uk> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] Xref: biosci bionet.software:9493 bionet.software.acedb:445 [Note: followups to bionet.software only] Ben Davis (bjd12@cus.cam.ac.uk) wrote: : Rajan Nair (rnair@umich.edu) wrote: : : > I can make some PostScript files, using GCG in Sun machines. I would be : grateful, if : : > you could recommend any particular programme that I can use to view : these .ps files in a To view postscript files on a Mac, there are at least two possibilities: - Ghostscript is free software, clumsy to use, ugly fonts - Adobe Illustrator is expensive, slow and converts postscript into objects which can then be manipulated. : There's quite a few very good shareware programs for printing ps : files directly from the mac. MacLPR is the one we use - just drop the ps : or ascii text icon onto it, and it prints - fast, easy to use (it sorts : out whether its ps or ascii itself). The "LaserWriter Utility" which comes either with your Mac or your Apple LaserWriter is able to download Postscript directly to your printer. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "People are DNA's way of making more DNA." (Edward O. Wilson, 1975) */ From owner-acedb@net.bio.net Fri Sep 30 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 1 Oct 1994 02:00:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 322 Sender: daemon@net.bio.net Distribution: world Message-ID: <199410010900.CAA04078@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. 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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: