From owner-acedb@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!nihs.go.jp!taka From: taka@nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: plural aceservers on the same machine Date: 1 Apr 1996 22:36:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604020633.AA00986@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net Hello, I have a question about the aceserver system. Is it possible to run plural aceservers on the same machine simultaneously? I added two aceservers both in /etc/rpc and in /etc/inetd.conf. I can operate each aceserver separetely, but cannot operate these simultaneously. Am I prohibited from doing such a kind of operation? Thank you in advance. Takako Igarashi Division of Chem-Bio Informartics National Institute of Health Sciences 1-18-1,Kamiyoga,Setagaya-ku,Tokyo,Japan 158 tel +81-3-3700-1141 ext.296 fax +81-3-5717-7180 email taka@nihs.go.jp From owner-acedb@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!sprout.nal.usda.gov!usenet From: Doug Bigwood Newsgroups: bionet.software.acedb Subject: Re: plural aceservers on the same machine Date: Tue, 02 Apr 1996 09:44:41 -0500 Organization: Genome Informatics Group, NAL, USDA Lines: 13 Message-ID: <31613D59.30D@gig.usda.gov> References: <9604020633.AA00986@nihs.nihs.go.jp> NNTP-Posting-Host: locus.gig.usda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.5 sun4m) Yes, this is possible. We run several (more than 10) on one machine (a SPARC) without problems. If you send me your rpc and inetd.conf entries I will attempt to debug them. Doug Bigwood dbigwood@gig.usda.gov Takako Igarashi wrote: > I have a question about the aceserver system. > Is it possible to run plural aceservers on the same > machine simultaneously? From owner-acedb@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!csn!news-1.csn.net!ub!newsstand.cit.cornell.edu!news.tc.cornell.edu!newsserver.sdsc.edu!news.cerf.net!news From: "Eric E. Snyder" Newsgroups: bionet.software.acedb Subject: IMAGE cDNA library as ACEDB Grid? Date: Tue, 02 Apr 1996 14:53:30 -0800 Organization: Sequana Therapeutics, Inc. Lines: 18 Message-ID: <3161AFEA.56D5@sequana.com> NNTP-Posting-Host: 198.207.137.13 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) CC: eesnyder@sequana.com Greetings, We recently obtained a gridded cDNA library from Research Genetics. The library consists of 11 filters containing a total of about 250000 cDNAs on the grid. I would be interested to know if anyone has set up this library as a grid in ACEDB? If anyone has set this up before, I would be interested in getting a copy of the database or the program used to create the grid-to-plate reference system. In fact, I would be down right grateful for any tips on making this work. Thanks, Eric E. Snyder, PhD Sequana Therapeutics, Inc. 11099 North Torrey Pines Road, Suite 160 La Jolla, CA 92037 N 32 54'32" W 117 14'26" (619) 646-8279; (619) 452-6653 fax; eesnyder@sequana.com http://beagle.colorado.edu/~eesnyder/eesnyder.html From owner-acedb@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!nihs.go.jp!taka From: taka@nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: Re: plural aceservers on the same machine Date: 3 Apr 1996 00:53:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604030850.AA07372@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net Thank you Dr.Thierry-Mieg, Dr.Bigwood, and Dr.Holt for advising me about "plural aceservers". They all taught me that it is possible to run plural aceservers on the same machine simultaneously. Dr.Thierry-Mieg sent me examples of aceserver configuration files. He also let me use new ace4.3d. Thank you for your kindness, Dr.Thierry-Mieg. I am sorry, but my two aceservers have not run simultaneously on the same machine yet, even on ace4.3d. Only just after rebooting the machine, I can run one of the aceservers. But once I ran one of the aceservers, the other aceserver cannot be run at all, untill next rebooting. Only the aceserver which I started just after rebooting can be run. When I attempted to run the other aceservers, I got the error message by aceserver program, "//! cannot establish connection". I found that once I accessed one of the aceservers, the corresponding rpc.acedbd process remained permanently, though I finished the corresponding aceclient process. (Of course, that rpc.acedbd process was vanished after rebooting.) I use SGI/IndigoII irix5.3. I am glad if anyone tell me the information of aceserver system on irix. Dr.Bigwood kindly told me that he would attempt to debug the entries of rpc and inetd.conf. Then I added corresponding my entries. wwwace 20000100 rpc.acedbd wwwace2 20000200 rpc.acedbd wwwace/1 stream rpc/tcp wait taka /usr/local/bin/rpc.acedbd rpc.acedbd /usr/peop le/taka/wwwace 20000100 600:600:0 wwwace2/1 stream rpc/tcp wait taka /usr/local/bin/rpc.acedbd rpc.acedbd /usr/peo ple/taka/wwwace2 20000200 600:600:0 I am sorry to bother you with my question. Thank you very much in advance. Takako Igarashi Division of Chem-Bio Informartics National Institute of Health Sciences 1-18-1,Kamiyoga,Setagaya-ku,Tokyo,Japan 158 tel +81-3-3700-1141 ext.296 fax +81-3-5717-7180 email taka@nihs.go.jp From owner-acedb@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: multi servers Date: 3 Apr 1996 12:30:48 +0100 Lines: 57 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4jtnh8$imh@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk a) time outs rpc.acedbd is declared wait in inetd.conf hence 1) it is forked only if it does not yet exists 2) it is not killed by unix at end of connection however, aceserver commits suicide after its own time out which is a parameter on the command line here 600 seconds since the decalration is: wwwace2/1 stream rpc/tcp wait taka /usr/local/bin/rpc.acedbd rpc.acedbd /usr/people/taka/wwwace2 20000200 600:600:0 *********************** b) declarations are required i think in 3 places: /etc/inetd.conf, /etc/rpc /etc/services these are the entries on my own machine: /etc/services # These are acedb databases servers cele 20000100/tcp rpc.acedbd igd_ace 20000200/tcp rpc.acedbd # These are acedb/jade netclients worm 20100/tcp #aceclient /etc/rpc #acedb worm data server cele 20000100 rpc.acedbd igd_ace 20000200 rpc.acedbd /etc/inetd.conf # experimental ACE client to use with java scripts worm stream tcp nowait mieg /usr/local/bin/netclient netclient -host beta -port 20000100 cele/1 stream rpc/tcp wait mieg /usr/local/bin/rpc.acedbd rpc.acedbd /local1/worm 20000100 1200:1200:0 igd_ace/1 stream rpc/tcp wait mieg /usr/local/bin/rpc.acedbd rpc.acedbd /local1/igd/ace 20000200 1200:1200:0 I suspect that you may be missing the entry in /etc/services in particular I think that it is crucial in services to associate the service to its port and to its executable (here rpc.acedbd) I beleive the system runs corectly on sgi, but i have myself set it up only on a dec alpha (with the precious help and collabortion Bigwood & co) and on a Solaris with Donn Davy) If this system does not work, please let me know. *********************** c) rebooting In principle, one should not reboot, just restart the correct daemons, but in my experience, i always end up rebooting, becasause after killing and restarting a few daemons, acedbserver may well run, but some other service like nfs or whatelse is unhappy. From owner-acedb@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!nihs.go.jp!taka From: taka@nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: Re: plural aceservers on the same machine Date: 4 Apr 1996 01:33:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604040930.AA13330@nihs.nihs.go.jp> References: <31628B2F.7045@gig.usda.gov> NNTP-Posting-Host: net.bio.net I would like to thank Dr.Thierry-Mieg and Dr.Bigwood for advising me on aceserver again. At last I could run two aceservers on the same machine!! At first I tried to run CSNDB (the database for cell signaling networks, which I demonstrated at the ace95 workshop) and the new database. But this combination of databases did not work expectedly at all. Next I tried to run the new database and the copy of the new database, then I succeeded to run these two aceservers ! Though I am not sure what is wrong with CSNDB, some of modifications on CSNDB may cause some trouble. I will continue investigating the cause of trouble with CSNDB. Anyway I received much advice on how to use aceserver. It was a great help for me. I would like to appreciate for the kindness. Takako Igarashi Division of Chem-Bio Informartics National Institute of Health Sciences 1-18-1,Kamiyoga,Setagaya-ku,Tokyo,Japan 158 tel +81-3-3700-1141 ext.296 fax +81-3-5717-7180 email taka@nihs.go.jp From owner-acedb@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: grid Date: 4 Apr 1996 09:11:18 +0100 Lines: 37 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4k0076$g1a@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk I got a qustion on grid display: how to use it for my own data The important thing is to declare a grid object and a corresponding view: for the worm they go as follow: Grid : "POLY1" view "GRID-1" View : "GRID-1" Grid_map 2 Colour BLUE Grid_map 2 Surround_colour GREEN Grid_map 2 Tag "Hybridizes_to" Grid_map 1 Colour LIGHTBLUE Grid_map 1 Surround_colour YELLOW Grid_map 1 Tag "Hybridizes_weak" Grid_edit_default "Hybridizes_to" Grid_edit_menu "Hybridizes_weak" Grid_edit_menu "Hybridizes_to" the full grid object reads Grid : "POLY1" Title "Yac polytene filter 1" Lines_at 3 4 Space_at 12 8 View "GRID-1" Row 1 Clone "Y48A1" "Y47C7" "Y11A1" "Y40G6" "Y24C9" Row 2 Clone "Y48A12" "Y53F10" "Y38H4" "Y26A2" "Y53H11" Row 3 Clone "Y11D8" "Y56F10" "Y54C1" "Y42E1" "Y50D2" From owner-acedb@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: 6 Positions to establish UK plant database network Date: 4 Apr 1996 16:22:54 +0100 Lines: 90 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4k0pge$haq@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Scottish Crop Research Institute Institute of Grassland and Environmental Research John Innes Centre Nottingham Arabidopsis Stock Centre UK CROP PLANT BIOINFORMATICS NETWORK -------------------------------------------------------------------- The Biotechnology and Biological Sciences Research Council (BBSRC) has initiated a programme involving several posts to develop and apply plant genome bioinformatics in the UK. The role of the network will be to develop bioinformatics as a research tool The following positions are available:- 1. Scottish Crop Research Institute, Dundee To develop a new genome database for barley and establish links with other international bioinformatics resources. (REF: BIONET.1) 2. Institute of Grassland and Environmental Research, Aberystwyth To develop a new genome database for the forage grasses and to establish links with genome research in other cereals. (REF:1996\6) 3. John Innes Centre, Norwich To coordinate the Network and develop applications and comparative mapping software for the Arabidopsis, Brassica and cereal databases. (REF: BIONET.2) 4. John Innes Centre, Norwich To link cereal genome data from wheat, barley, millet and rice with GrainGenes and MilletGenes databases. (REF: BIONET.3) 5. John Innes Centre, Norwich To develop a new Brassica database with links to the existing Arabidopsis databases. (REF: BIONET.4) 6. Nottingham Arabidopsis Stock Centre, The University of Nottingham To develop the Arabidopsis database, AtDB, for UK data. Provide training support for the UK group and develop user interfaces to the network databases. (REF: BIONET.5) All appointments will be for a fixed term of three years duration. Appointments 1, 2 and 3 will be to Pay Band 6 within the salary range 13,951 to 24,174 per annum (UK pounds sterling). Appointments 4 and 5 will be to Pay Band 7 within the salary range 11,929 to 20,665 (UK pounds sterling). Previous experience of bioinformatics (knowledge of UNIX, ACEDB, and programming in C or Perl for the Band 6 and RA1A posts) is preferable. A relevant biological background in genetics with an interest and aptitude for applying computer database methods Application forms and general details on the projects can be obtained by writing to the Personnel Officer at the John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH. Specific details relating to individual positions are available from: 1. Dr Robbie Waugh, (SCRI) Tel: (01382) 562731, E-Mail rwaugh@scri.sari.ac.uk 2. Dr Mike Hayward, (IGER) Tel: (01970) 828255, E-Mail mike.hayward@bbsrc.ac.uk 3. Dr Mike Bevan, (JIC) Tel: (01603) 452571, E-Mail bevan@bbsrc.ac.uk 4. Dr M D Gale, (JIC) Tel: (01603) 452571, E-Mail jeffrey@bbsrc.ac.uk 5. Dr Martin Trick (JIC), Tel (01603) 452571, E-Mail trick@bbsrc.ac.uk 6. Dr Mary Anderson, (NASC) Tel: (0115) 9791216, E-Mail arabidopsis@nottingham.ac.uk The BBSRC and University of Nottingham are Equal Opportunities Employers. The closing date for completed applications is 3 May 1996. From owner-acedb@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!nihs.go.jp!taka From: taka@nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: Re: plural aceservers on the same machine Date: 4 Apr 1996 23:42:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604050740.AA17902@nihs.nihs.go.jp> References: <9604041216.AA05585@kaa> NNTP-Posting-Host: net.bio.net Greetings, Dr.Thierry-Mieg taught me that Ace4 released prior to September '95 dose not support multiple aceservers. It is supported only after Ace4.1. Exactly, I use Ace4.0 for our CSNDB ! I transferred our CSNDB from on Ace4.0 to on Ace4.3d, then I succeeded to run correctly multiple aceservers. Dr.Thierry-Mieg, thank you very much for your help. Takako Igarashi Division of Chem-Bio Informartics National Institute of Health Sciences 1-18-1,Kamiyoga,Setagaya-ku,Tokyo,Japan 158 tel +81-3-3700-1141 ext.296 fax +81-3-5717-7180 email taka@nihs.go.jp From owner-acedb@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!news.uky.edu!gatech!swrinde!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!news!jschultz From: jschultz@EMBL-Heidelberg.DE (Joerg Schultz) Newsgroups: bionet.software.acedb Subject: ?LongText Date: 08 Apr 1996 09:15:47 GMT Organization: EMBL Heidelberg Lines: 11 Distribution: world Message-ID: NNTP-Posting-Host: kite.embl-heidelberg.de Hello, I just started to work with ACEDB and have some problems with the LongText class. First, words in a LongText entry are not found by any search. Second, the Hypertext mechanism does not work. I created the KeySet as said in the manuals but it just does not find the words corresponding to objects in the database. I use the ace4.1 distribution, namely the binaries for Irix5. Hope you can help me Joerg From owner-acedb@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!oleane!tank.news.pipex.net!pipex!newsfeed.internetmci.com!csn!news-1.csn.net!ub!newsstand.cit.cornell.edu!news.tc.cornell.edu!newsserver.sdsc.edu!news.cerf.net!news From: "Eric E. Snyder" Newsgroups: bionet.software.acedb Subject: ACEDB Workshop Date: Thu, 11 Apr 1996 12:03:04 -0700 Organization: Sequana Therapeutics, Inc. Lines: 11 Message-ID: <316D5768.3F03@sequana.com> NNTP-Posting-Host: 198.207.137.13 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) Is there any information yet on when and where the ACEDB workshop will be? I saw Otto Ritter's note to this group last week saying that it would not be at DKFZ. ...but he didn't indicate where it might be. Any news? Eric E. Snyder, PhD Associate Director, Genome Analysis Sequana Therapeutics, Inc. 11099 North Torrey Pines Road, Suite 160 La Jolla, CA 92037 N 32 54'32" W 117 14'26" (619) 646-8279; (619) 452-6653 fax; eesnyder@sequana.com From owner-acedb@net.bio.net Tue Apr 16 23:00:00 1996 Path: biosci!rutgers!gatech!news.mathworks.com!hookup!news.join.ad.jp!news.imnet.ad.jp!usenet.seri.re.kr!news.kreonet.re.kr!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: 17 Apr 1996 17:42:50 GMT Organization: Dendrome, A genome database for forest trees Lines: 1168 Approved: news-answers-request@MIT.Edu Message-ID: <4l3aiq$hue@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:890 news.answers:63475 Archive-name: acedb-faq Last-modified: 4/17/96 Version: 1.28 ACEDB FAQ ********* Curated by: Bradley K. Sherman Frequently Asked Questions about ACEDB ++++++++++++++++++++++++++++++++++++++ o Q0 : What is ACEDB? o -------------------- o Q1 : What is the current version of ACEDB? o ------------------------------------------- o Q2 : What hardware/software do I need to run ACEDB? o ---------------------------------------------------- o Q3 : Where can I get ACEDB? o ---------------------------- o Q4 : !What ACEDB databases exist? o ---------------------------------- o Q5 : What documentation exists for ACEDB? o ------------------------------------------ o Q6 : What other resources are available for ACEDB? o --------------------------------------------------- o Q7 : How should ACEDB be cited? o -------------------------------- o Q8 : Is ACEDB object-oriented? o ------------------------------- o Q9 : How does one get on/off the ACEDB announcements mailing list? o ------------------------------------------------------------------- o Q10 : When and where is the next ACEDB Workshop? o ------------------------------------------------- o Q11 : Who prepared this document & where is the current version? o ----------------------------------------------------------------- Questions marked with '+' are new, those with '!' have substantially changed answers. Q0: What is ACEDB? ++++++++++++++++++ A0: +++ ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [Q4 gives contact information]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions Q1: What is the current version of ACEDB? +++++++++++++++++++++++++++++++++++++++++ A1: +++ (This answer refers to the software not the C. elegans data.) Current version is 4_1 (as of 10 August 1995). A test (beta) version of ACEDB 4.0b4 (5/95) is available. A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q9. Return to List of Questions Q2: What hardware/software do I need to run ACEDB? ++++++++++++++++++++++++++++++++++++++++++++++++++ A2: +++ The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. o Unix and X11: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series o PC 386/486/Pentium with Linux (free Unix) Jeff Bryer, jbryer@darwin.mbb.sfu.ca and Ken Clark provide a linux version of 4.2 and a complete C. elegans data set at trog.mbb.sfu.ca in /pub/acedb as bin.linux.4_1.tar.Z and in ELF binary as ftp://trog.mbb.sfu.ca/pub/acedb/bin.linux.4_2.elf.tar.gz . o There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o Macintosh: o [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a 17" color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. o ACEDB for The NEC EWS4800 is available via anonymous ftp at ftp.nec.co.jp (192.135.93.2) in /pub/packages/acedb/ace2. Contact Tohru Sano Fundamental Research Laboratories NEC Corporation Tsukuba, 305, JAPAN, e-mail: sano@exp.cl.nec.co.jp, FAX: +81-298-56-6136, VOICE: +81-298-50-1507 (Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems SPARCstation II, and users can interact using Macintoshes and PC-clones by using X11 implementations for the personal computers and a LAN. --bks) X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions Q3: Where can I get ACEDB? ++++++++++++++++++++++++++ A3: +++ The standard ACEDB source and binaries are available in the following public access accounts (anonymous ftp sites) accessible via Internet: o lirmm.lirmm.fr in pub/acedb o cele.mrc-lmb.cam.ac.uk in pub/acedb o ncbi.nlm.nih.gov in repository/acedb o bioinformatics.weizmann.ac.il in pub/databases/acedb. MacAce is available from: o genome.lbl.gov in pub/macace o cele.mrc-lmb.cam.ac.uk in pub/acedb/macace Linux; ACEDB version 4.1 (and earlier versions) for Linux 2-10: o trog.mbb.sfu.ca /pub/acedb as bin.linux.4_1.tar.Z. ACEDB for The NEC EWS4800: o ftp.nec.co.jp[obsolete? --bks] in /pub/packages/acedb/ace2. Return to List of Questions Q4: What ACEDB databases exist? +++++++++++++++++++++++++++++++ A4: +++ In alphabetic order by Database name ------------------------------------ [Curators, please submit changes as new paragraphs] Database : AaeDB Species : Aedes aegypti (Mosquito) Last_update : December 1994 ACEDB_version : 3.0 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Database : AAtDB Species : Arabidopsis thaliana Current version : 3-5 Last_update : August 1995 PI : J. Michael Cherry Curator : David Flanders Contact : arab-curator@genome.stanford.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : genome-ftp.stanford.edu in arabidopsis/aatdb FTP : ncbi.nlm.nih.gov in repository/aatdb FTP : probe.nalusda.gov in pub/aatdb Gopher : genome-gopher.stanford.edu/11/Arabidopsis Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://genome-www.stanford.edu WWW : http://probe.nalusda.gov:8300/plant/ Database : AboutDB Curator : Staffan Bergh, staffan@biochem.kth.se Subject : ACEDB itself (meta-meta-metadata) ACEDB_version: 3.0 Last_update : July 1995 WWW : http://www.biochem.kth.se/AboutDB.html Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@mrc-lmb.cam.ac.u Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Last_update : August 1995 Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ DataBase : AceMap Species : Homo sapiens Subject : Physical mapping data for human chromsome X ACEDB_version : 4.1 Curator : Hugues Roest Crollius, croillius@mpimg-berlin-dahlem.mpg.de PI : Hans Lehrach FTP : ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap Comment: Get the README file in the directory above. Contact : Max-Planck-Institut fur Moleulare Genetic, Ihnestrasse 73, 14195 Berlin, Germany Availability : beta release of the X chromosome data/models via anonymous ftp FTP : ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap Last_update : August 1994 Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu Last_update : March 1994 ACeDB_version : 3.0 Subject: Contains extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe yeast); interacting loci via defined Interactions for each locus Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 Last_Update : July 1995 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 4.1 Last_updated : September 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Last_update : August 1995 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Last_update : September 1995 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : CoolGenes Species : Cool Season Fool Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edubr> ACEDB_version : 3.0 Last_update : January 1996 Gopher : gopher://probe.nalusda.gov:7000/11/genome.databases/coolgenes/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 Last_update : January 1995 (version 95.1) ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ Database : CSNDB Focus : Cell Signalling Molecules and Interactions Contact : Takako Igarashi, National Insitute of Health Sciences, Division of Chem-Bio Informatics, Setagaya-ku, Tokyo, Japan 158, taka@nihs.go.jp Database : EofD (Encyclopaedia of the Drosophila) Species : Drosophilidae (primarily D. melanogaster) Availability : Macintosh CD-ROM and SunOS executables via anonymous ftp Last_update : November 1995 ACEDB_version : 4.1 Developer : Suzanna Lewis, suzi@fly2.berkeley.edu Developer : Cyrus Harmon, sly@fly2.berkeley.edu Developer : Edward Welbourne, eddy@gen.cam.ac.uk Collaborator : The FlyBase Consortium, flybase-help@morgan.harvard.edu Collaborator : The Berkeley Drosophila Genome Project, flygenome@maillink.berkeley.edu FTP : fruitfly.berkeley.edu in pub/EofD Gopher : fly.bio.indiana.edu:70+/11/Flybase WWW : http://shoofly.berkeley.edu WWW : http://fly2.berkeley.edu:3512/EofD.html Database : EthnobotDB (orldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Last_update : June 1995 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Last_update : May 1995 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : GrainGenes Species : Wheat, barley, oats, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_1 Data_version : 1.5+ Last_update : November 1995 FTP : probe.nalusda.gov in pub/graingenes Gopher : greengenes.cit.cornell.edu/ Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://wheat.pw.usda.gov/graingenes.html Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr WWW : http://moulon.inra.fr/acedb/igd.html Description : IGD (Integrated Genomic Database) aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : LeishDB Species : Leishmaia major, L. infantum, L. peruviana, L. donovani and others PI : Jennie Blackwell PI : Al Ivens Last_update : September 1995 ACEDB_version : 4.1 Contact : Matin Aslett, ma10025@cus.cam.ac.uk FTP : ftp://parsun1.path.cam.ac.uk [obsolete? --bks] WWW : http://parsun1.path.cam.ac.uk/ Curator : Martin Aslett Curator : Howard Cobb Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie-Paule Lefranc Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr Database : MaizeDB Species : Zea mays L. ssp. mays and related species Latest_release : April 1995 Acedb_version : 3.3 Comment : MaizeDB is a periodically extracted ACeDB front end for the Maize Genome Database, MaizeDB, a SYBASE database, implemented using Genera software, developed by Stan Letovsky. Comment : Genera provides (1) up-to-the-minute form internet access to SYBASE databases, both for query (WWW and APT) and data entry (APT only); (2) database design alterations by systems administrators; (3) gopher file extraction. Comment: MaizeDB uses WWW record-to-record hard-links to 16 external databases for (1) annotated sequences: GenBank, dbEST, GenoBase, PIR, SwissProt, Prosite, ENZYME; (2) other species genome information: AAtDB(Arabidopsis), RiceGenes, GrainGenes, SaachDB (yeast), CGSC(E. coli), XLocus, RiceGenes, GrainGenes (3) germplasm: GRIN. Data : Over 100,000 records include: 6513 mapped loci (located to chromosome or better) including 1081 mapped genes and 1937 mapped probed sites (gene candidates); 2448 probes; 2460 map scores; 1551 gel patterns (Probe/Enzyme/Stock); 8777 stocks; 18,100 Variations (alleles, DNA polymorphisms, rearrangements, etc); 596 phenotypes; 317 traits; 715 gene products; 6158 bibliographic references; 2200 researchers with addresses. FTP : probe.nalusda.gov in pub/maizedb Gopher : gopher.agron.missouri.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: corncob WWW : http://www.agron.missouri.edu/top.html WWW : http://probe.nalusda.gov:8300/plant/ WWW Genera information : http://gdbdoc.gdb.org/letovsky/genera/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe, ed@teosinte.agron.missouri.edu Curator : Mary Polacco, maryp@teosinte.agron.missouri.edu Assoc Curator : Pat Byrne, byrne@teosinte.agron.missouri.edu QTL data Assoc Curator : Georgia Davis, gdavis@teosinte.agron.missouri.edu Map data Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic Stock data Assoc Curator : Christiane Fauron, FAURON@GENE1.med.utah.edu Mitochondrion genome Assoc Curator : Carolyn Wetzel, cmwetzel@iastate.edu Chloroplast genome Assoc Curator : Steve Rodermel, S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome Design : Stan Letovsky, letovsky@gdb.org Design : Mary Berlyn, mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock, dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 11 April 1995 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Last_update : July 1995 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : Millet Genes Species : Pennisetum Glaucum (Pearl Millet) ACEDB_version : 4.1 Availablity : Local Curator : Matt Couchman, couchman@bbsrc.ac.uk Curator : Katrien Devos, devos@bbsrc.ac.uk DataBase : Mousedb Species : Musculus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD Last_update : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_vertion : 4.0 Last_update : June 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : MsqDB Species : Interspecies Mosquito database Last_update : March 1996 ACEDB_version : 4.1 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Contact : aaedbmgr@klab.agsci.colostate.edu Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. Curator : Staffan Bergh, staffan@biochem.kth.se Curator : Stewart Cole, stcole@pasteur.fr Last_update : November 1995 ACEDB_version : 4.1 Data_version : 4-9 (November 1995) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au Curator : Gail Juvik, gjuvik@nalusda.gov - ACEDB version ACEDB_vertion : 4.0 Last_update : September 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Last_update : June 1995 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 Last_update : September 1995 FTP : ftp.sanger.ac.uk in pub/PomBase Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Last_update : June 1995 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susah McCouch ACEDB_version : 4.1 Last_update : November 1995 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 2.0, MacAce 2.0b4 Last_update : September 1995 Data_version : 2.4.12 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB Gopher : genome-gopher.stanford.edu WWW : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Rita Schmidt, bleb@genome.stanford.edu Curator : Barbara Dunn, bdunn@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Programmer : Karen Davis, karen@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu PI : Steve Tanksley Release : ACEDB 3.0 Last_update : May 1995 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 Last_update : September 1995 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker Curator : David Grant, dgrant@iastate.edu Assistant_curator : Marica Imsamde, mimsande@mendel.agron.iastate.edu Contact : David Grant, dgrant@iastate.edu ACEDB-Version : 3.7 Last_update : October 1995 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://mendel.agron.iastate.edu:8000/main.html Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server Last_update : October 1994 FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Database : Toxo Species : Toxoplasma gondii PI : Jennie Blackwell PI : Jim Ajioka Last_update : September 1995 ACEDB_version : 4.1 Contact : Martin Aslett, ma10025@cus.cam.ac.uk FTP : parsun1.path.cam.ac.uk WWW : http://parsun1.path.cam.ac.uk/ Curator : Martin Aslett Curator : Howard Cobb Database : TreeGenes Species : Forest trees ACEDB_version : 3.0 Last_update : July 1995 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ Database : Trypbase Species : Trypanosoma brucei PI : Sara Melville Curator : Martin Aslett, ma10025@cus.cam.ac.uk Curator : Howard Cobb, hc102@econ.cam.ac.uk Contact : sm160@mole.bio.cam.ac.uk ACEDB_version : 4.1 (Sun and Linux) FTP : parsun1.path.cam.ac.uk WWW : http://parsun1.path.cam.ac.uk Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Last_update : April 1994 FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Database : 11Db Species : Homo sapiens Subject : Physical and Genetic mapping of Human Chromosome 11 Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk) PI : Peter Little (p.little@bc.ic.ac.uk) ACEDB_version : based on 4_1 with added map displays. ACEDB_version : based on 3_6 with added map displays. Data version : 1.0 Last Update : December 1995 WWW : http://chr11.bc.ic.ac.uk FTP : ftp.cc.ic.ac.uk Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Database : 22ace Species : Homo sapiens Subject : Physical map of human chromosome 22, genomic sequencing and more ACEDB_version : 4.1 Curator : Ian Dunham, id1@sanger.ac.uk Curator : Gareth Maslen, glm@sanger.ac.uk PI : Ian Dunham Last_update : August 1995 FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu Last_update : September 1993 ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions Q5: What documentation exists for ACEDB? ++++++++++++++++++++++++++++++++++++++++ A5: +++ From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000 . Primary documents from the developers are: o acedb -- A C. elegans Database: I. Users' Guide. o acedb -- A C. elegans Database: II. Installation Guide. o acedb -- A C. elegans Database: III. Configuration Guide. o Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z . The files are in TeX (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/index.html A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html . Japanese language guides: _Japanese ACEDB Guide Ver.1.2._ _ACEDB ver.2 for NEC engineering workstation EWS4800 series_ are available in PostScript via anonymous ftp at ftp.nec.co.jp as /pub/packages/acedb/acemanjp.1_2.ps.Z . There is a Japanese language ACEDB FAQ available at http://www.cbi.or.jp/~sano/acemanjp12/index.html SampleDB, by Dave Matthews, is an ACEDB database constructed to demonstrate features of ACEDB, especially map and sequence displays. Anonymous ftp to probe.nalusda.gov:pub/acedocs/sampledb You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angistute.ps and angistute.hqx available by anonymous ftp at ncbi.nih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). URL : http://genome-www.stanford.edu/docs/aatdb_man.html . A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. URL : http://probe.nalusda.gov:8000/acedocs/overview.html . Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. Return to List of Questions Q6: What other resources are available for ACEDB? +++++++++++++++++++++++++++++++++++++++++++++++++ A6: +++ Perl and WWW tools ++++++++++++++++++ The AGIS server at the National Agricultural Library provides a tool set for integrating version 4 of ACEDB with perl and the World-Wide Web. The archive is ftp://probe.nalusda.gov/pub/tools/acelib.tar.gz For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/ . The Developers' Archive +++++++++++++++++++++++ Mike Cherry maintains an archive of tools that may be useful in curating ACEDB databases via gopher at gopher://genome-gopher.stanford.edu:70/11/ftp If you have a contribution send a message to Mike (cherry@genome.stanford.edu). The Biosci conference bionet.software.acedb +++++++++++++++++++++++++++++++++++++++++++ There is a USENET/Biosci conference titled bionet.software.acedb created expressly for discussion of ACEDB. The best way to interact with the Biosci conferences is via a newsreader like rn, trn, tin or a WWW browser. Consult your system administrator for more information. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. All of the articles in biosci.software.acedb are archived by Biosci at http://www.bio.net:80/hypermail/ACEDB/ and by Mike Cherry at http://genome-www.stanford.edu/cgi-bin/biosci_acedb. If your WWW browser is configured properly you may be able to read the newsgroup at news:biosci.software.acedb . And more ++++++++ The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: o http://moulon.inra.fr/acedb/acedb.html for C. elegans data o http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data o http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html A how-to manual on the Moulon server is available at http://keck.tamu.edu/cgi/staff/ace-mosaic-howto.html The Genome Computing Group, Lawrence Berkeley Laboratory, has an anonymous ftp service at machine genome.lbl.gov which contains: o flydb - LBL's Drosophila Acedb-style database o 21bdb - LBL's Human Chromosome 21 Acedb-style database o querdb - LBL's query-language extensions to Acedb o metadata - LBL's compendium of Acedb database schema variants o macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version o There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to dataabases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: o 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). o 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier Jean Thierry-Mieg et al), and the Interated Genome Database project in Heidelburg (Otto Ritter, Detlef Wolf et al). Return to List of Questions Q7: How should ACEDB be cited? ++++++++++++++++++++++++++++++ A7: +++ From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions Q8: Is ACEDB object-oriented? +++++++++++++++++++++++++++++ A8: +++ From the ACEDB User's Guide: A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions Q9: How can I get on/off the ACEDB announcements mailing list? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A9: +++ To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q6 for details] is on the mailing list. Return to List of Questions Q10: When and where is the Next ACEDB Workshop? +++++++++++++++++++++++++++++++++++++++++++++++ A10: ++++ The 1996 Workshop is not yet scheduled. If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, there are online collections: o by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; o by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; o and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions Q11:Who prepared this document & where is the current version? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A11: ++++ This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu as pub/usenet/news.answers/acedb-faq . If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html and http://s27w007.pswfs.gov/Homepage/acedbfaq.html There is a Japanese language FAQ available at http://www.cbi.or.jp/~sano/acemanjp12/index.html Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov Major contributions in getting this FAQ off the ground were made by Mike Cherry, John McCarthy, and Doug Bigwood. Other contributors include: o Lisa Lorenzen o David Matthews o Edie Paul o Donn Davy o Eric De Mund o Sam Cartinhour Please cite as: Sherman,B.K., ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993,1994,1995,1996 approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome Research Program. Return to List of Questions End of ACEDB FAQ --bks From owner-acedb@net.bio.net Wed Apr 17 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.cais.net!newsfeed.internetmci.com!news.msfc.nasa.gov!bcm.tmc.edu!usenet From: Corey Lovitt Newsgroups: bionet.software.acedb Subject: Looking for transformation scripts Date: Thu, 18 Apr 1996 15:12:55 -0500 Organization: Baylor College of Medicine Lines: 11 Message-ID: <3176A247.4D97@bcm.tmc.edu> NNTP-Posting-Host: grok.imgen.bcm.tmc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) Hello, I'm interested if anyone in the ACeDB community has written scripts or knows of scripts which create an ACE readable database from a relational one. I'm interested in ACE's visualization tools but we have all our data stored in a relational type format. Thanks in advance for any replies and help. Cheers, Corey From owner-acedb@net.bio.net Wed Apr 17 23:00:00 1996 Path: biosci!CUTTER.LBL.GOV!davy From: davy@CUTTER.LBL.GOV (Donn Davy) Newsgroups: bionet.software.acedb Subject: Re: Looking for transformation scripts Date: 18 Apr 1996 14:13:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3176A247.4D97@bcm.tmc.edu> Reply-To: Donn Davy NNTP-Posting-Host: net.bio.net On Thu, 18 Apr 1996, Corey Lovitt wrote: > I'm interested if anyone in the ACeDB community has written scripts or > knows of scripts which create an ACE readable database from a relational > one. I'm interested in ACE's visualization tools but we have all our > data stored in a relational type format. > There is an awk script called "line2ace" which converts a tab-delimited dump of tabular material (like from a relational db) in the archives of acedb somewhere (at ncbi, I think). I have written something similar in perl: enclosed below. The 1st line is gives the Class name then acedb 'field' tags, succeeding lines have tab-separated data. The output is a .ace file suitable for loading a particular acedb class. I plan a variant which will do the update directly, using the aceclient/aceserver. --------------------------------------------+------------------ Donn F. Davy, Computer Systems Engineer / (510) 486-4162 Lawrence Berkeley National Laboratory \ MS 50F-129, One Cyclotron Rd / Berkeley, CA 94720 \ fax (510) 486-5548 -----------------------------------------+--------------------- ----------- begin enclosed matter ------------- #!/usr/local/bin/perl #l2a - convert tabular delimited data to .ace # assumptions: # - class object ID is column 1 # - tag names are column titles in row 1 # - for rows w/ blank col 1 (ID): any values on line accrue to prev object $lno = 0; LINE: while (<>) { if (/^\s*$/) { next LINE}; ## skip blank lines $lno++; if ($lno == 1) { chop; @fields = split(/[\t]/); next LINE; } chop; split(/[\t]/); unless ($_[0] =~ /^[ \t]*$/) { $_[0] =~ s/"//g; ## strip out all double quotes print "\n$fields[0] : \"$_[0]\"\n"; } for ($i = 1; $i <= @fields; $i++) { unless ($_[$i] =~ /^[ \t]*$/) { $_[$i] =~ s/"//g; ## strip out all double quotes print "$fields[$i] \"$_[$i]\"\n"; } } print "\n"; } From owner-acedb@net.bio.net Sun Apr 28 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!in2.uu.net!EU.net!Germany.EU.net!Dortmund.Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.ruhr-uni-bochum.de!news.uni-stuttgart.de!news.belwue.de!News.Uni-Marburg.DE!usenet From: Michael Otto Newsgroups: bionet.software.acedb Subject: xcontigview (!) Date: Mon, 29 Apr 1996 08:41:59 +0200 Organization: Hochschulrechenzentrum der Universitaet Marburg Lines: 27 Message-ID: <318464B7.41C67EA6@Mailer.Uni-Marburg.DE> NNTP-Posting-Host: su2002.humangenetik.humanmedizin.uni-marburg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 4.1.4 sun4m) CC: otto@Mailer.Uni-Marburg.DE Hi Newsgroup, is there someone with experiences compiling/installing the program Xcontigview (Version 1, Release 1) by Hugues Roest Crollius ? The program was presented at the ACEDB'95 Workshop (in Berlin ?) and it looks like something we can need. I tried the install it on a SUN SparcStation 20 (32 Mbyte Memory), pathnames should be correct (I believe), but the Makefile stops with errors at the very first source-file telling me that it did not find some procedures (>imageformats< and >load_image_proc<). Using grep, I found, that these procedures do not belong to the program itself. Don't know what's missing - can anyone help me - I also tried to install it on an IBM/AIX system (RS6000). Here the Makefile works without any error messages, but the executable dumps (!) - any help would be very welcome - thanks in advance Michael Otto From owner-acedb@net.bio.net Sun Apr 28 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!EU.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!rag2.rz-berlin.mpg.DE!crollius From: crollius@rag2.RZ-Berlin.MPG.DE (Hugues Roest Crollius) Newsgroups: bionet.software.acedb Subject: Re: xcontigview (!) Date: 29 Apr 1996 14:05:42 GMT Lines: 79 Message-ID: <4m2ibm$2mu@fu-berlin.de> References: <318464B7.41C67EA6@Mailer.Uni-Marburg.DE> NNTP-Posting-Host: rag2.rz-berlin.mpg.de (141.14.130.102) NNTP-Posting-User: crollius X-Access: 16 25 816 Hello Michael, Just to give a few precisions and give credit back to who deserves it: In article <318464B7.41C67EA6@Mailer.Uni-Marburg.DE>, Michael Otto writes: |> Hi Newsgroup, |> |> is there someone with experiences compiling/installing the program |> Xcontigview (Version 1, Release 1) by Hugues Roest Crollius ? I didn't write a single line of code. Huw Griffith in our lab at the ICRF in London wrote xcontigview, to help data entry in acedb. Ralph Muhlhaus from the MPI in Berlin did a few modifications and I think that he got in touch with you regarding the problems you mentioned, which are solved now I believe. To inform those who don't know xcontigview and who might be interested, below is the introduction of the README file which goes with the program. Hugues H. Roest Crollius Abt. Lehrach Max-Planck-Institut fuer Molekulare Genetik Ihnestrasse 73 14195 Berlin Germany e-mail: roest@mpimg-berlin-dahlem.mpg.de ********************************************************************************* By Huw Griffiths, Genome Analysis Laboratory, ICRF, London (huw@gea.lif.icnet.uk) (1994) xcontigview Version 1 , Release 1 README Introduction Xcontigview is an X Windows based program designed to allow the entry of maps from a sheet of paper into a format suitable for use by an AceDB type database. It is built using the Athena widget set and it is therefore neccessary to have Xaw library which is distributed with X11. It will read images in Tiff format though it is possible to hook on routines to read different image formats. It will also read Hips images for which it need the public domain Hips library libhipspub. As this program has been developed independently of AceDB it has had to incorporate a degree of configurability to allow for changes made to Acedb. It will allow a user to set, by the use of a configuration file, the type/name of the objects he wishes to enter, eg. clone, probe etc. Data is transformed into correct AceDb format using an awk script as a filter. The progam comes with awk scripts suitable for AceDB Version 1 & 3 formats. From owner-acedb@net.bio.net Mon Apr 29 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: bug fix report Date: 30 Apr 1996 16:55:11 +0100 Lines: 220 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4m5d4v$pkq@mserv1.dl.ac.uk> Original-To: dok432@mbp-sgi5.embnet.dkfz-heidelberg.de, o.ritter@dkfz-heidelberg.de Final test fro distribution 4.3 Test was ran under 4.3h I found two missing feature that i added to 4.3i The constraints which was missing in 4.1 and is only supported in parse.c, The new feature is to be able to follow complex-questions, i.e. Follow A#B or Follow A = "aaa" Everything now works correctly as far as I know. Detlef found after release 4.1 that the main remaining problems were: 1) the query used in IGD for single-chromosome subset selection is still not parsed, nor does the query 2) where find Probe probe_clone_data = "vector_type" AND NEXT = "Plasmid" work. Then he gave a list of current problems sorted by priority. I checked all of then in 4.3 and added in his lists some comments ------------------------------------------------------- :NAME: tagvqry :PRIORITY: 5 :SUMMARY: queries on values after tags works in 4.3h Example: acedb> clear // 0 Active Objects acedb> query Find n R = aaa AND NEXT = bbb // Found 1 objects // 1 Active Objects acedb> show N : "nn1" R aaa bbb A better syntax now is: acedb> query Find n R:2 = bbb // Found 1 objects ------------------------------------------------------- :NAME: parsubq :PRIORITY: 4 :SUMMARY: parameter substitution in queries in complex cases works in 4.3h ------------------------------------------------------- :NAME: abnmqry :PRIORITY: 3 :SUMMARY: find M "" should find the M object called works in 4.3h ------------------------------------------------------- :NAME: cttab :PRIORITY: 3 :SUMMARY: constructed types and parameter passing in table definitions works in 4.3h ------------------------------------------------------- :NAME: nnmqry :PRIORITY: 3 :SUMMARY: queries for objects whose name is a number works in 4.3h ------------------------------------------------------- :NAME: aqdump :PRIORITY: 2 :SUMMARY: turn attached query results on/off in write command works in 4.3h ------------------------------------------------------- :NAME: atqry :PRIORITY: 2 :SUMMARY: attached queries from root of objects; show attached data works in 4.3h example: acedb> find A1 // Found 1 objects in this class // 1 Active Objects acedb> show A1 : "a1" T a2 U V W a2 X a4 Y // 1 object dumped // 1 Active Objects acedb> show -a A1 : "a1" T "a2" "this should be picked up by the attached query" T "a2" "multi-valued should work" T "a2" U "just to make sure that only part of the a2 object is attached" U "this should be displayed by the U @'>T\; B' query in model of A1" U V W "a2" "this checks attach from within a constructed type" V W "a2" X "a4" "a2" X "a4" //!! Internal error : condMatch should not parse FIND Y // This crash is correct, you have to attach locally, not a whole class. // 1 object dumped // 1 Active Objects acedb> ------------------------------------------------------- :NAME: cnstrain :PRIORITY: 2 :SUMMARY: constraints should be evaluated when loading data works in 4.3i was nullified in 4.1 except on read new models, actually we do not use it for nematode or anywhere else that i know ------------------------------------------------------- :NAME: dblqot :PRIORITY: 2 :SUMMARY: double quotes in data and names and queries works in 4.3h example: acedb> parse // Type in your data in .ace format, then CTRL-D to finish N "quo\"ed" M "bizre{ data\"\\" // 1 objects read with 0 errors// 1 Active Objects acedb> find N quo"ed // Found 1 objects in this class // 1 Active Objects acedb> show N : "quo\"ed" M bizre{ data"\ // 1 object dumped ------------------------------------------------------- :NAME: ppcont :PRIORITY: 2 :SUMMARY: loading erroneous data with pparse works in 4.3 ------------------------------------------------------- :NAME: followct :PRIORITY: 1 :SUMMARY: query that uses follow into a constructed type: follow A#B works in 4.3i i had forgotten that one, i just fixed it now. This was never in the acedoc, but i remember Otto wanted it for a long time. The same system now allows: N : "nn1" R aaa bbb M mm1 cc1 mm2 cc2 cc3 acedb> query Follow M = mm1 // -> cc1 acedb> query Follow M = mm2 // -> cc2 , cc3 ------------------------------------------------------- :NAME: tables :SUMMARY: some tests on complex tables works in 4.3h you must "" otherwise the text a is mixed with the tag a the correct condition is "%3" = "%2" ------------------------------------------------------- Everything else in Detlef script is ok except: /* :SUMMARY: "help query" shows query help text :PRIORITY: 1 :STATUS: not clear :FEATURE: :HISTORY: :MODEL: :DATA: :RESULT: fails in: ace950522a4n -- "help query" gives wrong result on first invocation, works on subsequent :SCRIPT: */ help: dbinit wspec.mini // help system tace help1: do -e help query help2: do -e help query exit Comment: I cannot reproduce the bug outside of aquila. ****** /* :SUMMARY: model command does not work for renamed classes :PRIORITY: 1 :STATUS: fail, Comment: but is it a bug ? the local model file should be remaned ****** /* :SUMMARY: constructed types and parameter passing in table definitions :PRIORITY: 3 :STATUS: nearly ok, comment: The table definition should say Next_Key rather than text to access a a#b in table. This is a half bug, because it works but the interface is not natural. ****** CONCLUSION: No remaining bug: From owner-acedb@net.bio.net Mon Apr 29 23:00:00 1996 Path: biosci!GENOME.LBL.GOV!beauheim From: beauheim@GENOME.LBL.GOV (Catherine Beauheim) Newsgroups: bionet.software.acedb Subject: (none) Date: 30 Apr 1996 11:31:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604301828.AA28085@genome.lbl.gov> NNTP-Posting-Host: net.bio.net subscribe From owner-acedb@net.bio.net Tue Apr 30 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 1 May 1996 02:01:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605010900.CAA14311@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-acedb@net.bio.net Tue Apr 30 23:00:00 1996 Path: biosci!USSUN4E.GLAXO.COM!ehl21107 From: ehl21107@USSUN4E.GLAXO.COM (Eric Lai) Newsgroups: bionet.software.acedb Subject: Workshop and Class Date: 1 May 1996 08:41:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605011534.LAA11795@ussun4e> NNTP-Posting-Host: net.bio.net I was told that there is a Acedb class offered in England or France during the summer. Is this true and who offers this? Is there a Acedb workshop in 1996? Eric Lai GlaxoWellcome Inc,