From owner-acedb@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!library.ucla.edu!humc.edu!news.cerf.net!news Newsgroups: bionet.software.acedb Subject: protein and peptide objects in acedb Message-ID: <3112631C.3514@zone.org> From: Jason Martin Date: Fri, 02 Feb 1996 11:16:44 -0800 Organization: CERFnet NNTP-Posting-Host: 198.207.137.33 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b4 (X11; I; SunOS 5.4 sun4m) CC: jason@sequana.com Lines: 44 Ace users, developers: I am interested in storing exon translations from gene-prediction programs as Protein/peptide objects. We want to do this because of the following sitatuation that can occur at exon splice boundaries: SPLICE exon1 | exon2 ACC GAG|GAT AGG --- --- --- --- the 'show translation' feature would give THR GLU ASP ARG the correct translation for exon2, and we would be :) but occasionally we get this: SPLICE exon1 | exon2 C CGA G|GA TAG G the 'show translation' feature would choke on this - --- ---- --- - because it doesn't know what frame to translate the . ARG GLY * . second exon in. What we would like to do is store the translation directly as a pepetide, that we could access by going to the 'corresponding_protein' of each exon. Once there, we could hopefully export the peptide as an AA sequence. I've tried to store peptides in an analagous manner to storing DNA features, but there doesn't seem to be any back-end built into aCEdb for displaying the translation. Any ideas or help would be greatly appreciated. (sorry if you didn't view this with a non-proportional font!) Jason --------------------------------------- Jason Martin Biocomputational Scientist Sequana Therapeutics, Inc. 11099 North Torrey Pines Rd. Suite 160 La Jolla, CA 92037 (619)-452-6550 (619)-452-6653 [FAX] jason@sequana.com --------------------------------------- From owner-acedb@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: ACEDB3 -> ACEDB4.1 Date: 3 Feb 1996 13:47:42 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <9602032145.AA02646@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > Also, are there other things I need to know when upgrading from > 3.0 to 4.1? Has anyone written any documentation on upgrading? Well, not really. The best I know of is SampleDB, a small sample ace4 database that's supposed to function as "executable documentation". The main things you need to work on, as far as I recall, are: 1. Some of the magic tags that drive particular features of the GMAP display have changed. See SampleDB's models.wrm and the explanations in Magic Tags and The Genetic Map Display. 2. The GMAP display is now configurable, and configurations can be saved in objects of class ?View. See "The Genetic Map Display". SampleDB contains some Views that are better than the configuration you get if you don't use a default View at all. 3. The traditional online help system now runs via Mosaic, using html files in a new directory $ACEDB/whelp. This requires a script in the new directory wscripts. See SampleDB. 4. Pick_me_to_call no longer assumes the data files are in $ACEDB/ externalFiles. To invoke xv now on those same files now, replace "Pick_me_to_call xv my.gif" with "Pick_me_to_call display my.gif" and create the following executable script named $ACEDB/wscripts/display: #!/bin/csh xv $ACEDB/externalFiles/$1 & - Dave From owner-acedb@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!mongol.sasknet.sk.ca!canopus.cc.umanitoba.ca!news From: Brian Fristensky Newsgroups: bionet.software.acedb Subject: ACEDB3 -> ACEDB4.1 Date: 2 Feb 1996 21:19:25 GMT Organization: University of Manitoba Lines: 96 Message-ID: <4etv4t$pl5@canopus.cc.umanitoba.ca> NNTP-Posting-Host: vogt.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4m) X-URL: news:bionet.software.acedb#4etud1$olf@canopus.cc.umanitoba.ca (I originally posted this message with no subject line. Sorry.) I am trying to upgrade from ACEDB3 to ACEDB4.1, but when I start ACEDB4.1, I get errors regarding my models. These models worked in ACEDB3. The errors seem to fall into 3 classes: ########################################################################### 1) Model error: non-tag ?Journal in column in model ?Paper //------------------------------------------------------------------ ?Journal Paper ?Paper XREF Journal //------------------------------------------------------------------ ?Paper Reference Title UNIQUE ?Text Journal UNIQUE ?Journal XREF Paper Unpublished Volume UNIQUE Text Text Pages UNIQUE Text Year UNIQUE Text Publisher UNIQUE Text Author ?Author XREF Paper Contained_in ?Paper XREF Contains Editor ?Author Medline_ID UNIQUE Int GenBank UNIQUE Text Accession UNIQUE Text Abstract ?LongText Type UNIQUE Text Contains ?Paper XREF Contained_in Image ?Image XREF Paper Refers_to ANY Keyword ?Keyword Remark Text Journal does, in fact appear as a tag in tags.wrm. ########################################################################### 2) Model error: tag Strain outside rooted subtree in model ?DNA_Sample //------------------------------------------------------------------ ?DNA_Sample Name Text Experiment ?Experiment XREF DNA_Sample Image ?Image Accession Text DNA_Type UNIQUE Plasmid ?Plasmid XREF DNA_Sample Vector ?Vector XREF DNA_Sample Genomic ?Species Strain Text Linear_DNA ?Linear_DNA XREF DNA_Sample Conc.[ug_per_ul] Float Freezer Text Box Text ########################################################################### 3) Model error: In model ?Library, tag Paper XREF's to tag Library in class ?Paper can't find tag Library in model ?Paper //------------------------------------------------------------------ ?Library Name Text // Full name Description ?Text // Description of material included Laboratory ?Laboratory Author ?Author Paper ?Paper XREF Library Experiment ?Experiment XREF Library REPEAT Donor_Species ?Species Strain Text Library_Type UNIQUE cDNA Genomic UNIQUE sheared Restriction_Enzyme Text Vector ?Vector Restriction_Site Text Text Host_Strain ?Bacterial_Stock Some class 3 errors are in models that are unchanged from the models.wrm as distributed with ACEDB3. Has model syntax changed, or is ACEDB4.1 just more fastidious at detecting errors? Also, are there other things I need to know when upgrading from 3.0 to 4.1? Has anyone written any documentation on upgrading? -- =============================================================================== Brian Fristensky | Department of Plant Science | A monarch's neck should always University of Manitoba | have a noose around it -- Winnipeg, MB R3T 2N2 CANADA | it keeps him upright. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Robert A. Heinlein FAX: 204-261-5732 | http://home.cc.umanitoba.ca/~frist/ =============================================================================== From owner-acedb@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!mongol.sasknet.sk.ca!canopus.cc.umanitoba.ca!news From: Brian Fristensky Newsgroups: bionet.software.acedb Subject: (no subject) Date: 2 Feb 1996 21:06:41 GMT Organization: University of Manitoba Lines: 92 Message-ID: <4etud1$olf@canopus.cc.umanitoba.ca> NNTP-Posting-Host: vogt.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4m) X-URL: news:bionet.software.acedb I am trying to upgrade from ACEDB3 to ACEDB4.1, but when I start ACEDB4.1, I get errors regarding my models. These models worked in ACEDB3. The errors seem to fall into 3 classes: ########################################################################### 1) Model error: non-tag ?Journal in column in model ?Paper //------------------------------------------------------------------ ?Journal Paper ?Paper XREF Journal //------------------------------------------------------------------ ?Paper Reference Title UNIQUE ?Text Journal UNIQUE ?Journal XREF Paper Unpublished Volume UNIQUE Text Text Pages UNIQUE Text Year UNIQUE Text Publisher UNIQUE Text Author ?Author XREF Paper Contained_in ?Paper XREF Contains Editor ?Author Medline_ID UNIQUE Int GenBank UNIQUE Text Accession UNIQUE Text Abstract ?LongText Type UNIQUE Text Contains ?Paper XREF Contained_in Image ?Image XREF Paper Refers_to ANY Keyword ?Keyword Remark Text Journal does, in fact appear as a tag in tags.wrm. ########################################################################### 2) Model error: tag Strain outside rooted subtree in model ?DNA_Sample //------------------------------------------------------------------ ?DNA_Sample Name Text Experiment ?Experiment XREF DNA_Sample Image ?Image Accession Text DNA_Type UNIQUE Plasmid ?Plasmid XREF DNA_Sample Vector ?Vector XREF DNA_Sample Genomic ?Species Strain Text Linear_DNA ?Linear_DNA XREF DNA_Sample Conc.[ug_per_ul] Float Freezer Text Box Text ########################################################################### 3) Model error: In model ?Library, tag Paper XREF's to tag Library in class ?Paper can't find tag Library in model ?Paper //------------------------------------------------------------------ ?Library Name Text // Full name Description ?Text // Description of material included Laboratory ?Laboratory Author ?Author Paper ?Paper XREF Library Experiment ?Experiment XREF Library REPEAT Donor_Species ?Species Strain Text Library_Type UNIQUE cDNA Genomic UNIQUE sheared Restriction_Enzyme Text Vector ?Vector Restriction_Site Text Text Host_Strain ?Bacterial_Stock Some class 3 errors are in models that are unchanged from the models.wrm as distributed with ACEDB3.Has model syntax changed, or is ACEDB4.1 just more fastidious at detecting errors? Also, are there other things I need to know when upgrading from 3.0 to 4.1? Has anyone written any documentation on upgrading? -- =============================================================================== Brian Fristensky | Department of Plant Science | A monarch's neck should always University of Manitoba | have a noose around it -- Winnipeg, MB R3T 2N2 CANADA | it keeps him upright. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Robert A. Heinlein FAX: 204-261-5732 | http://home.cc.umanitoba.ca/~frist/ =============================================================================== From owner-acedb@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: model syntax: Date: 3 Feb 1996 15:51:48 -0000 Lines: 125 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4f00ak$78o@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr 3 sort of problems were reported: ########################################################################### 1) Model error: non-tag ?Journal in column in model ?Paper //------------------------------------------------------------------ ?Journal Paper ?Paper XREF Journal //------------------------------------------------------------------ ?Paper Reference Title UNIQUE ?Text Journal UNIQUE ?Journal XREF Paper Unpublished Journal does, in fact appear as a tag in tags.wrm. ########################################################################### First of all, tags.wrm can be removed before constructing a new database, the file must stay if the database was constructed before 3.3 but really this does not apply to ace4 databases also the construction: Journal UNIQUE ?Journal XREF Paper Unpublished is not legal in a given column one should not mix up tags and class objects the corerect model should say ?Paper Reference Title UNIQUE ?Text J UNIQUE Journal ?Journal XREF Paper Unpublished in fact it is closer to real life ########################################################################### 2) Model error: tag Strain outside rooted subtree in model ?DNA_Sample //------------------------------------------------------------------ ?DNA_Sample Genomic ?Species Strain Text ########################################################################### This is indeed illegal only basic or constructed types may appear to the right of a pointer you should say ?DNA_Sample Genomic ?Species #St #St Strain Text or you can have ?DNA_Sample Genomic ?Species ?Strain ########################################################################### 3) Model error: In model ?Library, tag Paper XREF's to tag Library in class ?Paper can't find tag Library in model ?Paper //------------------------------------------------------------------ ?Library Name Text // Full name Description ?Text // Description of material included Laboratory ?Laboratory Author ?Author Paper ?Paper XREF Library Experiment ?Experiment XREF Library REPEAT Donor_Species ?Species Strain Text Library_Type UNIQUE cDNA Genomic UNIQUE sheared Restriction_Enzyme Text Vector ?Vector Restriction_Site Text Text Host_Strain ?Bacterial_Stock very true: you are trying to XREF to a non existing tag this is clearly a bug ##################################### The fatsest way to edit the models is to open emacs edit the models file and in a separate window to start tace and issue the command read_model this is much better for that task than using xace #################################### ace 4 models support DateType , look in the session object to see the date foramt correect dates are for example now today 1996 1992-01-25 1995-01-25_18:11:37 .. in addition the coming 4.2 supports COORD modificator inside sequence models to indicate numbers which may slide when an insertion is made say i insert a base in 200 then internally the code will edit every COORD > 200 to increase by 1 there is no esxternal interface yet for this thing but it is used by our sequence manipulation tools Jean From owner-acedb@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: models in ace 3 and ace4 Date: 3 Feb 1996 15:37:02 -0000 Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4evveu$6ee@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr the model syntax has not changed it is enriched a little but 100% compatible BUT, it is more strict and carefully checks the xref we then realised that ALL models used so far had glitches in the way we were using XREF and became fully convinced of the interest of the checking ! From owner-acedb@net.bio.net Sun Feb 04 22:00:00 1996 Path: biosci!agate!howland.reston.ans.net!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!news.kth.se!sibirien.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: ACEDB3 -> ACEDB4.1 Followup-To: bionet.software.acedb Date: 5 Feb 1996 08:19:42 +0100 Organization: Biochemistry, KTH, Stockholm Lines: 84 Sender: staffan@biochem.kth.se Distribution: world Message-ID: <4f4b2e$7t8@sibirien.physchem.kth.se> References: <4etv4t$pl5@canopus.cc.umanitoba.ca> NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Brian, you may already have had this answered by email, but as the news articles in this group are now available as a searchable archive and the documantation is lagging behind, I think it would be nice to have these comments available for all: In article <4etv4t$pl5@canopus.cc.umanitoba.ca> Brian Fristensky writes: >I am trying to upgrade from ACEDB3 to ACEDB4.1, but when I start >ACEDB4.1, I get errors regarding my models. These models worked >in ACEDB3. The errors seem to fall into 3 classes: > >########################################################################### > >1) Model error: non-tag ?Journal in column in model ?Paper > >//------------------------------------------------------------------ >?Paper Reference Title UNIQUE ?Text > Journal UNIQUE ?Journal XREF Paper > Unpublished ^ here you have tags and ?Objects mixed in column, which is not allowed. There will be one more error like this from the Paper model, after Contained_in > Volume UNIQUE Text Text > [some stuff deleted ...] > Contained_in ?Paper XREF Contains > Editor ?Author > Medline_ID UNIQUE Int > [some more stuff deleted ...] > >Journal does, in fact appear as a tag in tags.wrm. The tags.wrm, systags.wrm and sysmodels.wrm files are now obsolete, ACE constructs the list of tags from the models.wrm file. >########################################################################### > >2) Model error: tag Strain outside rooted subtree in model ?DNA_Sample >//------------------------------------------------------------------ >?DNA_Sample Name Text > Experiment ?Experiment XREF DNA_Sample > Image ?Image > Accession Text > DNA_Type UNIQUE Plasmid ?Plasmid XREF DNA_Sample > Vector ?Vector XREF DNA_Sample > Genomic ?Species Strain Text ^ a tag after a ?Object is not allowed, you have to use a constructed subtype >########################################################################### >3) Model error: In model ?Library, tag Paper XREF's to tag Library > in class ?Paper > can't find tag Library in model ?Paper The model for ?Paper included does not have a Library tag > >Some class 3 errors are in models that are unchanged from the >models.wrm as distributed with ACEDB3. As Dave has already pointed out, there are some changes in the 'magic' tags etc. Documentation on (at least some) of the magic stuff is at http://probe.nalusda.gov:8000/acedocs/index.html >Has model syntax changed, or is ACEDB4.1 just more fastidious at >detecting errors? ACEDB4.1 is much more picky. It now does error checking on the models ... Came as a shock to me also when moving MycDB from 3 to 4! Good Luck /staffan Staffan Bergh Biochemistry, KTH, S-100 44 Stockholm, Sweden email: staffan@biochem.kth.se + Don't let that horse eat that violin phone: int+46 8 790 9230 + cried Chagall's mother fax: int+46 8 24 54 52 + but he kept right on painting + -- Lawrence Ferlinghetti Webmaster and MycDB maintainer From owner-acedb@net.bio.net Mon Feb 05 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!gatech!news.emf.net!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: 6 Feb 1996 00:16:19 GMT Organization: Dendrome, A genome database for forest trees Lines: 1170 Approved: news-answers-request@MIT.Edu Message-ID: <4f66kj$bo9@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:838 news.answers:57802 Archive-name: acedb-faq Last-modified: 2/5/96 Version: 1.27 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 4.1 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_1.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 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 : 1.0 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 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 : 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 and ftp://weeds.mgh.harvard.edu/acedb_doc . 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. [text is available through ftp or gopher from weeds.mgh.harvard.edu] 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. [text is available through ftp or gopher from weeds.mgh.harvard.edu] 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. It can be reached by anonymous ftp at URL ftp://weeds.mgh.harvard.edu/acedb_dev/ or via gopher at gopher://genome-gopher.stanford.edu:70/11/ftp If you have a contribution place it in ftp://weeds.mgh.harvard.edu/acedb_dev/incoming/ and 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. o All of the articles in biosci.software.acedb are archived by Biosci at gopher://gopher.bio.net/1/ACEDB o Mike Cherry makes it possible to search past articles in biosci.software.acedb using WAIS at gopher://genome-gopher.stanford.edu:80/77/.index/acedb-biosci and at URL http://genome-www.stanford.edu/biosci_acedb.html . 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 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 Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!wizard.pn.com!brighton.openmarket.com!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!news From: Brian Fristensky Newsgroups: bionet.software.acedb Subject: Re: ACEDB3 -> ACEDB4.1 Date: 7 Feb 1996 18:46:36 GMT Organization: University of Manitoba Lines: 34 Message-ID: <4fas2c$768@canopus.cc.umanitoba.ca> References: <4etv4t$pl5@canopus.cc.umanitoba.ca> <4f4b2e$7t8@sibirien.physchem.kth.se> NNTP-Posting-Host: vogt.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4m) X-URL: news:4f4b2e$7t8@sibirien.physchem.kth.se staffan@biochem.kth.se (Staffan Bergh) wrote: ..deleted >In article <4etv4t$pl5@canopus.cc.umanitoba.ca> Brian Fristensky writes: > >>I am trying to upgrade from ACEDB3 to ACEDB4.1, but when I start >>ACEDB4.1, I get errors regarding my models. These models worked >>in ACEDB3. The errors seem to fall into 3 classes: .. error descriptions deleted... >ACEDB4.1 is much more picky. It now does error checking on the models ... Came >as a shock to me also when moving MycDB from 3 to 4! > Yes. All of my problems stemmed from doing things in 3.0 that 4.1 wouldn't let me get away with. After a bit of tedium, I now have tighter models and a database that works under 4.1. >Good Luck /staffan > >Staffan Bergh >Biochemistry, KTH, S-100 44 Stockholm, Sweden > Many thanks to those who responded to my original post. =============================================================================== Brian Fristensky | We've heard 3 or 4 times this morning that, Department of Plant Science | out of 85,000 works funded by the NEA, University of Manitoba | only 20 were controversial. I don't know Winnipeg, MB R3T 2N2 CANADA | why anyone would cite that as something to frist@cc.umanitoba.ca | be proud of. Office phone: 204-474-6085 | FAX: 204-261-5732 | Garrison Keillor, testimony to Congress in http://home.cc.umanitoba.ca/~frist/ defense of Natl. Endowment for the Arts =============================================================================== From owner-acedb@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: converting to .ace format Date: 8 Feb 1996 11:50:47 -0000 Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4fco2o$f2i@mserv1.dl.ac.uk> Original-To: carson@abacus.mc.duke.edu acedb 4.2 now reads fasta format 4.1 does not i think (i can t remember if it does in fact) fasta format is a file called mydna.ace (other wise the file chooser won t prompt for it) >ZC23A junk that will be kept as a remark atgc aggttdtggttc atgcATGCTGATGC TGA TTGGTGG ace format differs by the title line: DNA ZC23A atgc aggttdtggttc atgcATGCTGATGC TGA TTGGTGG that is it: read the file there will be a new sequence called ZC23A pick it and run genefinder you can then exports the translation to blast it etc From owner-acedb@net.bio.net Mon Feb 12 22:00:00 1996 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: escaping "//" in acediff Date: 13 Feb 1996 12:35:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9602132031.AA24048@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net The Configuration Guide says that in .ace files, "Two consecutive forward slashes (//) signify the start of a comment. Any text following them is ignored. You can escape one of them with a backslash if you really want two forward slashes." This works for xace, but acediff seems to ignore everything after "\//" or "\/\/" too. Is there any way to escape the // in acediff? - Dave From owner-acedb@net.bio.net Mon Feb 12 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: bug in acediff Date: 13 Feb 1996 23:40:32 -0000 Lines: 4 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4fr7hg$v3@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr Dave says: acediff does not escape \/\/ this is an ovious bug we ll try to patch it soon, sorry From owner-acedb@net.bio.net Thu Feb 15 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.tamu.edu!algodon!lazo From: lazo@sun.com (Gerard R. Lazo) Newsgroups: bionet.software.acedb Subject: Re: escaping "//" in acediff Date: 16 Feb 1996 14:33:24 GMT Organization: Sun Microsystems, Inc. Lines: 16 Distribution: world Message-ID: <4g24jk$a6j@news.tamu.edu> References: <9602132031.AA24048@greengenes.cit.cornell.edu> Reply-To: lazo@sun.com NNTP-Posting-Host: algodon.tamu.edu I tried using "//" in the datainfo.wrm file to highlight a web site. Everthing beyond "//" was taken as comments/ I tried "\/\/" also, but "\/\/" was printed. I settled on "/ /", but you need to know that the space shouldn't be there. --- Gerard R Lazo .-.-. USDA-ARS Southern Crops Research Laboratory -. .-. .-. .-. .-. ).). .-. .-. .-. .-. .-. .-. .-. .-. .-. ||X|||\ /|||X|||\(.( .) .)\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /||| |/ \|||X|||/ \|||X(_( ._)||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ ' `-' `-' `-' `-//\)`-' `-' `-' `-' `-' `-' `-' `-' `-' `-' lazo@tamu.edu (( 2765 F&B Rd, College Station, TX 77845-9592 From owner-acedb@net.bio.net Thu Feb 22 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB update for C.elegans 4-14 Date: 23 Feb 1996 15:06:07 -0000 Lines: 86 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4gkl4v$f1d@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. ACEDB data update 4-14 for C. elegans ===================================== The additions since 4-13 are: - more genomic sequence data (there are now 986 cosmids totalling 29,930,126 bases). - electronic entries in WBG 14 Number 2 have been added - a physical map update (January 24) - some medline references have been added together with connections to sequences from these and cgc_references - years have been added to wbg citations - new data submitted by email to the CGC in Cambridge or direct to Sylvia has been entered - a number of errors and problems have been fixed - names of proteins and motifs have been made more systematic, removing some duplications The total database size after adding updates 4-1 to 4-14 is approximately 260 Mbytes. The last 10% of the update, where the protein naming is fixed, is unfortunately extremely slow to read in. Also at this point the update window will flicker. Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb ftp.sanger.ac.uk in England, in pub/acedb lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password: your user id or email address cd repository/acedb # change to relevant directoy binary # IMPORTANT dir # display files in this directory get README get NOTES get INSTALL cd ace4 # change to ace4 directory get bin.sunos.4_1.tar.Z # get program cd ../celegans # change to worm data directory mget update* # get all update files quit -------------------------------- Get any update.4-n.tar.Z that you do not have already and read the file NOTES before proceeding further. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb"), click "Yes" to accept initialising the database if starting from scratch, then choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button. If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Comments about the data should be sent to the data curator, Sylvia Martinelli (sylvia@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- From owner-acedb@net.bio.net Fri Feb 23 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: possible ACEDB update problem Date: 24 Feb 1996 02:42:15 -0000 Lines: 21 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4gltu7$7hc@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk I have had a reliable report of a crash while loading the update 4-14 announced yesterday, using the standard 4_1 software on a Sun computer. This has not happened with previous updates, or on other computers of other types that we know load this update OK. We don't know yet if the problem is with the specific environment where it crashed, or is more general. This type of crash generates the message "segmentation fault" in the Unix shell window from which you started acedb. If there is a message "malloc failure..." then you have run out of memory and should add swap space using mkfile and swapon (not hard, see your system manager or man pages for help if necessary). We will look for a fix/workaround for the segmentation fault problem, but it may take several days (I will be away for 4 days myself from now). If this crash happens to you please email Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) and myself (rd@sanger.ac.uk). That way you will be notified about the fix. Richard Durbin From owner-acedb@net.bio.net Mon Feb 26 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!ddsw1!news.mcs.net!van-bc!unixg.ubc.ca!news.bc.net!news.sfu.ca!trog.mbb.sfu.ca!jbryer From: jbryer@trog.mbb.sfu.ca (Jeff Bryer) Newsgroups: bionet.software.acedb,bionet.celegans Subject: ANNOUNCE: Linux binary for ACEDB v4.2 Date: 27 Feb 1996 02:32:39 GMT Organization: IMBB, Simon Fraser University Lines: 51 Distribution: world Message-ID: <4gtqg7$f20@morgoth.sfu.ca> NNTP-Posting-Host: trog.mbb.sfu.ca Xref: biosci bionet.software.acedb:851 bionet.celegans:822 I have made available both an a.out and an ELF version of ACEDB v4.2 for Linux on trog.mbb.sfu.ca in /pub/acedb (the normal location). I assume that the files will migrate over to the ncbi site shortly. These files are based on the February 14th release of the 4.2 code. For the C. elegans community I will be making available a mult-part archive containing all data releases up to and including 4-14 (same location). The readme's follow: Jeff jbryer@darwin.mbb.sfu.ca ------------- README.LINUX.4_2 February 26, 1996 This is the a.out binary version of ACEDB v4.2 for Linux and can be found at ftp://trog.mbb.sfu.ca/pub/acedb/bin.linux.4_2.tar.gz and soon at ftp://ncbi.nlm.nih.gov/repository/acedb/ace4/bin.linux.4_2.tar.gz If your Linux system cannot handle the a.out format, an ELF version is also available. ftp://trob.mbb.sfu.ca/pub/acedb/bin.linux.4_2.elf.tar.gz Linux is a free Unix-like OS available for the Intel [3456]86 platform. You can find out more about Linux in the comp.os.linux.* groups on usenet. Acedb runs very well on Linux, but you will need a fairly loaded system. I reccomend at _least_ 16MB of RAM and a 486/33. You will also want a large disk that can accomodate the database's growth. More RAM is much better than a faster processor. A 486/66 with 32MB RAM will blow the doors off a Pentium/100 with 8M. You should have 32MB of swap for updates. You should be running Linux 1.0 or better and either the a.out shared libraries (I am using libc 4.5.26) or the ELF libraries (I am using libc 5.0.9). Other versions should work, but are untested. Jeff Bryer jbryer@darwin.mbb.sfu.ca -- ------- Jeff Bryer | "Maybe VR.12 turns you into Fabio." jbryer@darwin.mbb.sfu.ca | -Duncan in Parallel Lives (VR.5) From owner-acedb@net.bio.net Tue Feb 27 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!news.cis.okstate.edu!news.ksu.ksu.edu!pstpm.pp.ksu.edu!user From: PST@KSU.KSU.Edu (Paul St. Amand) Newsgroups: bionet.software.acedb Subject: MacACE 4.1b1 and map display problem Date: 28 Feb 1996 21:52:24 GMT Organization: USDA/ARS and KSU Agronomy Dept. Lines: 13 Message-ID: NNTP-Posting-Host: pstpm.pp.ksu.edu X-Newsreader: Yet Another NewsWatcher 2.1.7 We are using MacACE 4.1b1 and can not display maps at all. If a map name is double-clicked, a window opens and then the machine crashes. We had no trouble with version 2. We have tried numerous models all with the same result. Any suggestions? Thanks, Paul C. St. Amand (PST@KSU.KSU.Edu) USDA Research Geneticist // \\ // \\ // \\ // \\ // 2004 Throckmorton Hall, KSU // | :,\\': | \\ // | :,\\': | \\ // | Manhattan KS 66506-5501\\ // | | // \\ | |\\ // | | // \\ | | \\ // | | (913) 532-6168 \\ | :,\\': | // \\ |:,\\': | // \\ | :,\\': | // Fax (913) 532-6167 \\ // \\ // \\// \\ // \\ // \\ // From owner-acedb@net.bio.net Wed Feb 28 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!news.uiowa.edu!news.physics.uiowa.edu!newsrelay.iastate.edu!news.iastate.edu!macgrant.agron.iastate.edu!user From: dgrant@iastate.edu (David Grant) Newsgroups: bionet.software.acedb Subject: images in MacACE Date: 27 Feb 1996 21:30:40 GMT Organization: Iowa State University Lines: 105 Message-ID: NNTP-Posting-Host: macgrant.agron.iastate.edu Colleagues, A while back I posted a message asking how to get MacACE to display images the way the UNIX versions of ACeDB would. No one had an answer then but after some poking around I have found a method that works. The biggest problem I had was that although the images distributed with MacACeDB 4-1b1 are labeled as JPEGs, they are actually PICTs. Only PICTs will work with MacACE. I discovered this for myself but later found that the images distributed with MacAAtDB_3-6 are correctly labeled as PICT. The PICT images must be in a folder named 'pictures' in the same folder as MacACE, and the database and wspec folders. This is in contrast to our UNIX ACeDB where the GIF files were stored in a folder named 'externalFiles'. I altered our models.wrm and options.wrm to change 'Image' to 'Picture' to match MacACeDB. Later I found that 'Image' is used in MacAAtDB so the exact name is apparently not important. The 'Picture' line in my options.wrm was lifted verbatum from the MacACeDB file. The equivalent line in MacAAtDB is somewhat different though I don't know the significance of the differences. All of our *.ace files that used the tag 'Image' were modified to use 'Picture'. I left in the 'Pick_me_to_call' line although I am fairly certain it is not needed. The following shows the before and after versions of my *.wrm files. original SoyBase UNIX version in options.wrm _VImage -H in displays.wrm _DDtImage -g TEXT_FULL_SCROLL -t "Image" -width .6 -height .4 -help Image in models.wrm ?Image Probe ?Probe XREF Image Locus ?Locus XREF Image Pathology ?Pathology XREF Image Gene ?Gene XREF Image Pick_me_to_call UNIQUE Text Text ... ... ... Last_update UNIQUE Text ?Gene Name Gene_class UNIQUE ?Gene_Class XREF Gene Correct_name ?Gene XREF Other_name Other_name ?Gene XREF Other_name Image ?Image XREF Gene ... ... ... Last_update UNIQUE Text Macintosh SoyBase version in options.wrm _VImage -H _VPicture -H -D DtImage (this line added) in displays.wrm (unchanged from UNIX original) _DDtImage -g TEXT_FULL_SCROLL -t "Image" -width .6 -height .4 -help Image in models.wrm (all instances of 'Image' in the other classes also changed to 'Picture') ?Picture Probe ?Probe XREF Picture Locus ?Locus XREF Picture Pathology ?Pathology XREF Picture Gene ?Gene XREF Picture Pick_me_to_call UNIQUE Text Text ... ... ... Last_update UNIQUE Text ?Gene Name Gene_class UNIQUE ?Gene_Class XREF Gene Correct_name ?Gene XREF Other_name Other_name ?Gene XREF Other_name Picture ?Picture XREF Gene ... ... ... Last_update UNIQUE Text I make no claims to being a MacACE expert and it is possible that some of the changes I made are unneeded. I would be glad to hear from anyone who understands ACeDB better than I as to what the changes I made are doing and which, if any, should be reversed or modified. David Grant dgrant@iastate.edu -- David Grant dgrant@iastate.edu (515) 294-1205 From owner-acedb@net.bio.net Wed Feb 28 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!gatech!newsxfer2.itd.umich.edu!chi-news.cic.net!news.uiowa.edu!news.physics.uiowa.edu!newsrelay.iastate.edu!news.iastate.edu!macgrant.agron.iastate.edu!user From: dgrant@iastate.edu (David Grant) Newsgroups: bionet.software.acedb Subject: Re: MacACE 4.1b1 and map display problem Date: 29 Feb 1996 17:33:25 GMT Organization: Iowa State University Lines: 15 Message-ID: References: NNTP-Posting-Host: macgrant.agron.iastate.edu In article , PST@KSU.KSU.Edu (Paul St. Amand) wrote: > We are using MacACE 4.1b1 and can not display maps at all. If a map name > is double-clicked, a window opens and then the machine crashes. We had no > trouble with version 2. We have tried numerous models all with the same > result. Any suggestions? > I had the same problem. Reverting to 4.0 allowed map displays. I don't remember where I got this version but I'll send it to you if you can't find it. -- David Grant dgrant@iastate.edu (515) 294-1205 From owner-acedb@net.bio.net Thu Feb 29 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!btnet!zetnet.co.uk!usenet From: chris.ctran@zetnet.co.uk (Chris Tranter) Newsgroups: bionet.software.acedb Subject: Internet timer Date: Fri, 01 Mar 1996 08:05:06 GMT Lines: 7 Message-ID: <4h5eml$kop@irk.zetnet.co.uk> NNTP-Posting-Host: man-b2.zetnet.co.uk X-Newsreader: Forte Free Agent 1.0.82 Internet/modem useage logger and timer program now available! Please E-mail for download info! CTran From owner-acedb@net.bio.net Thu Feb 29 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 1 Mar 1996 02:01:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 149 Sender: daemon@net.bio.net Distribution: world Message-ID: <199603011000.CAA02079@net.bio.net> NNTP-Posting-Host: net.bio.net I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We have three sponsors to date with a couple more pending. The process is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we hope to have new and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Statistics are for the four week period from 22 Jan. - 18 Feb. 1996 and usage continues to grow. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5000 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 600 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. ----------------------------------------------------------------------