From owner-acedb@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!CS.UNC.EDU!singh From: singh@CS.UNC.EDU (Raj Kumar Singh) Newsgroups: bionet.software.acedb Subject: BioSCAN -- Biosequence Similarity Analysis Tool Date: 3 May 1994 11:55:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 136 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9405031855.AA29058@polaris.cs.unc.edu> NNTP-Posting-Host: net.bio.net ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + + + BBBBBB OOOOO SSSSSS CCCCCC AAA N N + + B B @ O O S C A A NN N + + B B i O O S C A A N N N + + BBBBBBB ii O O SSSSS C AAAAAAA N N N + + B B ii O O S C A A N N N + + B B ii O O S C A A N NN + + BBBBBB iii OOOOO SSSSSS CCCCCC A A N N + + + + _ _ ___ + + | | |_| _ ___________ _____ _____ __/ / + + | |__ _ ____ | |__ / _____/ // _ // _ // / + + | || || . || | /__ // / // __// ___// / / + + |__|_||_||__ ||__|_|/_____// __//____//____//____/ + + |_____| /_/ "Computer!" + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL Department of Computer Science CB #3175 Sitterson Hall Chapel Hill, NC 27599-3175 Tel: (919) 962-1744 Fax: (919) 962-1799 o AUTOMATIC E-mail Server -- bioscan@cs.unc.edu o ANONYMOUS FTP Server for Client Software -- Host: ftp.cs.unc.edu (presently 152.2.128.159) -- Path: /pub/bioscan o Other Information (Human interface) -- bioscan-info@cs.unc.edu ============================================================================ BioSCAN: A Scalable Multiprocessor System for Biopolymer Similarity Analysis ============================================================================ o DESCRIPTION BioSCAN (Biological Sequence Comparative Analysis Node) is a massively parallel computer system designed for biological sequence similarity analysis. This system performs rapid, rigorous, searches of DNA, RNA, and protein sequence databases and is compatible with popular software packages such as BLAST and FASTA. BioSCAN uses a rigorous implementation of linear similarity methods used in the BLAST systems. It is also well suited to multiscore applications using multiple PAM and BLOSUM scoring matrices. o OVERVIEW o Speed is independent of query sequence length. o System performance is scalable. Maximum query sequence length is determined by the size of the system. (Current VMEbus based design allows up to 12,992 characters in query sequence) o Rigorous implementation of linear similarity method as used in the BLAST system; well suited to multiscore search application using multiple PAM and BLOSUM scoring matrices. o CONCEPT o Combination of hardware and software carefully chosen to provide high performance without sacrificing flexibility. o Simple linear similarity algorithm implemented in hardware reports significant alignments in the database at high speed. o Core algorithm is implemented in a full-custom VLSI chip. o Layered software allows changes and further development of system components without impacting the applications". o FEATURES o Suitable for DNA, RNA and Protein sequences. o Can perform simultaneous searches with multiple LOG-ODDs matrices such as PAM and BLOSUM. o Can perform simultaneous searches of multiple query sequences. o Software architecture supports stand-alone, Client-Server , and E-mail access to the system. o An Application Programming Interface (API) provides easy interface for third-party application software development. o PERFORMANCE o Each VLSI chip scans a maximum of 2 million elements (DNA and RNA bases or amino acid residues) per second. o System scans GenBank 77 database (size 139 million bases) in 71 seconds and SWISS-PROT 25 database (size 10 million residues) in 5 seconds. o GETTING STARTED o To receive the current set of instructions on using the BioSCAN e-mail server, send an e-mail to the address "bioscan@cs.unc.edu". Put the word "HELP" on a line by itself in the body of the message. o A tutorial can be obtained via anonymous FTP from "ftp.cs.unc.edu". The directory is /pub/bioscan and the file is called "tutor.txt". o Please direct problems with the server and other inquries to "bioscan-info@cs.unc.edu". * ACKNOWLEDGEMENTS This research was supported in part by: o NSF, under Grant No. MIP-9024585 o MCNC, under Design Initiative Research Program ============================================================================== Prof. Raj K. Singh Dept. of Computer Science UNC Chapel Hill CB # 3175 Sitterson Hall Chapel Hill, NC 27599-3175 Off: (919) 962-1744l Fax: (919) 962-1799 E-mail: singh@cs.unc.edu From owner-acedb@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!news.tamu.edu!rigel.tamu.edu!grl6732 From: grl6732@rigel.tamu.edu (Gerard R. Lazo) Newsgroups: bionet.software.acedb Subject: Data entry for ACeDB models? Date: 4 May 1994 11:29 CDT Organization: Texas A&M University OpenVMScluster Lines: 13 Distribution: world Message-ID: <4MAY199411294718@rigel.tamu.edu> NNTP-Posting-Host: rigel.tamu.edu News-Software: OpenVMS/VAX VNEWS 1.41 Has anyone written a simple program for entering data for various model data sets in ACeDB? I'd prefer to enter data from within Sun OpenWindows or X-Windows, but a program on the PC, Mac (or even PowerPC) would be alright. This would make things a bit easier than just straightforward text editing. Any assistance would be appreciated. I might give it a try, but if one is already available..... / Gerard R. Lazo . %. (=) GLAZO@tamsun.tamu.edu USDA-ARS (.( .) / Off: 409-260-9533 Southern Crops Research Lab. ( ( .) .) -> (=) Lab: 409-260-9522 Route 5, Box 805 %_( ._) / Fax: 409-260-9333 College Station, TX 77845 //\| (=) (( / From owner-acedb@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!slavsing.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Re: Data entry for ACeDB models? Followup-To: bionet.software.acedb Date: 5 May 1994 15:14:07 GMT Organization: Lawrence Berkeley Laboratory Lines: 38 Distribution: world Message-ID: References: <4MAY199411294718@rigel.tamu.edu> <2q9sut$f44@overload.lbl.gov> NNTP-Posting-Host: slavsing.lbl.gov In article <2q9sut$f44@overload.lbl.gov>, bks@s27w007.pswfs.gov (Bradley K. Sherman) wrote: > In article <4MAY199411294718@rigel.tamu.edu> grl6732@rigel.tamu.edu (Gerard R. Lazo) writes: > >Has anyone written a simple program for entering data for various > >model data sets in ACeDB? > > Most of the work seems to be translations of existing sets rather > than straight data entry. I would bet that most of the curators > have developed various tools based on awk, sed and so forth. > > You might consider something like Filemaker Pro as an input tool > and then transferring the comma-separated text fields to your Unix > box for transformation into an ACE file. > > --bks > > -- > Bradley K. Sherman P.O. Box 245 > Computer Scientist Berkeley, CA, 94701 > Dendrome Project 510-559-6437 FAX: 510-559-6440 > Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov -- Lawrence Berkeley Laboratory has a couple of nawk programs that assist with translation from tab (or other unique character) delimited fields to .ace format files and vice versa -- line2ace and ace2line. You can get them via anonymous ftp from genome.lbl.gov in the directory /pub/SWAP.SOFTWARE/ace2stuff/ If you need to input data "from scratch," you can combine these, as Brad suggests, with a user-friendly data entry tool like FileMaker Pro. +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: Data entry for ACeDB models? Date: 5 May 1994 04:33:33 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 19 Distribution: world Message-ID: <2q9sut$f44@overload.lbl.gov> References: <4MAY199411294718@rigel.tamu.edu> NNTP-Posting-Host: s27w007.pswfs.gov In article <4MAY199411294718@rigel.tamu.edu> grl6732@rigel.tamu.edu (Gerard R. Lazo) writes: >Has anyone written a simple program for entering data for various >model data sets in ACeDB? Most of the work seems to be translations of existing sets rather than straight data entry. I would bet that most of the curators have developed various tools based on awk, sed and so forth. You might consider something like Filemaker Pro as an input tool and then transferring the comma-separated text fields to your Unix box for transformation into an ACE file. --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!CS.UNC.EDU!singh From: singh@CS.UNC.EDU (Raj Kumar Singh) Newsgroups: bionet.software.acedb Subject: BioSCAN Update Date: 4 May 1994 18:30:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9405050130.AA02280@rigil.cs.unc.edu> NNTP-Posting-Host: net.bio.net BBBBBB OOOOO SSSSSS CCCCCC AAA N N B B @ O O S C A A NN N B B i O O S C A A N N N BBBBBBB ii O O SSSSS C AAAAAAA N N N B B ii O O S C A A N N N B B ii O O S C A A N NN BBBBBB iii OOOOO SSSSSS CCCCCC A A N N *************************** * U P D A T E -- 5/4/94 * *************************** o The BioSCAN e-mail server databases have been updated. The current versions are: GenBank Release 81.0, SWISS-PROT Release 28, and Protein Information Resource (PIR) Release 38. o BioSCAN is a computational tool for biosequence similarity analysis. The e-mail server can be accessed by sending a specially formated message to "bioscan@cs.unc.edu". Send "help" on a line by itself in the body of the message to receive further instructions. Please send your questions and comments to "bioscan-info@cs.unc.edu". o Searches: bioscan@cs.unc.edu, User support: bioscan-info@cs.unc.edu o This research was supported in part by NSF under grant MIP-9024585. ======================================================================= Raj K. Singh singh@cs.unc.edu +1 (919) 962-1744 From owner-acedb@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!dog.ee.lbl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Getting Map Distances from ACEDB Date: 5 May 1994 21:50:06 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 14 Distribution: world Message-ID: <2qbpme$5il@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov Is there a fast and/or easy way to get map distances out of ACEDB? E.g.: What is the distance between egl-44 and mab-3 on C. elegans chromosome II? --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!news From: cgr@poplar1.cfr.washington.edu (Carl G. Riches) Newsgroups: bionet.software.acedb Subject: Re: Data entry for ACeDB models? Date: 5 May 1994 16:29:58 GMT Organization: University of Washington Lines: 24 Distribution: world Message-ID: <2qb6u6$f11@news.u.washington.edu> References: <2q9sut$f44@overload.lbl.gov> Reply-To: cgr@poplar1.cfr.washington.edu NNTP-Posting-Host: poplar1.cfr.washington.edu In article <4MAY199411294718@rigel.tamu.edu> grl6732@rigel.tamu.edu (Gerard R. Lazo) writes: >Has anyone written a simple program for entering data for various >model data sets in ACeDB? > i've developed a set of c programs to take some mapmaker 3 data files and translate them to comma-delimited files that can be used for rdbms input. i then take these files, input them into r:base and use r:base reporting tools to generate various files in acedb update format for voxpop data entry. some of these tools are available for anonymouse ftp or gophering at the poplar molecular network's data center: poplar1.cfr.washington.edu in the directory /pub/acedb. (i've recently added a tool to extract qtl information from mapmaker-- i'll try to get the new stuff into the ftp/gopher site soon.) carl --- carl g. riches college of forest resources internet: cgr@poplar1.cfr.washington.edu university of washington ar-10 voice: 206-543-2764 seattle, wa 98195 fax: 206-543-3254 From owner-acedb@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: arithmetical queries Date: 6 May 1994 15:37:17 +0100 Lines: 14 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2qdkmt$slq@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk In reply to Brad Sherman, who asked if there was a fast way to get map distances out of ACEDB: No, that is not easy yet. The query package does in fact recognize and handle arithmetic operations, but the output of a query must always be a database object, or a set of objects. In this case you want a numeric result. Those are obtainable in tablemaker, but I still don't think tablemaker supports what you want. You would have to just obtain the map positions ofthe two genes in tablemaker, and export the table to some other system which would do the subtraction. Richard From owner-acedb@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!agate!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 May 1994 17:52:21 GMT Organization: Dendrome, A genome database for forest trees Lines: 906 Approved: news-answers-request@MIT.Edu Message-ID: <2qe04l$shd@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. Archive-name: acedb-faq Last-modified: 5/6/94 Version: 1.11 Xref: biosci bionet.software.acedb:261 news.answers:16659 ---------------------------------------------------------------------- Common Questions, with Answers, about ACEDB. Q0: What is ACEDB? Q1: What is the current version of ACEDB? Q2: !What hardware/software do I need to run ACEDB? Q3: Where can I get ACEDB? Q4: !What ACEDB databases exist? Q5: What written documentation exists for ACEDB? Q6: Where can I find further information about ACEDB? Q7: How should ACEDB be cited? Q8: Is ACEDB object-oriented? Q9: What's all this about Gopher|WAIS|ftp|WWW|URL ... Q10: How can I get on/off the ACEDB announcements mailing list? Q11: When and where is the next ACEDB Workshop? Q411:Who prepared this document & where is the current version? Questions marked with + are new, those with ! have substantially changed answers. ---------------------------------------------------------------------- Q0: What is ACEDB? A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [see Q4]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the European integrated Genome Project. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage -missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. ---------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: As of January 1994, ACEDB has undergone a bifurcation. Those involved with C. elegans will want to to track the 2.x series under the stewardship of Richard Durbin and all other groups should probably track the 3.x series of Jean Thierry-Mieg. Thierry-Mieg writes "... 2 and 3 differ only at the level of displays ..." Version 2.0 was released in December, 1993 and version 3.0 was released in January, 1994. To retrieve the software see Q3. To be kept informed of new releases see Q10. [This question refers to the software not the C. elegans data.] ---------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: Unix and X11: Any machine running SunOS 4.x SPARCstation 10 under Solaris [Probably all Solaris, then --bks] DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series PC 386/486 with Linux (free Unix) There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu MSDOS/Windows/NT: A port to NT is rumored to be in the works. Macintosh: [Contributed by Frank Eeckman] macace 2.0 is now available from genome.lbl.gov (131.243.224.80) under ftp/pub/macace. 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 from the same source. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a decent color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. For cost savings, a combination of a high-end Intel platform with Linux appears very attractive. 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. [This section should be expanded to have a more thorough discussion of X11 interactions. --bks] ---------------------------------------------------------------------- Q3: Where can I get ACEDB? A3: All the files are available in the following public access accounts (anonymous ftp sites) accessible via Internet: lirmm.lirmm.fr (193.49.104.10) in pub/acedb cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb (version 1-10 is available in repository/aatdb) bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb. A typical session would be: ftp ncbi.nlm.nih.gov login: anonymous password: your email address cd repository/acedb/ace3 binary ls get README_3 get NOTES get INSTALL get bin.sparc.3.0.tar.Z quit ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alphabetic order by Database name. Curators, submit changes as new paragraphs.--bks] Database : AAnDB-1.0 Species : Aspergillus nidulans PI : Leland Ellis Last_update : February 1994 ACEDB_version : 3.0 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : AAtDB Species : Arabidopsis thaliana Availability : Curator : John Morris Current version: 1-5 Contact : curator@frodo.mgh.harvard.edu Last_update : Sept. 1993 Database : ABtDB-1.0 Species : Bovine, Bos taurus ACEDB_version : 3.0 extended PI : Leland Ellis Last_update : February 1994 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : ACeDB Species : Caenorhabditis elegans Current version: 2-9 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@mrc-lmb.cam.ac.uk Contact : mieg@kaa.crbm.cnrs-mop.fr Last_update : March 1994 Database : AceMap Species : Homo Sapiens (Saccaromyces Pombe, Mus musculus in development) Focus : Physical mapping of human chromosomes X and 21 Curator : Hugues Roest Crollius Contact : hrc@gea.lif.icnet.uk PI : Hans Lehrach PI : Hugues Roest Crollius Last_update : 22 Feb 1994 Database : AGhDB Species : Gossipium hirsutum (cotton) PI : Russ Klhel Curator : Stephanie Crouch Last_update : March 1994 Contact : scrouch@tamsun.tamu.edu Database : AGsDB A Genus species Database Species : Aspergillus nidulans Species : Neurospora crassa Species : cow w/ human anchor loci Species : cotton (demo) Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast PI : Leland Ellis Curator : Leland Ellis Last_update : March 1994 ACeDB_version : 3.0 (beta still), with extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe) yeast); interacting loci via defined Interactions for each locus Models : as of 3.13.94 Data : as of 3.13.94 Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux (ducoux@moulon.inra.fr). URL : http://keck.tamu.edu/ibt.html Contact : leland@straylight.tamu.edu Database : ASbDB Species : Sorghum bicolor PI : Keith Schertz Curator : Stephanie Crouch Last_update : March 1994 Contact : scrouch@tamsum.tamu.edu Database : ChlamyDB Species : Chlamydomonas PI : Elizabeth Harris Contact : chlamy@acpub.duke.edu Availability : Still under construction Phone : 919-684-5243 (till 6/94) Fax : 919-684-5412 (till 6/94) Last_update : 30 Sept. 1993 Database : EcoDB Species : E. coli PI : Staffan Bergh Contact : staffan@biochem.kth.se Availability : Still under construction Last_update : 11 Oct. 1993 Database : FlyBase Species : Drosophila melanogaster Availability : gopher or gopher+ ftp.bio.indiana.edu Availability : ACeDB-style interface to SyBase server due by end of 1994 Curator : Edward Welbourne Contact : eddy@gen.cam.ac.uk Contact : flybase@morgan.harvard.edu PI : William Gelbart PI : Michael Ashburner PI : Thomas Kaufman PI : Kathy Matthews PI : John Merriam Database : Flydb Species : Drosophila melanogaster Availability : by request only, via ftp Curator : Suzanna E. Lewis Contact : SELewis@lbl.gov Focus : STS content mapping project summary PI : Gerald Rubin PI : Mike Palazzolo PI : Dan Hartl PI : Alan Spradling Last_update : Sept. 1993 Database : GrainGenes Species : Wheat, barley, oats, relatives Availability : Anonymous ftp from probe.nalusda.gov:pub/grains Availability : Gopher greengenes.cit.cornell.edu port 70 Availability : Gopher probe.nalusda.gov port 7002 Curator : David E. Matthews PI : Olin D. Anderson Contact : matthews@greengenes.cit.cornell.edu Contact : oandersn@wheat.usda.gov URL : gopher://greengenes.cit.cornell.edu/1/ Data_version : 1.3 Released : 12 Jan 1994 Based_on : acedb.1-10 Availability : See following WWW URL URL : http://probe.nalusda.gov:8000/acedbs/acedbs/graingenes/index.html Last_update : Feb. 1994 Database : human.c17 Species : Homo sapiens Availability : the database is under development Contact : lsprilus@weizmann.weizmann.ac.il Focus : mapping & sequencing of Human Chromosome 17 Based_on: acedb.3-0 Last_update : Jan. 1994 Database : Maize Species : Zea mays L. ssp. mays Focus : Maize genome Acedb_version : 1.9 FTP : probe.nalusda.gov, pub directory; anonymous ftp Comment : Maize is an acedb front end for the Maize Genome Database, MaizeDB, a SYBASE database. Comment : MaizeDB is updated daily and has WWW connectivity to external databases: GenBank (loci, alleles and probes), SwissProt (gene products) and the E. coli Stock Center (loci). Data : Major data categories: 4522 mapped loci (located to chromosome or better) including 684 mapped genes and 1423 mapped probed sites (gene candidates); 982 probes; 1850 map scores; 1533 gel patterns (Probe/Enzyme/Stock); 4231 stocks; 5105 Variations (alleles, DNA polymorphisms, rearrangements, etc); 465 phenotypes; 223 traits; 547 gene products; 5314 bibliographic references; 1979 persons with addresses. Gopher : host = teosinte.agron.missouri.edu, port = 70 Telnet : telnet teosinte.agron.missouri.edu login as guest, use password 'corncob' HTTP : http://teosinte.agron.missouri/top.html HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant Genome Database Comment : Genera is a software toolkit for creating and extracting data from Sybase databases; used to create MaizeDB and Worldwide Web connectivity. HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu Curator : Pat Byrne byrne@teosinte.agron.missouri.edu Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu Curator : Mary Polacco maryp@teosinte.agron.missouri.edu Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Curator : Christiane Fauron FAURON@GENE1.med.utah.edu Curator : Carolyn Wetzel cmwetzel@iastate.edu Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU Design : Stan Letovsky letovsky-stan@CS.YALE.EDU Design : Mary Berlyn mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 25 April 1994 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. PI : Staffan Bergh PI : Stewart Cole PI : Doug Smith Curator : Staffan Bergh Contact : staffan@biochem.kth.se Last_update : Apr. 1994 WWW : http://kiev.physchem.kth.se/MycDB.html ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb Database : RiceGenes Species : Rice (O. sative) Availability : under development, login at own risk Curator : Edie Paul Contact : epaul@nightshade.cit.cornell.edu Last_update : Sept. 1993 Database : SolGenes Coverage: Solanaceae - tomato, potato, pepper (eventually) Availability : Beta ACEDB via login or tar file Curator : Edie Paul Contact : epaul@nightshade.cit.cornell.edu Last_update : Sept. 1993 Database : SoyBase Species : Soybeans Curator : Lisa Lorenzen PI : Randy Shoemaker Contact : lorenzen@mendel.agron.iastate.edu Phone : 515-294-0421 Fax : 515-294-2299 Last_update : Sept. 1993 Database : TreeGenes Species : Forest trees Availability : alpha, contact curator ACEDB_version : 1-10 Curator : Bradley K. Sherman PI : David B. Neale Contact : Dendrome@s27w007.pswfs.gov Contact : bks@s27w007.pswfs.gov Contact : dbn@s27w007.pswfs.gov Last_update : March 1994 URL : gopher://s27w007.pswfs.gov/ URL : http://s27w007.pswfs.gov/ URL : ftp://probe.nalusda.gov/pub/trees Database : 21Bdb Species : Homo sapiens Availability : by request, via ftp, world-wide-web Based_on : acedb.1-10 plus moulon server URL : ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z URL : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy Contact : DFDavy@lbl.gov Contact : aggarwal@genome.lbl.gov Focus : STS content mapping & sequencing of Human Chromosome 21 PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng Last_update : Apr. 1994 Database : VoxPop Species : Populus spp. Availability : contact curator Curator : Carl G. Riches PI : Reinhard F. Stettler Contact : cgr@poplar1.cfr.washington.edu Contact : STETTLER@coyote.cfr.washington.edu Last_update : Sept. 1993 Database : ? PI : Scott Chasalow Species : Potato Contact : Scottish Crop Institute, Dundee Last_update : Sept. 1993 Database : ? PI : George Murphy PI : David Flanders Species : Arabidopsis thaliana Contact : John Innes Center, Norwich, England Last_update : Sept. 1993 Database : ? Species : Homo sapiens Focus : Physical mapping of human chromosomes 22 and X Curator : Ian Dunham Contact : idunham@crc.ac.uk id1@sanger.ac.uk PI : Ian Dunham PI : David Bentley Last_update : 28 Sep 1993 ---------------------------------------------------------------------- Q5: What written documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000. Primary documents from the developers are: acedb -- A C. elegans Database: I. Users' Guide. acedb -- A C. elegans Database: II. Installation Guide. acedb -- A C. elegans Database: III. Configuration Guide. Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z And ftp://weeds.mgh.harvard.edu/acedb_doc The files are in tex and postscript. [I have had some difficulty printing these. Jean Thierry-Mieg suggests latex xxxx.tex, dvi2ps xxxx.dvi > xxxx.ps, lpr xxxx.ps.] You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1993) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press (in press). [text is available through ftp or gopher from weeds.mgh.harvard.edu] Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1993) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. (Academic Press) (review, in press). [text is available through ftp or gopher from weeds.mgh.harvard.edu] ---------------------------------------------------------------------- Q6: Where can I find further information about ACEDB? A6: There is a Usenet/Biosci conference titled bionet.software.acedb. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. Mike Cherry has set up an ACEDB Developer's archive. For anonymous ftp use the hostname weeds.mgh.harvard.edu and look in the acedb_dev directory. If you wish to contribute you can put files in the incoming directory. Send a message to Mike (cherry@genome.stanford.edu) that you have put something in that directory then Mike will move it out for general access. For gopher you can connect to weeds.mgh.harvard.edu (132.183.190.21) and ... --> N. FTP Archives for Molecular Biology/ then --> M. ACEDB Developer's archive/ [N and M are integers which are subject to change.] The bionet.software. acedb.conference is archived and can be searched using WAIS. Here is a Gopher-style link to the WAIS archive. (This is also courtesy of Mike Cherry.): # Type=7 Name=ACEDB BioSci Electronic Conference Path=7/.index/acedb-biosci Host=genome-gopher.stanford.edu Port=70 The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. Other URL's that readers with mosaic clients might want to examine are: http://moulon.inra.fr/acedb/acedb.html for C. elegans data http://moulon.inra.fr/acedb/mycdb.html for Mycobacterium data http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html http://moulon.inra.fr/acedb_conf.html (en francais) The Genome Computing Group, Lawrence Berkeley Laboratory has an anonymous ftp service at machine genome.lbl.gov (131.243.224.80) which contains: flydb - LBL's Drosophila Acedb-style database 21bdb - LBL's Human Chromosome 21 Acedb-style database querdb - LBL's query-language extensions to Acedb metadata - LBL's compendium of Acedb database schema variants macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version There is also a repository of contributed software for data conversions and the like. 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). ---------------------------------------------------------------------- Q7: How should ACEDB be cited? A7: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit, available by Anonymous FTP from ... Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. ---------------------------------------------------------------------- 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. ---------------------------------------------------------------------- Q9: What's all this about Gopher/WAIS/ftp/WWW ... A9: These terms all refer to Internet protocols. An excellent introduction to the Internet is: _The Whole Internet User's Guide & Catalog_, by Ed Krol, O'Reilly & Associates, 1992. Or ask your system administrator to provide you with a gopher client or mosaic client and begin navigating on your own. URL is a Universal Resource Locator on the World-Wide Web (WWW). There are many free Internet browsers available that allow you to use an Internet connection and a URL to access services. Mosaic may be the most popular and it is available for Mac, PC or Unix via anonymous ftp from ftp.ncsa.uiuc.edu. ---------------------------------------------------------------------- Q10: How can I get on/off the ACEDB announcements mailing list? A10: To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list. ---------------------------------------------------------------------- Q11: When and where is the Next ACEDB Workshop? From Jean Thierry-Mieg: DATES: The acedb '94 workshop will be held july 2 to 16, in Saint Matthieu de Treviers, a small village, 20 km north of Montpellier, at the foot of the Pic Saint Loup. HOUSING: We have booked a place meant for family vacations which includes ample space, a nice conference room and ten studios meant for 5 people (bathroom, shower, kitchenette, terrace, all nice and clean) that we plan to share among 3 to 4 participants. Meals will be taken at a local restaurant. The place is ideal for work and informal discussions and will be well equiped with computers. The situation is nice for hiking and allows volley-ball, ping-pong, tennis and petanque. We can provide lists of possible hotels for those who would prefer more privacy or find ways of accomodating families if you let us know very soon (school ends early july in France). Cost for 2 weeks is 1000 FF (about 200 US dollars) for housing on site plus 2500 FF for full meals. We may get enough funding to reduce this cost, but cannot pay for travel. PROGRAM: Formal presentations and general discussions will take place in the mornings and the evenings, alternating network aspects, data handling, displays and genome data analaysis. The afternoons will be dedicated to data manipulation, programming and writing documentation. The idea is to actually implement during the meeting many of the ideas that will come up, to fuse and coallesce the now numerous acedb-based applications into a working modular package, and to import and consolidate large sets of additional data. Towards this goal, we will broadcast the following announcement ACEDB'94 Genome Database Workshop. Montpellier, July 2-16, 1994 This meeting will cover the use and development of the ACEDB database manager central to several major genome projects, including C.elegans, A.thaliana, human, and a number of other plant and animal species. We wish to encourage people with large sets of data on other organisms to attend this workshop. They will be helped to build, during the meeting, a friendly graphic presentation of their own data, in return for discussing their own experience. ******************************************************************* FORMAT: This meeting will be much longer than the 2 previous acedb workshops (Cambridge 92 and Boston 93), in the hope of initiating new collaborations and allowing concrete results. This format is usual in physics summer schools and often very productive. The workshop may be coupled to a 2 days presentation of acedb, open to the general audience, and yet to be organised. We anticipate at least the participation of people from: Berkeley, Boston, Cambridge, Heidelberg and Montpellier, including Richard Durbin (LMB and Sanger Centre, Cambridge), John McCarthy (LBL, Berkeley), Otto Ritter (DKFZ, Heidelberg), Danielle and Jean Thierry-Mieg (CNRS, Montpellier). Please confirm your participation and forward this announcement to your colleagues. Danielle and Jean Thierry-Mieg CNRS-CRBM BP 5051, 34033 Montpellier, France. email mieg@kaa.crbm.cnrs-mop.fr (if this address fails, fall back on mieg@ncbi.nlm.nih.gov) Tel: (33) 67 61 33 24 Fax: (33) 67 52 15 59 ---------------------------------------------------------------------- Q411:Who prepared this document & where is the current version? [Note to international readers: 411 is the phone number for information in the USA. --bks] This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net (134.172.2.69) as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu (18.70.0.209) as pub/usenet/news.answers/acedb-faq. Answer 3 demonstrates a sample FTP session. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html http://s27w007.pswfs.gov/Homepage/acedbfaq.html Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov Major contributions in getting this FAQ off the ground were made by John McCarthy and Mike Cherry. Other contributors include: Lisa Lorenzen David Matthews Edie Paul Donn Davy Eric De Mund Sam Cartinhour Please cite as: Sherman, Bradley K. (1994) "ACEDB Genome Database FAQ." Usenet news.answers. Available via Universal Resource Locator ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome Research Program. --bks ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Sun May 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!eddy From: eddy@eddy.gen.cam.ac.uk (Edward Welbourne (Genetics)) Newsgroups: bionet.software.acedb Subject: Re: Data entry for ACeDB models? Date: 09 May 1994 17:08:02 GMT Organization: University of Cambridge, England Lines: 22 Distribution: world Message-ID: References: <4MAY199411294718@rigel.tamu.edu> <2q9sut$f44@overload.lbl.gov> NNTP-Posting-Host: eddy.gen.cam.ac.uk In-reply-to: bks@s27w007.pswfs.gov's message of 5 May 1994 04:33:33 GMT In article <2q9sut$f44@overload.lbl.gov> bks@s27w007.pswfs.gov (Bradley K. Sherman) writes: > In an earlier article, grl6732@rigel.tamu.edu (Gerard R. Lazo) writes: > >Has anyone written a simple program for entering data for various > >model data sets in ACeDB? > > Most of the work seems to be translations of existing sets rather > than straight data entry. I would bet that most of the curators > have developed various tools based on awk, sed and so forth. and for those playing with SyBase -> ACeDB data transfers, I can now offer my syquery program (technically, it should do SyBase -> anything you understand how to specify; but I've only explored it for ace). It's still in development and prone to dreadful slowness (there are optimisations I really ought to explore ...). If you e-mail me I'll tell you more. If enough do, I'll add to this. Eddy. -- ... Few indeed are those who, travelling it, have crossed the dark and yawning Abyss of Implementation to Delivery. Many, yea, many in truth stagnate yet in the Desert of Delay, or linger ever in the ghastly limbo called Perpetual Beta. (from the LOGINATAKA) From owner-acedb@net.bio.net Mon May 09 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: kirbym@har-rbu.mrc.ac.uk Newsgroups: bionet.software.acedb Subject: Cytogenetic Data in AceDB Date: 10 May 1994 16:27:33 +0100 Lines: 239 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2qo955$mf0@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Does anyone using acedb have cytogenetic data? If so, do you find it handles this data adequately/some of it/not at all? Are there any improvements that you would like to see? Having tried to convert my data into acedb3 format it is still extremely frustrating to find that yet again, it is impossible to enter cytogenetic data and get it to display on appropriate maps. It seems to me that very little thought has actually been given to the representation of this data. With the next workshop approaching (July 1994), this would be a good time to get some improvements made that will be useful to everyone and, more importantly, get them incorporated into the main version of acedb. The following are based mainly on my own requirements. If these need to be more generic, or you can see a better way to do the same thing, then please comment. Data ---- The acedb philosophy is that "objects" displayed on a map are defined either as a single Locus or as an Interval which is composed of two end points or Loci. (Boston workshop) In practice, map locations are defined in the ?map_location model and are defined numerically. Mouse cytogenetic data is of two types. Genes with locations derived mainly from hybridisation in situ (HIS) and somatic cell (SC) techniques, and chromosomal anomalies (or rearrangements) with breakpoint data, eg insertions, translocations, etc. Breakpoints can be regarded as Loci in acedb. If an anomaly has two breakpoints on the same chromosome then the intervening region forms a segment or interval. In all cases the location is given as chromosome bands. Improvements to Existing Models and Code Wanted ----------------------------------------------- 1. The ?map_location model allow - locations to be given as chromosome bands. - end points be specified to indicate ranges Eg human Xq21.1-Xq27.3 This means the computer works out the numeric coordinates required for placing loci and intervals on the map(s) from the Chrom_Band definitions. If the band is defined in terms of the tags Contains and Contained_in then the algorithmn will have to recurse until it can either get a numeric definition or fail. 2. The computer find the missing bands in that range if the full complement of bands is needed elsewhere. (They usually are if the bands in the Chromosome column on the map(s) are to be highlighted correctly.) 3. If a set of ?Chrom_Bands forms an idiogram for a chromosome, is there any way the same idiogram can be used on several maps without having to redefine the Chrom_Bands for each map? At the very least then, the ?map_location model would be: ?map_location UNIQUE Position UNIQUE Float Float Multi_Position Float Float Ends Left UNIQUE Float Float Right UNIQUE Float Float Chrom_Band ?Chrom_Band ?Chrom_Band Junction ?Chrom_Band ?Chrom_Band where Chrom_Band refers to a location within a band or a range of bands and Junction refers to a point at the junction of two adjacent bands. (Yes, we do have this data.) Except that Left and Right currently define the Interval end points and should have Chrom_Band definitions as well. (Also, I am for ever being told by the scientists at Harwell that Left and Right are meaningless and to use the proper terms instead, ie Proximal and Distal.) Problems with ?map_location Model --------------------------------- 1. Locations are numeric and have to be specified fairly accurately. Cytogenetic data is given as chromosome bands and is often imprecise. For example, a deletion is from mouse band 4E2 to the end of the chromosome (4E2-4ter). 2. The data in the ?map_location model are separated from any supporting data in the rest of the parent model (eg Locus). This is not a problem if there is only one position in the map_location model and the parent model refers to only one location. However, nearly all chromosome anomalies have two or more breakpoints. Some of these will be listed in the same data structure, eg Translocations. Some have BOTH genetic and cytogenetic data which has to be linked to the correct location. 3. Most of the confusion and problems that I have experienced stem from the fact that ?map_location is used to define BOTH single points on a map and intervals (two points) on a map. Proposal -------- If this proposal is going to cause immense work by changing some of the fundamental data definitions, at least consider the possibility of creating new models for cytogenetic data where these changes can be implemented. For instance, instead of the model Interval there could be a CytoInterval. The suggestion is that: i. ?map_location be used for SINGLE locations only. ii. All locations are defined by two points. - If they are the same, the location is a single point - If different, the location is a range (Apparently this would preempt the time when molecular information will be available and positions will be ranges on the physical map.) iii. All Intervals are defined by pairs of double points. - If the end point is a range then either the mid point of the range would be used to draw the Interval, or, an error bar could be drawn to indicate the extent of the uncertainty. - If only ONE point is given then the end of the Interval is from the single point to the end of the chromosome. A dotted line continuing on from the main part of the Interval (solid line) could indicate the uncertainty at that end on the map. iv. Intervals (or CytoIntervals) are composed of two Locus definitions which in turn access the ?map_location model. v. All anomaly breakpoints be treated as Loci (ie use the model Locus). vi. Can we agree on a common definition for Chromosome Anomalies (Rearrangements)? The model definitions would thus become: ?map_location Position Float Float Chrom_Band ?Chrom_Band ?Chrom_Band Junction ?Chrom_Band ?Chrom_Band ?Locus Identifier UNIQUE Text Location Map ?Map XREF Locus #map_location ... // rest of model definition ?Interval Identifier UNIQUE Text Type ?Text // anomaly type, eg deletion, etc. Location Map ?Map Proximal #Locus Distal #Locus Contains Locus ?Locus Fragment ?Interval Contained_in ?Chrom_Anomaly XREF Interval 1. The new ?map_location model does not have to affect numeric positions for single Loci. The existing arrangement could continue. However, any chromosome band information would have to conform to the above schema and changes would be required to implement the new Interval or CytoInterval. 2. #Locus is preferable to ?Locus because in the majority of cases the Locus model will only be used for the map location data. For anomaly breakpoints which may have need of the rest of the Locus model it may still be preferable. It is easier to see all the data displayed together under one tree (model) rather than have to go to other trees to see different parts of the data. Besides I object to having to define x number of loci for the same anomaly (given that there could be many breakpoints involved) and don't see why they should be lumped in with genes and given identities of their own. HOWEVER, being in sub objects makes it difficult to get at the location data and there is an efficiency tradeoff. What will happen when the linkage data is added to each breakpoint? 3. Treating a set of Chrom_Bands as an idiogram will be necessary in order to find the end of the chromosome when the location is very uncertain. 4. For human chromosome anomalies which contain large repeats of data (such as Simon Mercer's data) Intervals can be defined as belonging to or containing other Intervals. 5. Chromosome Anomaly Definitions. Any definition for chromosomal anomalies needs to be able to cope with both the Long and Short nomenclature forms. The most simplistic model would be: ?Chrom_Anomaly Identifier UNIQUE Text Type ?Text // eg deletion, etc. Chromosome Text Location Cytogenetic_location Text Contains Fragment ?Interval XREF Chrom_Anomaly Bkpt #Locus Foreign_gene ?Locus XREF Chrom_Anomaly ... // rest of model definition - With this model it is relatively easy for the computer to pick up the Intervals and Loci and display them on the map but some clarity regarding which breakpoints belong to which Type is lost. - For complex anomalies involving several different types, how useful would it be to explicitly identify these? Part of a definition that I have been using does this: ?Chrom_Anomaly Identifier UNIQUE Text Type Deletion ?Interval Duplication ?Interval Insertion Donated_segment ?Interval Recipient_bkpt #Locus Inversion ?Interval Translocation Bkpt1 #Locus Bkpt2 #Locus HSR #Locus // Homogeneously Staining Region Robertsonian Tertiary_nullisomic Extra_seg1 ?Interval Extra_seg2 ?Interval Tertiary_trisomic Missing_seg1 ?Interval Missing_seg2 ?Interval Transgene #Locus Foreign_gene ?Locus Transposition ?Interval Monosomy ?Text Trisomy ?Text ... // rest of model definition - The disadvantage with this definition is that the computer has a lot more work to do to find the map locations. - Heterochromatin's or Homogeneously Staining Regions (HSR's) are unidentifiable regions of foreign DNA whose size is often specified by + or ++ only. Would it be adequate to define their endpoints by those of the regions into which they have been inserted on the host chromosome? Please comment. - Representing circular chromosomes may be more difficult. 6. The Location subtree is often used by several models, eg Locus, Interval, Chrom_Anomaly and in the Homology model developed by Jo Dicks and myself. Can we agree on a common definition for it? I apologise for sending such a long letter to the bulletin board but it is difficult to convey the complexities of dealing with chromosomal anomalies in acedb. In defence of the charge that all of this should have been discussed last November when Jean first put forward his proposals: well I did send a detailed reply to the bulletin board (Nov 24 1993) but no one took any notice. If any of the above is useful to other people please say so. I have code that implements a small part of the above proposal but it needs a significant amount of work to extend it to do all of the above. A stable model definition would help. I would be happy to work on this but suspect that it will also involve substantial changes to parts of the acedb code. Merging new code into the main acedb code each time there is a new version released is a real pain and I don't want to waste any more of my time on it. It would be better if the authors of acedb were involved. Many thanks to Simon Mercer for the recent helpful discussion. Michelle Kirby (email kirbym@har-rbu.mrc.ac.uk) From owner-acedb@net.bio.net Tue May 10 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!EU.net!uunet!munnari.oz.au!hippo.ru.ac.za!ucthpx!c-pc76.mrc.ac.za!JHHAUMAN From: JHHAUMAN@eagle.mrc.ac.za (John Hauman) Newsgroups: bionet.software.acedb Subject: MS Windows browsers and MycDB Date: Wed, 11 May 1994 11:20:42 Organization: SA Medical Research Council Lines: 20 Distribution: world Message-ID: NNTP-Posting-Host: c-pc76.mrc.ac.za X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hi all Has anyone out there successfully used an MS Windows www browser (Cello or Mosaic) to access MycDB (URL http://kiev.physchem.kth.se/MycDB.html), in particular things like physical maps and so on. When we accessed a page with a physical map, we got what looked like a textdump of a postscript file, so set up Ghostscript for Windows as follows (for Mosaic 2.04): TYPE1=application/postscript application/postscript="c:\gs\gswin -Ic:\gs %ls" application/postscript=.ps,.eps,.ai but still got the same thing (or, if we moved the .ini file out of the \windows directory, a warning that a postscript viewer was needed) What are we doing wrong???? Please help! Thanks in advance John Hauman ------------------------------------------------------------------------ Dave Yamey DYAMEY@EAGLE.MRC.AC.ZA Medical Research Council,South Africa ------------------------------------------------------------------------ From owner-acedb@net.bio.net Wed May 11 23:00:00 1994 Path: biosci!ic.ac.uk!b.arnold From: b.arnold@ic.ac.uk Newsgroups: bionet.software.acedb Subject: Comments on Cytogenetic Data in AceDB May 10 kirbym@harwell-rad Date: 12 May 1994 02:22:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 82 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <15317.9405120927@bccsb.bc.ic.ac.uk> NNTP-Posting-Host: net.bio.net Hello , I've recently joined the ACEDB community (about a month ago) so bear with me if it seems that I'm making erroneous assumptions or outright mistakes. Just a few comments prompted by Michelle Kirby's message of a couple of days ago I'm currently working with Peter Little's group on chromosome 11 specifically to look at the possibility of using acedb to display our data. The ideas that Peter has had regarding how the data should be displayed are as follows : 1. As much of the data obtained is relational between genes, cosmid clones YACs etc there is little or no chance of being able to map anything to specific points on the chromosome, it is far simpler to map things with regard to intervals along the chromosome. (i.e. everything is mapped relative to its neighbours and not to pre-determind numerical positions.) 2. As more is found out about the order of loci/genes etc. along the chromosome this data could be entered and remains fixed until further information is found that leads to a change in the order of the loci/genes. With the above in mind it would be nice if acedb had a display function that could recognise such words as left of, fight of ,or between (yes, I don't use proximal or distal too often), and create a map based solely on these positional pointers rather than relying on an exact numerical location to be properly positioned. This would require something akin to a linked-list (my c/c++ programming is practically nil so this term is used in the hope that it is correct), where as the data is read in to the display matrix the order in which data is entered is not relevant but can be placed into the matrix at the required point relative to its neighbours and is displayed, on an arbitrary scale where distance data is not known, and at specific separations where map distances/ sequence length data is known. This approach is a little more general to the one you propose but could probably be more easily tailored to a wider variety of mapping problems with regard to relative positions rather than point locations. An example would be : It is known that genes a-h map in interval 1-3, with a,b and c mapping to interval 1-2 within interval 1-3, the order of a,b and c has been determined as b a c and no further information is known about d-h. The display Peter and I envisage would look something like the following : 1 - | b | a | c 2 - d,e,f,g,h | | | | | | 3 - If it were later found that d and e mapped closer to 3 than to 2 it would be possible to break interval 2-3 down into two intervals called 2.1 and 2.2 with d and e being mapped between 2.2 and 3 and f-h mapping between 2 and 2.1. As can be seen this would eventually lead to smaller and smaller intervals until one would eventually arrive at the actual sequence level of display to which a particular gene or locus would map. A tentative model may look something like : ?Interval Name text Position Left_of ?Interval XREF Right_of #overlap Right_of ?Interval XREF Left_of #overlap Where overlap is a constructed type that indicates to what degree the intervals overlap. (A rough percentage overlap would do). Please feel free to contact me if there is anything you don't understand above and I'll try and explain it better. Benedict Arnold (email b.arnold@ic.ac.uk) From owner-acedb@net.bio.net Fri May 13 23:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!olivea!charnel.ecst.csuchico.edu!psgrain!library.ucla.edu!agate!doc.ic.ac.uk!uknet!daresbury!not-for-mail From: radek@chem.pg.gda.pl (R. Pladzyk) Newsgroups: bionet.software.acedb Subject: none Date: 14 May 1994 11:40:45 +0100 Lines: 3 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2r29rd$18b@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk hi! My name Radek and I would like know somthing about us.I'm interested programmning for biochemistry (I prefer Turbo Pascal). Sorry for my English. No to czesc wam wszystkim. From owner-acedb@net.bio.net Fri May 13 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!doc.ic.ac.uk!news.lif.icnet.uk!hrc From: hrc@gea.lif.icnet.uk (Hugues Roest Crollius) Newsgroups: bionet.software.acedb Subject: X chromosome mapping data Date: 14 May 1994 18:14:17 +0100 Organization: Imperial Cancer Research Fund Lines: 43 Sender: hrc@news.lif.icnet.uk Distribution: world Message-ID: <2r30t9$435@gea.lif.icnet.uk> NNTP-Posting-Host: gea.lif.icnet.uk Keywords: ANNOUNCEMENT =========== ICRF HUMAN X CHROMOSOME PHYSICAL MAPPING DATA ============================================= Physical mapping YAC data for the human X chromosome are now available by anonymous ftp from ftp.icnet.uk (give user name as "anonymous", password as your email address). The data are below the directory icrf-public/GenomeAnalysis/X The data comprise YAC contigs generated in the ICRF Genome Analysis Laboratory, integrated with published contigs from the Reference Library System. The data will be of interest to people working on mapping the X chromosome and to computer scientists who wish to write new ordering algorithms. The data comprise four files in the directory icrf-public/GenomeAnalysis/X: README Explanation file raw.tar.Z Raw hybridisation data (compressed tar) Xcontigs.log.Z Summary information of X YAC contigs (compressed) Acemap.tar.Z acedb3 dump of X YAC contigs (compressed tar) Questions, Comments and Suggestions can be emailed to: andy@gea.lif.icnet.uk (Andrei Grigoriev) hrc@gea.lif.icnet.uk (Hugues Roest Crollius) humanX@gea.lif.icnet.uk (Mark Ross) rmott@gea.lif.icnet.uk (Richard Mott) or by post to:- Genome Analysis Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX UK From owner-acedb@net.bio.net Sun May 15 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: acedb demos at CSH Date: 16 May 1994 17:58:46 +0100 Lines: 20 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2r88o6$ltq@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk I would like to thank everybody for the acedb demos that we were able to set up at CSH, and in particular Eric DeMund for providing kodak overheads in the nick of time. I think that the audience on the whole really appriciated the acedb approach, because of the mounting quality of the work, the data and the documentation, all teh results of our better coordination over the last year. I did bet to Marr that, with the premisse that acedb and genome topographer are more or less equivalent today, acedb in for year will be 10 fold better, not because any one of us is more clever than he is, but because the open sofware approch that we have adopted will, in my opinion, continue to feed a snowball effect that his proprietary database will not be able to match. The bet is a caisse of Champagne against Hallibut and lobster. If both system survive, we will just have a hell of a diner all together. From owner-acedb@net.bio.net Tue May 17 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!news-feed-2.peachnet.edu!news-feed-1.peachnet.edu!news.duke.edu!teer4.acpub.duke.edu!mps2 From: mps2@teer4.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: MultiMap capabilities of 3.0 Date: 18 May 1994 19:36:44 GMT Organization: Duke University; Durham, N.C., USA Lines: 15 Distribution: world Message-ID: <2rdqoc$35e@news.duke.edu> NNTP-Posting-Host: teer4.acpub.duke.edu Keywords: I just learned about ACeDB two days ago, so pardon my ignorance. I am in the process of creating a set of models to accept .ace formatted information concerning Chlamydomonas foir Dr. Elizabeth Harris at Duke University. Since I have no expert top turn to, I must turn to the newsgroup when I am in a bind. One error I have that arises when trying to read in the .ace file is"Type of (something) does not check in B object (something)". This occurs for various things, and I cannot find the error. Granted that this a very general request, has anyone encountered this before or can anyone point out a possible direction to go in "debugging" the models.wrm file? My second problem is with the multimap option. When I try to look at a MultiMap the TableMaker comes up and says "No numerical column data". Where might this be debugged. Thank you so much for your help. Once I get used to the system more, I'm sure I will be able to see through mny own errors more easily. From owner-acedb@net.bio.net Tue May 17 23:00:00 1994 Path: biosci!MENDEL.AGRON.IASTATE.EDU!lorenzen From: lorenzen@MENDEL.AGRON.IASTATE.EDU (Lisa Lorenzen) Newsgroups: bionet.software.acedb Subject: Re: MultiMap capabilities of 3.0 Date: 18 May 1994 12:48:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 55 Sender: daemon@net.bio.net Distribution: world Message-ID: <9405181947.AA23430@mendel.agron.iastate.edu> NNTP-Posting-Host: net.bio.net Hi! I have also seen your first problem. Every time I have encountered this, I do not have one of my XREF's created properly, for example, in the model ?Probe: (a hypothetical example) ?Probe Locus ?Locus XREF Refers_to_this_probe Then, in the ?Locus class, I am MISSING the tag Refers_to_this_probe. Therefore, you enter a .ace file: Probe : "pA102" Locus "A102" You will get the 'something in B object doesn't check'. There might be other reasons, but this has always been the problem when I have seen this error. Lisa :-) ps. Sorry, I haven't had the pleasure of multi-maps yet :-( ----- Begin Included Message ----- From BIOSCI-REQUEST@net.bio.net Wed May 18 14:41:04 1994 Received: from net.bio.net by mendel.agron.iastate.edu (4.1/UW-NDC Revision: 2.21 ) id AA23414; Wed, 18 May 94 14:40:56 CDT Received: (from daemon@localhost) by net.bio.net (8.6.8.1/8.6.6) id MAA09262 for acedb-list; Wed, 18 May 1994 12:40:32 -0700 Received: (from news@localhost) by net.bio.net (8.6.8.1/8.6.6) id MAA09258 for acedb-arpanet; Wed, 18 May 1994 12:40:31 -0700 To: acedb@net.bio.net From: mps2@teer4.acpub.duke.edu (Maulin Piyush Shah) Subject: MultiMap capabilities of 3.0 Date: 18 May 1994 19:36:44 GMT Message-Id: <2rdqoc$35e@news.duke.edu> Nntp-Posting-Host: teer4.acpub.duke.edu I just learned about ACeDB two days ago, so pardon my ignorance. I am in the Status: R process of creating a set of models to accept .ace formatted information concerning Chlamydomonas foir Dr. Elizabeth Harris at Duke University. Since I have no expert top turn to, I must turn to the newsgroup when I am in a bind. One error I have that arises when trying to read in the .ace file is"Type of (something) does not check in B object (something)". This occurs for various things, and I cannot find the error. Granted that this a very general request, has anyone encountered this before or can anyone point out a possible direction to go in "debugging" the models.wrm file? My second problem is with the multimap option. When I try to look at a MultiMap the TableMaker comes up and says "No numerical column data". Where might this be debugged. Thank you so much for your help. Once I get used to the system more, I'm sure I will be able to see through mny own errors more easily. ----- End Included Message ----- From owner-acedb@net.bio.net Wed May 18 23:00:00 1994 Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!usc!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!news.duke.edu!teer4.acpub.duke.edu!mps2 From: mps2@teer4.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: Database bug or my bug? Date: 19 May 1994 15:34:17 GMT Organization: Duke University; Durham, N.C., USA Lines: 9 Distribution: world Message-ID: <2rg0tp$baf@news.duke.edu> NNTP-Posting-Host: teer4.acpub.duke.edu Hey y'all, its me again. I've overcome yesterdays errors and now I fully read in th .ace without trouble. When I click on bolds they go where they are supposed to in all but one case. In my ?Map I have a Locus ?Locus. So, when I click on the Locus listed I should expect to see the information from the ?Locus./ The problem is that instead I see the same screen pop up again (that is, the ?Map window). Its all rather circular instead of linear, the wway it should be. Any ideas, or is it just that sometimes there is a quirk in the program? Thanks a lot. Maulin From owner-acedb@net.bio.net Wed May 18 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!news.duke.edu!teer4.acpub.duke.edu!mps2 From: mps2@teer4.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: Sam Cartinhour Date: 19 May 1994 19:26:27 GMT Organization: Duke University; Durham, N.C., USA Lines: 2 Distribution: world Message-ID: <2rgeh3$jcg@news.duke.edu> NNTP-Posting-Host: teer4.acpub.duke.edu SAM!! Where are you? Has your email address changed? Please respond, thanx. (Sorry to all thos who had to read this) From owner-acedb@net.bio.net Wed May 18 23:00:00 1994 Path: biosci!GENOME.STANFORD.EDU!cherry From: cherry@GENOME.STANFORD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: "Next" function for browsing a keyset? Date: 19 May 1994 12:09:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <199405191910.MAA27186@stout.Stanford.EDU> NNTP-Posting-Host: net.bio.net > By which I think he means: given a keyset of tree objects, one of which is > currently displayed in the front window, it would be nice if there was an > easy way to call up the next (or previous) object for display in the same > window. > > This would be especially useful on small screens. I don't know what kind of > control should be used to invoke this. A button I guess. Special key > combinations are out of the question? Hmm, I guess the button would have to > be in the Keyset window rather than the tree window, if I assume correctly > that a tree window doesn't even know whether it came from a keyset or not. > This isn't so great. On the Unix version of ACEDB you can simply use the keyboard arrow keys to move through the keyset list. You click twice on an item in the keyset, then click back in the keyset (or on some window managers just move the mouse over the keyset window) then use the up and down arrows to move through the list. Works for all classes that I have tried. Mike From owner-acedb@net.bio.net Wed May 18 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: "Next" function for browsing a keyset? Date: 19 May 1994 11:34:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9405191838.AA02453@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net A user says, > I wish the AceDB > system provided a means to page through items in a class using the detailed > text windows instead of clicking on items in the list one at a time. By which I think he means: given a keyset of tree objects, one of which is currently displayed in the front window, it would be nice if there was an easy way to call up the next (or previous) object for display in the same window. This would be especially useful on small screens. I don't know what kind of control should be used to invoke this. A button I guess. Special key combinations are out of the question? Hmm, I guess the button would have to be in the Keyset window rather than the tree window, if I assume correctly that a tree window doesn't even know whether it came from a keyset or not. This isn't so great. - Dave Matthews From owner-acedb@net.bio.net Wed May 18 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: "Next" function for browsing a keyset? Date: 19 May 1994 12:32:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9405191937.AA02598@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > On the Unix version of ACEDB you can simply use the keyboard arrow > keys to move through the keyset list. You click twice on an item in > the keyset, then click back in the keyset (or on some window managers > just move the mouse over the keyset window) then use the up and down > arrows to move through the list. Works for all classes that I have > tried. > > Mike Wow, yes it does. That IS great. Also the left and right arrows do interesting and useful things. Thanks Mike! - Dave From owner-acedb@net.bio.net Wed May 18 23:00:00 1994 Path: biosci!agate!gmrubin11.berkeley.edu!user From: sly@fly2.berkeley.edu (Cyrus Harmon) Newsgroups: bionet.software.acedb Subject: MacAce 2.0b4 Released Followup-To: bionet.software.acedb Date: Thu, 19 May 1994 15:11:17 -0700 Organization: UC Berkeley Lines: 49 Message-ID: NNTP-Posting-Host: gmrubin11.berkeley.edu Macace 2.0b4 is now available by anonymous ftp. MacAce is the Macintosh version of ACeDB and is available from genome.lbl.gov (IP Address: 131.243.224.80) in the directory ~ftp/pub/macace. MacAce is also available at the European site cele.mrc-lmb.cam.ac.uk (IP Address: 131.111.84.1). The directory is ~ftp/pub/acedb/macace. European users have reported that transfers from this site are signifcantly faster than from genome. MacAce requires System 7 and runs on all Macintosh models with a 68030, 68040 or PowerPC processor. There are a number of new features in this version: * Native PowerPC Application * Greatly improved printing * Many Internal Bug Fixes * C. Elegans Data Release 2.10 (Thanks Richard!) The application and the C. Elegans data (release 2.10) are in the self-extracting archive MacAce2.0b4_Complete.sea.bin. The self-extracting archive (MacAce2.0b4_App_Update.sea.bin) contains the latest version of the macace Application and its wspec files. Only download this if you were using MacAce and have the release 2.10 database. If you already have the database you do not need to fetch the big file. Please be sure that you update both the application and the wspec folder. Do not use old wspec folders with the new version of the code. There are 3 partially redundant applications of macace in this archive: MacAce.68k for your good old 680x0 mac MacAce.ppc for your new fast powerPC box MacAce.fat, in so-called "fat-binary" contains both 680x0 and PowerPC code All three flavors are identical in functionality. We recommend using the fat binary, but if space is at a premium, you can use the smaller version for your processor. If you would like to add your name to our mailing, please send a brief message to eeckman@llnl.gov. We would appreciate your feedback and reports of any problems. Frank Eeckman eeckman@llnl.gov Cyrus Harmon sly@fly2.berkeley.edu From owner-acedb@net.bio.net Thu May 19 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!swrinde!pipex!uknet!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: "next" for keyset Date: 20 May 1994 06:34:16 +0100 Lines: 5 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2rhi4o$iac@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk The arrow keys work within a keyset, with the down key stepping correctly through the whole keyset. Isn't this what you want? Richard From owner-acedb@net.bio.net Thu May 19 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: "next" for keyset Date: 20 May 1994 15:16:14 GMT Organization: University of California, Berkeley Lines: 25 Distribution: world Message-ID: References: <9405201442.AA03349@greengenes.cit.cornell.edu> NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: matthews@GREENGENES.CIT.CORNELL.EDU's message of 20 May 1994 07:37:01 -0700 In article <9405201442.AA03349@greengenes.cit.cornell.edu> matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") writes: >... Oh I see, it works in MacX if you first click on the keyset window to >activate it, then hit the arrow key. I guess to be convenient it requires a >window manager that has a point-to-focus mode instead of click-to-focus. >- Dave Do NOT run Xace under Openwindows with "click-to-focus"!!!!! /usr/openwin/share/buglist.xnews: =>Bug Id: 1039020 =>Category: x11news =>SubCategory: olwm =>Synopsis: olwm locks up server in some situations =>Public Summary: => Running xnews and olwm, it is possible to lock up the server. => Olwm puts a passive grab on some frames when in click-to-type => mode. There seems to be a case where olwm will not respond => to middle mouse button press events when the event happens in => the middle of creating a window. Naturally this is Sun's default mode... -- Henry J. Cobb hcobb@fly2.berkeley.edu, SFB Tyrant-for-life "NT is aimed at a different way of working, thus YOU need to change the way you think." -Thomas F Lee From owner-acedb@net.bio.net Thu May 19 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: "next" for keyset Date: 20 May 1994 07:37:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9405201442.AA03349@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > The arrow keys work within a keyset, with the down key stepping > correctly through the whole keyset. Isn't this what you want? > > Richard Yes exactly, I just didn't know about it. ... Hmm, for some reason it doesn't seem to work for me with MacX, and my user reports it doesn't work with eXceed/W on Windows either. But I imagine you can't address all the deficiencies of every X server. ... Oh I see, it works in MacX if you first click on the keyset window to activate it, then hit the arrow key. I guess to be convenient it requires a window manager that has a point-to-focus mode instead of click-to-focus. - Dave From owner-acedb@net.bio.net Sun May 22 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: files from 2-day course Date: 23 May 1994 12:26:22 +0100 Lines: 27 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2rq3su$c62@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Mary O'Callaghan and I gave a two day course last Thursday and Friday on how to use ACEDB, and in particular how to edit in it, and adapt it to other data. In the process we made a number of miscellaneous files and it seemed a good idea to make them available to others. In particular Sam might want to add at least some of them to his documentation server. They are available by ftp as course.tar.Z on cele.mrc-lmb.cam.ac.uk in pub/acedb/ace2. The examples all run with the current public ace2 code and wspec -- sorry, that was just what was easiest for us. The archive contains: exercises with answers new-database script to make a new empty database with $ACEDB = pwd mini-db.ace small database with examples of most types of data examples.ace example ace file acediff/ info and examples for using acediff blast/ scripts for converting blast output to .ace files medline/ script for converting medline entries to .ace files editingmodels/ info and exercises on how to add to the models and classes. Also includes a complete annotated minimal set of models for ace2, containing only those tags used by the code, and briefly saying how they are used. There is a global README and a README in each subdirectory. Richard From owner-acedb@net.bio.net Sun May 22 23:00:00 1994 Path: biosci!BISON.LIF.ICNET.UK!mike From: mike@BISON.LIF.ICNET.UK (Mike Mitchell) Newsgroups: bionet.software.acedb Subject: Using ACeDb as a database management tool Date: 23 May 1994 02:20:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <199405230920.CAA27872@net.bio.net> NNTP-Posting-Host: net.bio.net I would greatly appreciate any information or pointers to information about using the ACeDb software to manage data. If this is a FAQ matter, I apologise, and would appreciate being pointed to the FAQ. Thanx in advance for your help. ************************************************************************** *Michael Mitchell * "All I know about babies is that you * *User Support * are not supposed to put them into * *Molecular Biology Software * washing machines. Makes the colours * *Imperial Cancer Research Fund * run, presumably." * *+44 (0)71 269 3115 * Tom Holt - Here Comes The Sun - 1994 * ************************************************************************** From owner-acedb@net.bio.net Sun May 22 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!news.duke.edu!teer4.acpub.duke.edu!mps2 From: mps2@teer4.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: ACeDB 3.0 Date: 23 May 1994 12:14:34 GMT Organization: Duke University; Durham, N.C., USA Lines: 6 Distribution: world Message-ID: <2rq6na$4oq@news.duke.edu> NNTP-Posting-Host: teer4.acpub.duke.edu Does anyone have something similar to what Richard is talking about concerning ACeDB 3? Even though I realize that most of the syntax is the same, I would really like to see some finished DB's, or ones that at least make use of the MultiMap and/or graphics capabilities more effectively. Thanks for your help. Maulin From owner-acedb@net.bio.net Tue May 24 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!nntp.msstate.edu!saimiri.primate.wisc.edu!news.doit.wisc.edu!f181-196.net.wisc.edu!user From: Kckim@students.wisc.edu (Konrad C. Kim) Newsgroups: bionet.software.acedb Subject: Biotechnology job Followup-To: bionet.software.acedb Date: 25 May 1994 21:54:55 GMT Organization: Univeristy of Wisconsin Lines: 52 Distribution: world Message-ID: NNTP-Posting-Host: f181-196.net.wisc.edu KONRAD C. KIM 16 White Deer Ct. Huntington, NY 11743 (516)549-5205 EDUCATION: University of Wisconsin-Madison: College of Letters and Sciences, B.S Zoology 1988-92Õ College of Agriculture and Life Sciences, B.S. Genetics 1993-94Õ Related Courses taken: Biochemistry, Cell Biology, Organic Chemistry, Endocrinology, Cell Physiology, Neurobiology, Microbiology, Soil Microbiology and Biochemistry, Human Genetics WORK EXPERIENCE: Junior Lab Technician, 6/92-6/93 University of Minnesota Hospital and Clinics Department of Therapeutic Radiology Radiation Oncology Radiation Biology Section Supervisor: Beth Auger. Assistant Professor Ph.D. Principal Investigator: Changwon Song. Professor Ph.D. 424 Harvard St. SE Minneapolis, MN 55455 612-626-6090 Biological Assistant, 1/92-6/92 Veterans Memorial Middelton Hospital Department of Neurology Supervisor: Jim Vann. Senior Lab Scientist and Manager 1134 Terrace Av. Madison WI 53715 SKILLS: Protein Isolation: SDS-PAGE, Affinity chromotography, Dialysis/Salting out, Agglutination Tissue Culture: Mark I Cesium Irradiation Chamber, Fsa2 and SCK Cell Types Genetics: Southern, Western, and Northern Blots, Gel Electrophoresis, PCR AWARDS AND HOBBIES: Eagle Scout University of Wisconsin All-String Orchestra 1988-92Õ References on request From owner-acedb@net.bio.net Wed May 25 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Linux xace3? Date: 26 May 1994 04:07:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <9405261111.AA09538@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Has anybody compiled acedb 3.x for Linux yet? If so I'd like to a get a copy from you. Thanks, - Dave Matthews From owner-acedb@net.bio.net Thu May 26 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: "Next" function for browsing a keyset? Date: 27 May 1994 16:17:20 +0100 Lines: 9 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2s52u0$mf0@mserv1.dl.ac.uk> Original-To: matthews@GREENGENES.CIT.CORNELL.EDU the arraow key does preciselly that. very fast indeed try it on a window of long text you ll be surprised so Query: FIND LongText you pop a keyset of texts use the arrow pad fast From owner-acedb@net.bio.net Sun May 29 23:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!agate!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!edvz.sbg.ac.at!wst!floeckn From: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Subject: C.Elegans CHRIII Message-ID: Lines: 22 Sender: floeckn@wst (Floeckner Hannes) Reply-To: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Organization: University of Salzburg / Austria Date: Mon, 30 May 1994 15:33:14 GMT Hello Netters! In NATURE Vol368 March 1994 I read an article about the CHRII sequence of C.elegans. There's also written that the sequences are submitted to EMBL and ACEDB database. I don't want to install the whole databases on my computer, since I only have very less space left, but I am very interested to get all sequences (of all 483 putative genes) in form of amino acid sequences. Any possibility to get only these sequences? Thank you Hannes =========================================================================== Floeckner Hannes e-mail: floeckn@dwst11.edvz.sbg.ac.at Inst.f. Chemie und Biochemie hannes@agnes.came.sbg.ac.at Universitaet Salzburg Jakob-Haringerstr. 1 A-5020 Salzburg AUSTRIA - EUROPE From owner-acedb@net.bio.net Sun May 29 23:00:00 1994 Path: biosci!agate!doc.ic.ac.uk!lyra.csx.cam.ac.uk!nntp-serv!esr From: esr@al.mrc-lmb.cam.ac.uk (Sonnhammer E./Durbin) Newsgroups: bionet.software.acedb Subject: Re: C.Elegans CHRIII Date: 30 May 94 19:27:20 Organization: /hgmp0/esr/.organization Lines: 20 Message-ID: NNTP-Posting-Host: al.mrc-lmb.cam.ac.uk floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) writes: ... I am very interested to get all sequences (of all 483 putative Any possibility to get only these sequences? Yes. The putative proteins found by the C. elegans sequencing project are distributed as the database Wormpep, which is available via anonymous FTP at ftp.sanger.ac.uk in /pub/databases/wormpep. The current release, Wormpep 5, contains 781 protein sequences. The Sanger Centre also maintains an up-to-date collection of the finished cosmid sequences, on the same server as above in /pub/databases/C.elegans_cosmids. _______________ Erik Sonnhammer Sanger Centre Cambridge UK From owner-acedb@net.bio.net Sun May 29 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!nntp-serv!esr From: esr@al.* (Sonnhammer E./Durbin) Newsgroups: bionet.software.acedb Subject: Re: C.Elegans CHRIII Date: 30 May 94 19:03:35 Organization: /hgmp0/esr/.organization Lines: 21 Message-ID: References: NNTP-Posting-Host: al.mrc-lmb.cam.ac.uk In-reply-to: floeckn@wst.edvz.sbg.ac.at's message of Mon, 30 May 1994 15:33:14 GMT floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) writes: ... I am very interested to get all sequences (of all 483 putative genes) in form of amino acid sequences. Any possibility to get only these sequences? Yes. The putative proteins found by the C. elegans sequencing project are distributed as the database Wormpep, which is available via anonymous FTP at ftp.sanger.ac.uk in /pub/databases/wormpep. The current release, Wormpep 5, contains 781 protein sequences. The Sanger Centre also maintains an up-to-date collection of the finished cosmid sequences, on the same server as above in /pub/databases/C.elegans_cosmids. _______________ Erik Sonnhammer Sanger Centre Cambridge UK From owner-acedb@net.bio.net Sun May 29 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: tag numbering problem in acedb3 Date: 30 May 1994 10:14:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <9405301719.AA13073@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net The distribution acedb 3.0 (bin.sparc.3_0.tar.Z on ncbi.nlm.nih.gov) seems to have some of the tag numbers for Map-related tags compiled-in and unchangeable. Symptom: clicking on a Locus name or a Map name produces only the tree window for the Map instead of the GMAP graphic, unless the tag numbers in tags.wrm are: Contains = 554, Map = 657, Position = 707. Also in classes.wrm, class Map must be numbered 110. I.e. these values must be the same as used in the Human Chromosome 21 wspec/tags.wrm included as part of that distribution. Also, to use Chrom_Band's, the tag numbers for Chrom_Band, Ends, Left, Right, Dark, Colour, etc. should be adjusted to match the Human 21 values. (Note, the symptoms are like those described by Maulin Shah in his recent message, and I'll bet this is the reason for his problem too.): - Dave Matthews :::::::::::::: To: acedb@net.bio.net >From: mps2@teer4.acpub.duke.edu (Maulin Piyush Shah) Subject: Database bug or my bug? Date: 19 May 1994 15:34:17 GMT Hey y'all, its me again. I've overcome yesterdays errors and now I fully read in th .ace without trouble. When I click on bolds they go where they are supposed to in all but one case. In my ?Map I have a Locus ?Locus. So, when I click on the Locus listed I should expect to see the information from the ?Locus./ The problem is that instead I see the same screen pop up again (that is, the ?Map window). Its all rather circular instead of linear, the wway it should be. Any ideas, or is it just that sometimes there is a quirk in the program? Thanks a lot. Maulin From owner-acedb@net.bio.net Sun May 29 23:00:00 1994 Path: biosci!agate!doc.ic.ac.uk!warwick!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: thoughts on july Date: 30 May 1994 08:26:56 +0100 Lines: 18 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2sc4g0$7es@mserv1.dl.ac.uk> Original-To: suzi@ux5.lbl.gov i agree 1000 per cent do you have nat goodman's emailk i would like him or one of his mcrowd to comt to streamline the interface is high on tyh e agenda we have schenes with otto in w6/action.c but all not perfect there is also the work of Henry & co at lbl and specific hooks like done by Richard on rna folding or as i did on dna assembly with phil yes yes yes, most important topic is to ease the interface from ace to outside wotrld From owner-acedb@net.bio.net Mon May 30 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!convex!news.duke.edu!teer4.acpub.duke.edu!mps2 From: mps2@teer4.acpub.duke.edu (Maulin Piyush Shah) Newsgroups: bionet.software.acedb Subject: A -T option for Subclasses? Date: 31 May 1994 20:16:26 GMT Organization: Duke University; Durham, N.C., USA Lines: 10 Distribution: world Message-ID: <2sg5uq$cq3@news.duke.edu> NNTP-Posting-Host: teer4.acpub.duke.edu In creating my Chlamydoimonas database, I want to represent a gene as merely a sub-class of Loci. However, when I display them on the Key Set window, I would like to a separate name appear in the window than the name of the Locus. That is, I would like the gene name to show in the window instead. Is there a possibility of doing this. How about something like a Title line in subclasses.wrm where I could specify the Tag I would like displayed? Has anyone overcome this in another way? Thanks. Maulin From owner-acedb@net.bio.net Tue May 31 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: A -T option for Subclasses? Date: 01 Jun 1994 15:17:27 GMT Organization: University of California, Berkeley Lines: 10 Distribution: bionet Message-ID: References: <2shgpo$2ah@mserv1.dl.ac.uk> NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: mieg@kaa.crbm.cnrs-mop.fr's message of 1 Jun 1994 09:27:36 +0100 To properly support aliasing we'd need an additional level of indirection. We probally need it anyway, if we want locks smaller than the size of the database anyway. -- Henry J. Cobb hcobb@fly2.berkeley.edu, Bad-Think Criminal "Do you realise the contribution auto pollution makes towards the killing of our lakes, rivers and oceans? A fish doesn't need just ONE bicycle." From owner-acedb@net.bio.net Tue May 31 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: kristoff (David Kristofferson) Newsgroups: bionet.software.acedb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 1 Jun 1994 02:00:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 319 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406010900.CAA17705@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. 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The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS, waismail, and gopher access. If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. 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For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-acedb@net.bio.net Tue May 31 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: A -T option for Subclasses? Date: 1 Jun 1994 09:27:36 +0100 Lines: 30 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2shgpo$2ah@mserv1.dl.ac.uk> Original-To: mps2@teer4.acpub.duke.edu if gene is a subclass of locus this means that some locus, say locus aaa is subclassified as a gene subclasses in ace are simply an automatic sorting system inside a class hence Locus aaa has the same name as Gene aaa, since there is a single object Keyset show the native names -Title is for tree displays however, you may alias any object so that 2 names will be used ace file is -A Locus aaa bbb now aaa and bbb will be recognized unfortunately aliases do not properly dump so this info should be keppt preciously ! from then on aaa and bbb will be recognized names an alternative is to have a separate class gene, XREF to locus, but this is probably less good From owner-acedb@net.bio.net Tue May 31 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: Suzanna Lewis Newsgroups: bionet.software.acedb Subject: Re: thoughts on july Date: 1 Jun 1994 20:57:13 +0100 Lines: 14 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2sip6p$8c5@mserv1.dl.ac.uk> Original-To: mieg@kaa.crbm.cnrs-mop.fr, nat@genome.wi.mit.edu Nat, Jean agrees 1000%. He's asked to be catch up on some (sorry) to be included in our technical correspondence. would you please send him whatever we've discussed so far. He says richard has put in some hooks for rna folding and some other work with otto. Jean, could you give me some details on your sequence assembly work? I met Sean Eddy here and he says the Wash. U. group are already using it in production. Suz. From owner-acedb@net.bio.net Tue May 31 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: A -T option for Subclasses? Date: 1 Jun 1994 19:20:07 +0100 Lines: 3 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2sijgn$2p6@mserv1.dl.ac.uk> Original-To: hcobb@fly2.berkeley.edu aliasing is supported, just not dumped properly by the Dump database function From owner-acedb@net.bio.net Tue May 31 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: workshop hardware, Internet, Macintosh AppleTalk bridge? Date: 1 Jun 1994 22:18:47 +0100 Lines: 34 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2sitvn$deh@mserv1.dl.ac.uk> Original-To: JLMcCarthy@lbl.gov plenty of workstations i hope 10 screens alphas and sun and xterms for 40 peole i think it is ok Internet connectivity yes Will you have a device so that those of us bringing Mac laptops would be able to connect to the network via AppleTalk (e.g., Gatorbox or some other ethernet=AppleTalk bridge/router)? i don t know how to set that i ll ask the local mac people here we connect some mac via an ethernet card i could have a mac with ethernet card If you do not have such hardware, perhaps Mike or someone else might be able to bring something that we could add to your local ethernet temporarily. bring all that is not too heavy we will have a sun tape drive probably a dec tape drive and several cdrom and a printer laser postscript B/W color in montpellier on the net plus plenty of cpu on the net but we do not have a permanaent line we pay for time of connection