From owner-acedb@net.bio.net Fri Apr 01 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!usc!aludra.usc.edu!not-for-mail From: sbflynn@aludra.usc.edu (Stephen Brooks Flynn) Newsgroups: bionet.software.acedb Subject: Survey Date: 2 Apr 1994 08:28:16 -0800 Organization: University of Southern California, Los Angeles, CA Lines: 129 Sender: sbflynn@aludra.usc.edu Distribution: world Message-ID: <2nk6f0$7sk@aludra.usc.edu> NNTP-Posting-Host: aludra.usc.edu SURVEY This is a short survey intended for developers and users of bio- technology software. The goal of the survey is to gain a better understanding of the needs and desires of the bioinformatics community. A key area of focus is object oriented technologies and their potential application. You may choose to complete any or none of the responses. The results of the survey will be used by ZumaSoft, a consulting firm not affiliated with any other entity, in their product development efforts and will be held confidential. Please note that this is not intended in any way as a commercial advertisement. Please feel free to collaborate with your colleagues. Thanks for your help. Ted Stevens President, ZumaSoft Section 1 - Graphical User Interfaces 1) What GUI/workstation do you use most often in your workplace ? MacIntosh ______ Windows ______ MSDOS ______ OS/2 ______ Silicon Graphics ______ Hewlett Packard ______ Sun OpenLook ______ NeXT ______ Other (specify) _________________________________ 2) Approximately what percentage of others in your workplace use this same GUI ? _______ 3) How many different applications is your organization likely to bring up this year on your answer to 1 ? ______ 4) How was your training on your main GUI obtained ? 1) Vendor training ______ 2) Independent training firm ______ 3) In house training program ______ 4) Other ______ 5) How well does the GUI metaphor (dialog...) specifically fit the domain space of your projects' tasks ? 1) Not at all ______ 2) Like a glove ______ 3) Somewhat greater than 50% ______ 4) Somewhat less than 50% ______ 5) It works ok but our technicians often get frustrated (please elaborate). _____________________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ Section 2 - Database technology 6) What type of database ( if any ) do you use ? 1) Relational (please specify) ____________________________________ 2) Object Oriented (please specify) ____________________________________ 3) None ______ 4) Other (please specify) ____________________________________ 7) Who designed and implemented your database schema ? 1) You ______ 2) IS department ______ 3) Other ______ 8) Approximately what level of effort (man months) went into designing and implementing your database schema ? ______ 9) How often do you modify your database schema ? ________________________ 10) How many people depend on your database ? ______ How many organizations ? ______ 11) How robust is your query language ? (please identify and elaborate) ______________________________________________________________________ ______________________________________________________________________ ______________________________________________________________________ ______________________________________________________________________ Section 3 - Programming 12) Do you use a high level language in your work ? (please specify) ______________________________________________________________________ 13) Have you previously investigated object oriented programmimng ? (please elaborate) ___________________________________________________ ______________________________________________________________________ 14) Which aspects of OO programming (inheritance, polymorphism, encapsulation, code reuse ...) have you found most encouraging ? (please elaborate) ____________________________________________________ _______________________________________________________________________ _______________________________________________________________________ Most problematic ? (please elaborate) _________________________________ _______________________________________________________________________ _______________________________________________________________________ Section 4 - General 15) Has your organization ever performed an EDP audit ? ______ 16) Has your system ever been attacked by a computer virus or worm ? ______ 17) Comments about anything _______________________________________________ _______________________________________________________________________ _______________________________________________________________________ _______________________________________________________________________ _______________________________________________________________________ Section 5 - Professional Info 18) Name, title, and organization _________________________________________ _______________________________________________________________________ 19) Main area of expertise ________________________________________________ 20) Address and phone number ______________________________________________ _______________________________________________________________________ Please return via email to 72674.3161@compuserve.com. Thank you. From owner-acedb@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: Lockup bug under Olwm. Date: 04 Apr 1994 18:50:27 GMT Organization: University of California, Berkeley Lines: 12 Distribution: bionet Message-ID: References: <2mp0l7$nqt@mserv1.dl.ac.uk> NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: hcobb@fly2.berkeley.edu's message of 04 Apr 1994 17:04:43 GMT Rats!, and I was so sure I had it this time. The iconification-hop eats up most of the window of vulnerability, but does not close it. A sufficently fast Sun can jump through all the hoops in time to hang itself. So, for the moment, if you run Ace (or any other non-sun tool) under OLWM, change focus policy to focus follows mouse. -- Henry J. Cobb hcobb@fly2.berkeley.edu, SFB Tyrant-for-life A "Bjorn again" programmer. From owner-acedb@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: memory leaks in ACEDB Date: 4 Apr 1994 19:05:23 +0100 Lines: 40 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2npkt3$rov@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Henry Cobb at Berkeley used "purify" to look for memory leaks in ACEDB. I hope it's OK to reproduce his results message here; they seemed to be of general interest. ----------------------- Date: Thu, 31 Mar 1994 14:11:39 -0800 From: "Henry J. Cobb" Message-Id: <199403312211.OAA03820@fly2.berkeley.edu> To: acedev@peru.lbl.gov Subject: Some questions about purity of essence. Status: R Just a few things pure spoted. wgraph/graphsub.c, line 131, what is the reference to gBox going here? Purify: Searching for all memory leaks... There are 16926 leaked bytes (0.27% of the 6263736 allocated bytes in the heap) There seems to be a small leak in ksetdisp that I'll look into, but the rest seems to be flydb porblems. ------------------------ The gBox reference picks up a global pointer to the current open box (if it exists, which it will if k is non-zero). We set the default foreground colour for the new box to the current foreground colour for gBox. (I am presuming you are referring to graphBoxStart() -- my coordinates are slightly off from yours.) Overall it looks like there is no major memory leak, but we would certainly like to hear of any you do find. In particular it would be nice to try after "Add Update". That seems to be very hard on the heap for some reason. Thanks Henry, Richard From owner-acedb@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: Lockup bug under Olwm. Date: 04 Apr 1994 17:04:43 GMT Organization: University of California, Berkeley Lines: 27 Distribution: bionet Message-ID: References: <2mp0l7$nqt@mserv1.dl.ac.uk> NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: mieg@kaa.crbm.cnrs-mop.fr's message of 23 Mar 1994 09:03:35 -0000 I have a fix for the lockup bug under click-to-focus OLWM, but you're not gonna like it... In wgraph/graphxt.c:YCreate() insert the following: ... XtSetArg(args[i], XtNiconName, graph->name); i++; XtSetArg(args[i], XtNiconic, True); i++; XtSetArg(args[i], XtNx, x ); i++; ... What happens is that each window is created iconic and then deiconified when it's activated (as part of its creation). The only problem is that this becomes visually distracting (look ma, exploding windows!) and the first two windows remain icons at program startup. (Because our variant pops up the help window at startup for users considered to be clueless, and this takes the activeness away from the first two windows. This would take just one extra round of window activations to fix). IMNSHO it'd just be eaiser for most of the workstation users in the universe (i.e. those with Suns) to switch to Motif (as they will be forced to do anyway. ;-). -- Henry J. Cobb hcobb@fly2.berkeley.edu, SFB Tyrant-for-life A "Bjorn again" programmer. From owner-acedb@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Seeing the whole genome Date: 5 Apr 1994 00:34:44 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 18 Distribution: world Message-ID: <2nqbn4$qr1@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov A pleasant addition to ACEDB would be a display that simultaneouly shows all of the linkage groups (a.k.a. chromosomes) in a genetic map. Possible features might include: * click on a linkage group to go to the gMap for that group * display members of a gene family * show related QTL's Just a suggestion, --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 Mon Apr 04 23:00:00 1994 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.software.acedb Subject: COMPMED 94 FINAL SCHEDULE Date: 5 Apr 1994 12:37:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404051938.AA08326@morpheus> NNTP-Posting-Host: net.bio.net FINAL PROGRAM ANNOUNCEMENT FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE AND PUBLIC HEALTH 24-28 April 1994 Hyatt on the Lake, Austin, Texas The final program for the First World Congress On Computational Medicine and Public Health has now been set. Over 200 speakers will be presenting work in a variety of applications areas related to medicine and public health. Registration is still open for attendees. Registration details and/or a copy of the schedule at a glance, schedule-in-detail may be requested by sending an email request to compmed94@chpc.utexas.edu or by calling 512-471-2472 or by faxing 512-471-2445 There is no ftp form of the conference schedule due to the size of the file. We will be happy to fax/send a copy to anyone who requests it. The conference proceedings will appear as a series of volumes published by World Scientific. If you are interested in possibly submitting a paper for the proceedings, please contact mwitten@chpc.utexas.edu or call 512-471-2457 The overwhelming response to this congress has already justified having a second world congress in the future. The tentative schedule is to have in in 3 years. If you are interested in participating at the 2nd World Congress On Computational Medicine and Public Health, please contact Dr. Matthew Witten Congress Chair mwitten@chpc.utexas.edu From owner-acedb@net.bio.net Tue Apr 05 23:00:00 1994 Path: biosci!VECTOR.NALUSDA.GOV!scartinh From: scartinh@VECTOR.NALUSDA.GOV (Sam Cartinhour) Newsgroups: bionet.software.acedb Subject: ACEDB Documentation Server Date: 6 Apr 1994 08:18:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 135 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404061516.AA01650@vector.nalusda.gov> NNTP-Posting-Host: net.bio.net Announcing the WWW/ACEDB Documentation Server at the National Agricultural Library U. S. Department of Agriculture 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: http://probe.nalusda.gov:8000 As ACEDB continues to evolve it is becomes increasingly urgent to document its features. Fortunately there is widespread interest in writing and editing documentation in the ACEDB community. We have received permission from many authors to present their work on the server. However, there is clearly room for much more writing to be done! We would like to issue an open invitation to everyone writing documentation to contact us when they are ready to release their (finished or unfinished) work for public consumption. Our view of documentation is that it can range from the formal to the informal, long to short, and programmer-oriented to user-oriented. If you have no experience with html (hypertext markup language) we can provide assistance. Please contact Sam Cartinhour if you would like to participate in this effort in any way (writing, markup, ideas, suggestions). Thank you, Sam Cartinhour (scartinh@vector.nalusda.gov) Plant Genome Database Project National Agricultural Library, USDA 10301 Baltimore Blvd. Beltsville, MD 20705 USA Brief description of ACEDB Documentation Server contents: ***Now Available I. User's guide--Durbin and Thierry-Mieg's original user's guide. Introduces ace and explains printing, help, window and mouse behavior, queries, basic display types, super-user status and updates. II. Installation guide--Durbin and Thierry-Mieg. Discusses installation of ACEDB (automatic and by hand) and setting up for more than one organism. How to initialise the database and recompile. III. Configuration guide--Durbin and Thierry-Mieg. wspec with emphasis on the models, .ace and update file syntax. ACEDB Frequently Asked Questions--The FAQ for the ACEDB newsgroup. Maintained by Brad Sherman. Please contact Brad to update an entry or include new material (acedbfaq@s27w007.pswfs.gov). ACEDB, A Tool for biological information--Mike Cherry and Sam Cartinhour. A non-technical introduction to ACEDB as a generic genome database. The ACEDB Genome Database--Durbin and Thierry-Mieg. Introduction to ACEDB. Discussion of software design issues. ***In Progress Exploring Models Design and Structure--Sam Cartinhour. Model components and how to modify them. Intended for new curators and advanced users. This is a draft version undergoing revision. ***Forthcoming (manuscripts received and being marked up) Syntactic Definitions--Thierry-Mieg and Durbin. Specification of syntax of models, .ace files, and the query language. A guide to models and ace files--Mary O'Callaghan. Describes model elements and function. Detailed look at ace files, including deletion, renaming, and comment options. User guide--Mary O'Callaghan. Introduces ACEDB. Discusses major display types, menu options, queries. The ANGIS ACEDB manual--Bruno Gaeta, Australian Genomic Information Centre, Sydney (gaeta@angis.su.oz.au). A detailed (and recently written) introduction for ACEDB users. ANGIS is the Australian National Genomic Information Service. Working on ACEDB: Modeling and More--Lisa Lorenzen. Her handouts from a minicourse taught at Iowa state University. Source Code Documentation--Provided by Simon Kelley. Descriptions of several ACEDB modules. For programmers. **Ideas for Documentation This is a call for contributions! Below are a few suggestions. If any of these appeal to you, or if you are pursuing other ideas for documentation projects, please let us know! TableMaker--This powerful utility needs a good introduction. Queries--We need documentation for query by example, the query builder, and the original query interface. Metabolic Pathways--Anticipating that this module (coded by Stan Letovsky) will be included in the standard ACEDB release, documentation is needed both for users and curators. Hints--This area might consist of an unlimited series of small essays contributed by many people dealing with very focused topics. You could examine a particular feature in detail (constructed types, attachments, acediff, keyset manipulation....the list goes on and on). If you are reluctant to undertake a large documentation project, try one of these. Proposals--This area might include descriptions of modifications or new features you would like to see. From owner-acedb@net.bio.net Tue Apr 05 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!gatech!swrinde!ihnp4.ucsd.edu!dog.ee.lbl.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 6 Apr 1994 21:22:09 GMT Organization: Dendrome, A genome database for forest trees Lines: 878 Approved: news-answers-request@MIT.Edu Message-ID: <2nv961$82i@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: 4/6/94 Version: 1.10 Xref: biosci bionet.software.acedb:215 news.answers:15183 ---------------------------------------------------------------------- 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 phil@decster.uta.edu MSDOS/Windows/NT: A port to NT is rumored to be in the works. Macintosh: A port to the Macintosh may become available real soon now. Beta versions of this *might* be found at the ACE archives. See Q3. Here is a note from Richard Durbin: There is now a tested Macintosh version. You need a Macintosh with >16Mb of memory and a decent monitor. You also need some way of obtaining the files from an ftp site (e.g. NCSA telnet, Versaterm Pro...) and Stuffit Deluxe, which I am told costs $65 in the USA, and is useful anyway for compressing/decompressing files. It turns out that Stuffit Deluxe can decompress Unix .tar.Z archive files. Frank Eeckman has now made available a .tar.Z archive of a complete C. elegans ACEDB database, with updates already read in. Ftp to genome.lbl.gov, folder pub/macace, and follow the instructions in README. Thank you Frank. 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 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 : Mace Species : Zea mays L. ssp. mays Focus : Maize genome Comment : Mace is the front end for maizedb, a relational (SYBASE) database. It is updated from maizedb by software written by Stan Letovsky. Maizedb is updated daily and will soon be accessible by public login. Curator : Ed Coe Curator : Pat Byrne Curator : Georgia Davis Curator : Mary Polacco Off-Site Curator : Marty Sachs Off-Site Curator : Christiane Fauron Off-Site Curator : Carolyn Wetzel Off-Site Curator : Steve Rodermel Off-Site Curator/Designer : Stan Letovsky Off-Site Curator/Designer : Mary Berlyn Systems Manager : Denis Hancock PI : Ed Coe Contact : maizedb@teosinte.agron.missouri.edu Last_update: 5 October 1993 Database : MycDB Species : Mycobacterium PI : Staffan Bergh PI : Thierry Garnier PI : Stewart Cole Contact : staffan@biochem.kth.se Contact : stcole@pasteur.fr Last_update : 18 March 1994 URL: http://kiev.physchem.kth.se/MycDB.html URL: ftp://kiev.physchem.kth.se/pub/MycDB URL: ftp://ftp.pasteur.fr/pub/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 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, gopher Curator : Donn F. Davy Contact : DFDavy@lbl.gov Contact : aggarwal@genome.lbl.gov Focus : STS content mapping & sequencing of Human Chromosome 21 PI : Jasper Rine PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng Last_update : Sept. 1993 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 version of the FAQ represents an attempt to bring an html version and a plain text version into congruence. Please let me know of any new errors that I may have introduced, and bear with me through the changeover. Thanks. --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 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/plant/acedbfaq.html [Until I get more familiar with HTML, it may not be totally synchronized with the plain FAQ. --bks] 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 Tue Apr 05 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: memory leaks in ACEDB Date: 06 Apr 1994 22:18:50 GMT Organization: University of California, Berkeley Lines: 64 Distribution: bionet Message-ID: References: <2npkt3$rov@mserv1.dl.ac.uk> NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: rd@mrc-lmb.cam.ac.uk's message of 4 Apr 1994 19:05:23 +0100 Had a few problems with the new file locking write access under purify, so I got the Sentinel program demo (from mike.simon@aib.com) and ran that. I added a comment to an item in the database and it complained about a leak of 510 bytes at wbs/bstree.c at line 341: bs->bt->cp = messalloc(strlen(BSbuffer)+1); And also: 0x19EC18 M messalloc() [/home/hgc/data14 malloc(532) 1 12 uArrayCreate() [/home/hgc/data14/Drosophila/flydb-v3.1/wfree/arraysub.c:56] arrayCopy() [/home/hgc/data14/Drosophila/flydb-v3.1/wfree/arraysub.c:164] makePaths() [/home/hgc/data14/Drosophila/flydb-v3.1/wbs/bssubs.c:1382] makePaths() [/home/hgc/data14/Drosophila/flydb-v3.1/wbs/bssubs.c:1365] makePaths() [/home/hgc/data14/Drosophila/flydb-v3.1/wbs/bssubs.c:1365] makePaths() [/home/hgc/data14/Drosophila/flydb-v3.1/wbs/bssubs.c:1365] bsMakePaths() [/home/hgc/data14/Drosophila/flydb-v3.1/wbs/bssubs.c:1331] objDecorate() [/home/hgc/data14/Drosophila/flydb-v3.1/wbs/bssubs.c:166] bsUpdate() [/home/hgc/data14/Drosophila/flydb-v3.1/wbs/bssubs.c:215] Which I suspect that:bssubs.c: line 1382 if (bsIsTag(bs) && bs->key != _ANY && !assInsert (ass,(void *)bs->key,arrayCopy(workPath))) forgets to release the copy of the array. Also lexsubs.c: line 899 LexHashTable[classe] = arrayCreate(1< NNTP-Posting-Host: s27w007.pswfs.gov For those of you who are desparate for an HTML version of the ACEDB FAQ, there is a version at URL: http://s27w007.pswfs.gov/Homepage/acedbfaq.html in addition to one at http://probe.nalusda.gov:8000/plant/acedbfaq.html I am attempting to keep the HTML version and the plain text versions congruent. Undoubtedly I have introduced errors. Please let me (or preferably acedbfaq@s27w007.pswfs.gov) know about any problems. Curators of ACEDB databases should be especially concerned. If you curate an ACEDB database, please send me a paragraph (formatted as in the FAQ) if you are not currently included or if there are errors. Feel free to improvise tags and add as many URL's as you like. I will take care of the HTML markup. Be sure to check out Sam Cartinhour's excellent documentaion at URL http://probe.nalusda.gov:8000/acedocs/index.html. --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 Apr 06 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: memory leaks in ACEDB Date: 07 Apr 1994 00:30:01 GMT Organization: University of California, Berkeley Lines: 17 Distribution: bionet Message-ID: References: <2npkt3$rov@mserv1.dl.ac.uk> NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: hcobb@fly2.berkeley.edu's message of 06 Apr 1994 22:18:50 GMT Again, RATS!! I've been fingering the wrong objects! In objcache.c:cacheDestroy() the comment says it all: case 1 : /* This cacheEntry has not been modified, thus we can still use it next time */ So the items that originally allocated the objects only did so because they were at a "high water" mark in the program and the objects that are holding the memory at program end are the real culprits. I'm gonna retest after chopping out the caching (for testing only). -- Henry J. Cobb hcobb@fly2.berkeley.edu, SFB Tyrant-for-life A "Bjorn again" programmer. From owner-acedb@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!csrgate8.lbl.gov!user From: jlmccarthy@lbl.gov (John McCarthy) Newsgroups: bionet.software.acedb Subject: Re: Seeing the whole genome Followup-To: bionet.software.acedb Date: 7 Apr 1994 11:39:43 GMT Organization: Lawrence Berkeley Laboratory Lines: 40 Distribution: world Message-ID: References: <2nqbn4$qr1@overload.lbl.gov> NNTP-Posting-Host: csrgate8.lbl.gov Arun Aggarwal and LBL is working with Richard Durbin and Simon Kelley at Cambridge to develop a much more general, user-configurable, multi-map display module that will allow users to specify arbitrary "columns" of information for multiple maps. It should be able to support the kind of functionality Brad Sherman suggests his recent posting (below). For a more complete description, see the subsequent news item reporting Richard's recent visit to LBL. -John McCarthy +=====================================================================+ | 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 | +=====================================================================+ In article <2nqbn4$qr1@overload.lbl.gov>, bks@s27w007.pswfs.gov (Bradley K. Sherman) wrote: > > > A pleasant addition to ACEDB would be a display that > simultaneouly shows all of the linkage groups (a.k.a. > chromosomes) in a genetic map. Possible features might > include: > > * click on a linkage group to go to the gMap for that group > * display members of a gene family > * show related QTL's > > Just a suggestion, > --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 Apr 06 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!csrgate8.lbl.gov!user From: jlmccarthy@lbl.gov (John McCarthy) Newsgroups: bionet.software.acedb Subject: Richard Durbin visit to LBL Followup-To: bionet.software.acedb Date: 7 Apr 1994 11:43:47 GMT Organization: Lawrence Berkeley Laboratory Lines: 97 Distribution: world Message-ID: NNTP-Posting-Host: csrgate8.lbl.gov Richard Durbin visited LBL on Tuesday, March 29. Those present included Frank Eeckman, Suzanna Lewis, Ed Theil, Eric DeMund, Arun Aggarwal, Marat Boshernitsan, and John McCarthy. This note summarizes our discussions: 1. CURRENT WORK AT CAMBRIDGE. Richard discussed work on ACEDB and related software currently under way in Cambridge at the Sanger Centre. [perhaps Richard and his group might want to write a brief summary of this at some point for the newsgroup. My notes are rather sketchy, but they clearly have a lot of interesting stuff going on. -JMc] Ed noted that LBL is interested in trying out and possibly using many of the analytic capabilties that Richard described. Arun will take the lead role here for installing, testing, and explaining them to the rest of the group at LBL. 2. ACE2 AND ACE3. Richard said that he basically likes most of the things Jean has done with ACEDB 3.0. It just happened so quickly that he was reluctant to go along with all the major model changes, etc. for the whole worm community before giving it a bit more consideration and testing. But their intention is to re-merge the two systems rather than to continue divergent development. This will require some time and effort, however, to get the two sets of code back into synch. 3. IMAGES. Frank Eeckman said that he and Cyrus Harmon had decided on a single image file format (PICT) for the Mac version of ACEDB. This has simplified things considerably. [Richard added the following: We also discussed images in detail during the afternoon, and came up with a new specification for the graphXxx calls that handle images, which Cyrus and I feel we can both implement: him using Mac PICT files and Friedemann/me using X images.] 4. SOURCE CODE FILE STRUCTURE. Cyrus and Frank have added new directories for mac code: w1mac, w2mac etc., without touching w1, w2 etc. They have also done some restructuring within those files; Frank suggests that we ought to consider adopting it for the standard distribution. 5. MAP DISPLAY. Richard outlined what he and Simon Kelly have been doing to rewrite the map display modules, with emphasis on user-configurable "columns" for different types of information. Arun Aggarwal explained and demonstrated work he has done to separate out 3 different levels of information in map displays: (1) entire display window; (2) one or more maps; and (3) columns within individual maps. Two major goals of this work are (a) capability to display multiple maps from different organisms simultaneously (e.g., human and mouse, or different plant species), and (b) capability to show simultaneously (side by side) multiple (zoom) levels of detail for a particular region (e.g., cytogenetic, genetic, physical, P1 clone, sub-clones, and DNA sequence). After some discussion, Richard concluded that the work Arun has done is nicely complementary to what they have been doing in Cambridge -- and that we should try to work together to develop a single map display module. Arun will send Email to Simon and they will try to work out details. Probably Simon will continue to work on column-level code, while Arun will work on map and display levels. Both of these will use the new map models Jean developed for ACEDB 3.0, and the new extensions to support multi-species homologies (though these may still require some further clarification and simplification). The goal is to have a joint prototype running for the July workshop. 5. ?LONGTEXT. We briefly discussed the still unresolved issue of how to deal with different types of text. Richard said that he and Jean had tentatively agreed to make array class objects "second class citizens" that must belong to some other B class object. If this were the case, then Longtext would become essentially another (special) datatype. We agreed that there needs to be a simple, consistent way to represent beginning and ending of Long (i.e., formatted) text, which may contain embedded spaces, carriage returns, etc. We also agreed that how to represent LongText within the system is a different (albeit closely related) question. For example, if Longtext is simply part of a standard object, it could be inially "collapsed" and could simply be expanded within the same tree display, or it could be displayed in a separate window (as is done at present). Richard pointed out that ACEDB does not currently have a multi-line text edit capability. We noted that Gary Aochi had developed such a capability last year, but it was not incorporated in the standard distribution. Eric will try to revive that code and merge it with ACEDB 3.0, for Richard and Jean to consider for possible incorporation in a future version of the standard distribution. -JLMc +=====================================================================+ | 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 Thu Apr 07 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: memory leaks Date: 8 Apr 1994 04:20:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404081124.AA20974@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > 2) i wonder if this discussion is not too technical for the bionet server ? Oh no Jean, we're all immensely enjoying this peek at the clockworks underneath ACEDB, even if we don't fully understand it. - Dave From owner-acedb@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: eventual memory leaks Date: 8 Apr 1994 12:10:03 +0100 Lines: 3 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2o3e2b$qff@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk bs->bt->cp = messalloc(strlen(BSbuffer)+1); is released by the function BTfree() From owner-acedb@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: memory leaks Date: 8 Apr 1994 12:07:16 +0100 Lines: 13 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2o3dt4$q6t@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk i don t see why under UNIX iu should release memory before exit(0) all teh memory in Cobb's message is necessary thoughout the life time of the process we do not release either the memory on the stack obviously. howver I added a comment to an item in the database and it complained about a leak of 510 bytes at wbs/bstree.c at line 341: bs->bt->cp = messalloc(strlen(BSbuffer)+1); would be serious, if indeed it is not release, ill check that one. 2) i wonder if this discussion is not too technical for the bionet server ? From owner-acedb@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: gels Date: 8 Apr 1994 13:05:21 +0100 Lines: 18 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2o3ha1$t5l@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk if the model should be Lane Marked Text Text UNIQUE Float >> Unmarked Text Text UNIQUE Float then since 2 texts are available, i don t see why we need to say marked, unmarked i may add a button to select in the display some templates for text 1 and 2 so that you could see for the 3 clones all their lanes, only some of them i mean for all the clones beeing displayed of couse, if a curator defines a class Lane, he coulpd associate FingerPrint as the preferd display for that classs in options.wrm the Text Text is excellent for genethon data useless for the nematode fp good enough for allele comparisons i think From owner-acedb@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Gel Patterns Date: 8 Apr 1994 12:55:19 +0100 Lines: 119 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2o3gn7$skc@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk In january i wrote a new display for finger print analysis adapted for the nematode then i reused it for the genethon data now i realise that it could be used more widely for any pattern 1) Present system The nematode ?Clone has a tag somewhere that syas FingerPrint UNIQUE Float REPEAT then in the pmap display i hooked a boxmenu on the clones that says fingerprint to invoke the fingerprint display, uou pick the menu in a displayed clone this starts the FP-display then you can import other clones like in GridDisp or KeySetAdd/Remove or import a whole keyset there is always a single active FP-display that coaligns all the patterns the lines in this pseudogel can be switched easilly, the common lines can be highlighted details on the object obtained by single and double clicks it zooms etc correctly 1.2) Difficulty the way to invoke the system is from pmap display only it can t be used in some other class 2) Genethon dta those are a bit more general what Cohen and co did is to cut yacs by several restriction enzymes then lightup those bands hybridizing to a repeated sequence THE so i have then a model ?Yac FingerPrint ?Probe ?Motif UNIQUE Float REPEAT Probe is THE or another one, Motif is the restriction enzyme used 3) A possible generalisation is to attach the FingerPrint display to nay object that will have the Fingerprint tag all of these could then be imported certainly the magic construct should be FingerPrint #FingerPrint nevertheless: How do we popup the FP-display to start with, from main menu ? how do we document this extra magic tag ? a possibility is to have a FP class, but i am rather against that ************************************* here is the proposal by Sam: I think we need a very general solution for band patterns, one that we can use to represent any banding pattern whether or not restriction enzymes are involved or if a locus is known--for example protein gels the minimum needed I believe is: a way to identify a lane a way to identify every band in the lane a way to give every band a size I could then use this to build more complicated things, e.g. to represent the plant genome database conception of "?Gel_Pattern". suppose this thing was called #Lane maybe it looks like this ?Lane Lane Text Text UNIQUE Float first Text is lane designation second Text is band designation third Float is band size so I could have Lane A Band1 12.5 Lane A Band2 9.3 Lane A Band3 4.2 Lane B Band1 9.7 Lane B Band2 0.8 etc in my higher level object I could annotate each lane as desired and associate it with enzymes, loci, etc? now how to display this? You would display only if you were looking at an object that had #Lane(s)? Sam ********* end of Sam's *********************** i dont really like that because in cases i know there are plenty of lines that nobody wants to name so FingerPrint Line Float MappedLine Text Float DoublyMappedLine Text Text Float is more economic, but is also very silly remeber that genethon data is several millions floats so silly tags are expansive ******* Feedback hoped for, Jean From owner-acedb@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: patterns Date: 8 Apr 1994 13:09:41 +0100 Lines: 28 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2o3hi5$8o@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk sam propses: ?Lane Lane Marked Text Text UNIQUE Float Unmarked Text Text UNIQUE Float > >first Text is lane designation ((would this be better as an INT)) >second Text is band designation >third Float is band size Marked bands could then be highlighted in the graphic display so I could have Lane : g2345HindIIIpop123 Lane A Marked Band1 12.5 Lane A Unmarked Band2 9.3 Lane A Unmarked Band3 4.2 Lane B Unmarked Band1 9.7 Lane B Marked Band2 0.8 > but this is wrong. in Lane B Marked Band2 0.8 the 0.8 would be assigned to text2 not to flaot so i vote against the Marked Unmarked tag From owner-acedb@net.bio.net Fri Apr 08 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: Gel Patterns Date: 9 Apr 1994 18:20:11 +0100 Lines: 62 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2o6o4b$94g@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk I am in favour of a general way to display gel patterns. Here are some immediate ideas to add to the discussion: Since there may be several patterns or lanes attached to any one object I suggest a two-level tag system: Fingerprint ?XXX #Fingerprint i.e. the display code will go one right of _Fingerprint before bsPushObj(). I can image it working two ways: With a single object you may want to show all the columns, each headed by name(xxx), where xxx is a key from class ?XXX. With a keyset of objects (as Jean uses it now approximately), you could pass an additional key yyy, and you would get one column per object in the keyset, given it had a key xxx that matched yyy. So e.g. you could show all the EcoRI digests of a set of clones. Note that I do not specify the class ?XXX. This might be ?Motif, for a restriction site, or ?Probe, or ?Text (anything). It may be meaningful in the object, but will just be used as a label by the gel display code. So it can be different in different models. Before you rush to say that you need both a motif and probe, read the next bit. #Fingerprint Bands Float UNIQUE Text Motif ?Motif // not ?Motif - may be double digest Probe ?Probe Text ?Remark ... Jean has essentially Bands UNIQUE Float REPEAT, i.e. a horizontal vector. Above I propose a vertical list of fragment lengths. It really should be more of a set. This allows adding and deleting bands more easily. It does forbid two distinct bands of exactly the same size. Is that a problem? The big win is that it allows an optional label to be attached for each band, as Sam wants, but if they are left off then you use the same memory as Jean's original solution. And any automatic matching code can ignore the labels. I'm not quite sure what other info one might want to put in the #Fingerprint structure, and how it will be displayed and used. Perhaps you could double click on something at the top of the column and see the #structure displayed as a tree (not possible with current treedisp code). Probably Fingerprint and #Fingerprint are not the best names. What about Fragment_set? Any other ideas? We have a direct application here for multiple fingerprints for a single clone, because the way David Bentley makes fingerprints he gets three per clone. As for starting the display. I'm not sure you should be able to start it from the main menu. Probably it should know how to apply the selected keyset to itself, or a single object by displayBlock() capture (as with probes for gridDisplay()). I think there could be specfic handles to start the window from menus or boxmenus in the map display and grid display. Actually, I guess the main menuy would also be harmless. Richard From owner-acedb@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: fwd: Re: gels Date: 11 Apr 1994 07:09:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404111413.AA23224@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Date: Mon, 11 Apr 94 14:59:59 +0100 >From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) To: matthews@greengenes.cit.cornell.edu Subject: Re: gels i see it is indeed a lane #Lane means it will never be used per se but yes i could have ?Lane it is indeed preferable From owner-acedb@net.bio.net Sun Apr 10 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: gels Date: 11 Apr 1994 04:58:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404111202.AA22975@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net This syntax, > Gel #Gel_Pattern > > #Gel_Pattern Bands UNIQUE Float REPEAT > Band Float Text // why Unique ? > Motif ?Motif > Probe ?Probe seems odd. Is there a reason the class is named #Gel_Pattern instead of ?Gel_Pattern like other constructed-types (?Colour, ?map_location)? I would favor going back to your previous name "Lane" instead of "Gel". Even if it does add a few more megabytes to the ace file, it seems to describe the entity better. - Dave From owner-acedb@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!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: gels Date: 11 Apr 1994 10:51:54 +0100 Lines: 81 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2ob6jq$8pa@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk Following various suggestions i think we all converge on the following: 1) a) A column of float is better because flaot are more general columns are easier to query than lines the treedisp will automatically come Closed showing the number of lines. b) however the lenght of the ace file may seem awkward 2) The second tag system is more versatile, and best used as a qualifier for the set of band values 3) Additional info may be requested Therefore i implement the following model 1) A magic tag: Gel (3 letters only because in ace files it may have to be repeasted millions of times 2) the folowing model: Gel #Gel_Pattern #Gel_Pattern Bands UNIQUE Float REPEAT Band Float Text // why Unique ? Motif ?Motif Probe ?Probe .... // this etc is left open to the curators my display code will use again a second tag approach here so you can use what you want The display code will be called DtGelPattern you can attach it to any class in options.wrm YThe dispaly will accept any object conatining Gel#Band (or Bands) the code is allready running, it has the following capabilitioes: zoom/center flip lanes import new lanes via blocksubs import keysets sort the lanes automatically (in test) it is invoked by the boxMenu in pmapdisp and by a button in dnaanalysis I will try to fus it with the artificial gel system which exists separatelly the only problem with Band in the the model is the ace format: MyClass myObj Gel Probe THE Gel Band 23.1 Gel Band 28.8 Gel Band 43 Gel Band 87 i.e. Gel Bands is repeated million times So i suggest to have an alternative Band or Bands up to the curator. The following selectors are implemented: In the window there are text box entries if filled only the patterns fitting these will be displayed other wise you may have 3 or more pattern per obj Actually i wonder if the ?XXX is useful since the same sort of info can be included in the #model for the genethon i would use Gel #Gel_Pattern #Gel_Pattern Bands Float REPEAT Enzyme ?Motif // one of ecor1 etc Probe ?Probe // THE etc From owner-acedb@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!VECTOR.NALUSDA.GOV!scartinh From: scartinh@VECTOR.NALUSDA.GOV (Sam Cartinhour) Newsgroups: bionet.software.acedb Subject: gels Date: 11 Apr 1994 06:52:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404111350.AA00304@vector.nalusda.gov> NNTP-Posting-Host: net.bio.net Hi, not to muddy the gel issue, but I wonder if the whole solution for gels and fragments could also be part of the solution for restriction maps and fragments. That is, can we come up with a representation for bands that would be versatile enough for both of these needs? I bring this up because Richard notes in his proposal: > It does forbid two distinct bands of exactly the same size If the gel/fragment model also supported restriction maps, it would need a list structure (REPEAT) to provide for same-sized fragments. I am not suggesting that the gel display and restriction map display be the same, only that their underlying models might share enough features that we could join them and have a single, unified representation for fragments. sam From owner-acedb@net.bio.net Sun Apr 10 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: Gel patterns Date: 11 Apr 1994 14:45:24 +0100 Lines: 33 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2obk9k$t37@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk I like the option of Bands or Band. I agree that Text following float does not have to be UNIQUE -- I just thought that by default only the first would be used as an explicit label. But removing the ?XXX makes an important difference. As you have it, wiuth Gel #Gel_Pattern you can only attach one pattern to an object. This is because the #Gel_pattern is a unique subobject. You could have two Probe entries in it and two Bands, but there would be nothing to attach one set of bands to a particular probe. The alternative Gel ?XXX #Gel_Pattern lets you attach a label to each gel_pattern, so you can differentiate them. It is very important. Of course in any one model you would have, e.g. Gel ?Text #Gel_Pattern but I thought that the DtGelPattern code might as well not care about the class of this first key -- just use it as a label. You could even have a tag: Gel Line1_fp #Gel_Pattern Line2_fp #Gel_Pattern Alu_pcr #Gel_Pattern In fact, I imagine that this could well be the most common usage. The .ace file would then say: Clone F37C3 Line1_fp Bands 2.3 4.8 4.9 15.6 Alu_pcr Bands 1.3 17.6 26.1 So I argue strongly that you are not using your marvellous invention of the second tag system in your proposal. Everything else looked good. Richard From owner-acedb@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!VECTOR.NALUSDA.GOV!scartinh From: scartinh@VECTOR.NALUSDA.GOV (Sam Cartinhour) Newsgroups: bionet.software.acedb Subject: gels Date: 11 Apr 1994 07:32:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404111430.AA00347@vector.nalusda.gov> NNTP-Posting-Host: net.bio.net I want to add one more thing to the idea of combining the band model with a restriction map model: people will probably want to show restriction map data on a gel display. I am hoping we could enter this data only once instead of twice, first to drive a restriction map display, and second to drive a gel simulation. I am assuming that someday there might be a restriction map display of some kind, motivating people to enter "ordered" fragment data. It does seem like a useful extension to physical maps. sam From owner-acedb@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!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: gels Date: 11 Apr 1994 15:44:40 +0100 Lines: 27 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2obnoo$458@mserv1.dl.ac.uk> Original-To: rd@cele i have a problem with my former proposal A contruicted type like #Lane is unique so it must be preceded by something Richard proposes Fingerprint ?XXX #Lane but maybe the #XXX should be a Text because it is really a description for a type of finger print experience or maybe we should have FingerPrint ?fp #Lane #Lane UNIQUE Bands UNIQUE Float REPEAT Band Float Text ?fp Probe ?Probe XREF fp Motif ?Motif .... this make sense because of course the whole purpose of fingerprinting is to aplly the same protocol to a great many clones or cells or whatever In this modification i transfer the deatailled description to the Fp class rather than to the lane subtype which just carries the floats and comments associted to a single value From owner-acedb@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!MENDEL.AGRON.IASTATE.EDU!lorenzen From: lorenzen@MENDEL.AGRON.IASTATE.EDU (Lisa Lorenzen) Newsgroups: bionet.software.acedb Subject: Restriction Maps Date: 11 Apr 1994 08:45:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404111544.AA24957@mendel.agron.iastate.edu> NNTP-Posting-Host: net.bio.net Not too change the subject too much, but I concur with Sam on the need for a restriction map display. I have used the regular map display to "mock up" restriction maps . . It works okay, but a "real" display would be nice :-) Lisa :-) ----- Begin Included Message ----- I want to add one more thing to the idea of combining the band model with a restriction map model: people will probably want to show restriction map data on a gel display. I am hoping we could enter this data only once instead of twice, first to drive a restriction map display, and second to drive a gel simulation. I am assuming that someday there might be a restriction map display of some kind, motivating people to enter "ordered" fragment data. It does seem like a useful extension to physical maps. sam ----- End Included Message ----- From owner-acedb@net.bio.net Mon Apr 11 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Testing, found bug, wanna fix my way, ok? Date: 12 Apr 1994 02:35:31 GMT Organization: University of California, Berkeley Lines: 25 Message-ID: NNTP-Posting-Host: fly2.berkeley.edu Hi, I'm working on a Tcl parsing version of Acedb for scripting. (See comp.lang.tcl). One of the things I'm using this for is to write standard tests of Ace. (Someday you might be able to say "make tests" and your installation will test itself against expected results). As I was going after an edge case, I found that: where {} will crash Ace. As the behaviour in this case was undefined, I'm not really surprised. (This kind of stuff is what testing scripts are for, no?) So the way I propose that I will fix this, if it's not a big headache for anybody, is to change the definition of braces in Ace to match that of Tcl, that is, as stackable quotes. OK? -- Henry J. Cobb hcobb@fly2.berkeley.edu, SFB Tyrant-for-life From owner-acedb@net.bio.net Mon Apr 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.intercon.com!udel!news2.sprintlink.net!news.sprintlink.net!indirect.com!nike From: nike@indirect.com (Laurence Canter) Newsgroups: bionet.software.acedb,ca.general Subject: Green Card Lottery- Final One? Date: 12 Apr 1994 07:44:44 GMT Organization: Canter & Siegel Lines: 34 Message-ID: <2odjhc$2dr@herald.indirect.com> NNTP-Posting-Host: id1.indirect.com Xref: biosci bionet.software.acedb:237 ca.general:2891 Green Card Lottery 1994 May Be The Last One! THE DEADLINE HAS BEEN ANNOUNCED. The Green Card Lottery is a completely legal program giving away a certain annual allotment of Green Cards to persons born in certain countries. The lottery program was scheduled to continue on a permanent basis. However, recently, Senator Alan J Simpson introduced a bill into the U. S. Congress which could end any future lotteries. THE 1994 LOTTERY IS SCHEDULED TO TAKE PLACE SOON, BUT IT MAY BE THE VERY LAST ONE. PERSONS BORN IN MOST COUNTRIES QUALIFY, MANY FOR FIRST TIME. The only countries NOT qualifying are: Mexico; India; P.R. China; Taiwan, Philippines, North Korea, Canada, United Kingdom (except Northern Ireland), Jamaica, Domican Republic, El Salvador and Vietnam. Lottery registration will take place soon. 55,000 Green Cards will be given to those who register correctly. NO JOB IS REQUIRED. THERE IS A STRICT JUNE DEADLINE. THE TIME TO START IS NOW!! For FREE information via Email, send request to cslaw@indirect.com -- ***************************************************************** Canter & Siegel, Immigration Attorneys 3333 E Camelback Road, Ste 250, Phoenix AZ 85018 USA cslaw@indirect.com telephone (602)661-3911 Fax (602) 451-7617 From owner-acedb@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!mrc-lmb.cam.ac.uk!rd From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB release 2-10: C. elegans data Date: 14 Apr 1994 05:57:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 140 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404141216.AA13695@cele.mrc-lmb.cam.ac.uk> NNTP-Posting-Host: net.bio.net This is a broadcast message to the ACEDB mailing list. If you do not want to be on the list, please send email to rd@mrc-lmb.cam.ac.uk. **** For Sun Sparc users, note the *IMPORTANT* message below. **** ACEDB data update 2-10 ====================== There is available a new data update for the C. elegans database. This does not affect version 3 of ACEDB, which is designed for human and other organism data. This is an incremental update, with new data but no change to the program. The next release will be a major release, including a new version of the program. Because this release is late it does in fact include the updated version of the genetic map (thank you Jonathan). However the external database of protein matches (proteins.???.tar.Z) has not been updated; it will be in the quarterly update. The main items in this data release are: Genetic map 3/94 Physical map 12/4/94 C. elegans DNA sequences in EMBL release 37 Mapping data sent to cgc@mrc-lmb.cam.ac.uk A major update of genes and rearrangements mentioned in papers listed in the CGC bibliography (thanks Theresa Stiernagle, Mark Edgeley and Larissa) New sequences from the genomic sequencing project, and changes to old ones. There are now 137 cosmids finished (about 4Mb). General edits and fixes (e.g. EMBL references brought up to date, and some sequences) New tutorial/manual =================== Bruno Gaeta and others at the Australian National Genome Information Service (ANGIS) wrote a very nice macintosh tutorial for ACEDB, full of screen images. They have kindly made this available for us to redistribute, and it is available in both postscript and compressed macintosh forms (angistute.*.*). Code ==== There is no new code release. You should use your existing version of the binary (2_0). ****** IMPORTANT ****** There is a bug in version 2_0 of the code that causes the program to crash ("bus error" or "segmentation violation") in some versions of the binary (particularly sparc) at the very end of reading the updates. This does not lose any data. It does remove the precalculation of the genetic and physical maps, which should speed up their display. You can do this precalculation by hand as follows: After adding the update, as the administrator (the person who installed ACEDB) Select "Write Access" from the main menu Select "Align Maps" from the main menu Press the "Make pMaps" button to make the physical maps Press the "Make gMaps" button to make the genetic maps Select "Save" from the main menu. ************************** Solaris versions ================ There are two Solaris versions, one for people with more recent Solaris releases that contain the X11R5 libraries (bin.solaris.2_0.tar.Z) and one for older releases with the X11R4 libraries (bin.solaris.2_0A.tar.Z). Some people have had continuing problems with Solaris libraries. If neither of these versions work, a more drastic solution is to establish symbolic links from /usr/lib to /usr/openwin/lib/libXaw.5*. Macintosh version ================= I understand the Macintosh version is now working in a number of labs. Again, the archive anonymous ftp site is genome.lbl.gov, folder pub/macace, and detailed enquiries should go to Frank Eeckman (eeckman@llnl.gov). Thank you again, Frank. Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb/ace2 cele.mrc-lmb.cam.ac.uk (131.11.84.1) in England, in pub/acedb/ace2 lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb/ace2 In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password 'your email address' cd repository/acedb/ace2 binary mget * get README y/n answer yes etc .. .. quit If installing for the first time -------------------------------- Get all the update tar.Z and read the files README and NOTES before proceeding further. If updating an existing system ------------------------------ Just get the last update.tar.Z file, plus INSTALL. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Please send any comments, especially about anything you think is wrong (program or data), to Richard Durbin (rd@mrc-lmb.cam.ac.uk) program Mary O'Callaghan (moc@mrc-lmb.cam.ac.uk) data -------------------- end of message -------------------- From owner-acedb@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!mcs.anl.gov!maltsev From: maltsev@mcs.anl.gov (Natalie Maltsev) Newsgroups: bionet.software.acedb Subject: a workshop announcement Date: 14 Apr 1994 10:39:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 164 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199404141739.MAA20519@juju> NNTP-Posting-Host: net.bio.net ------------------------------------------------------------------- Dear reader: Please bring this notice to the attention of persons you think might wish to participate. Workshop on Integration of Biochemical Databases June 8 - June 10, 1994 Pushchino, Russia (Registration deadline May 12) We invite all interested researchers to visit this major center of biomedical research in Russia and the former Soviet Union. The workshop will give you the opportunity to informally discuss how to integrate databases relevant to molecular biology and medicine. Several leading biological database experts from outside Russia will be present, and many interesting (and probably unfamiliar) Russian database projects will be demonstrated by their representatives. The workshop will be hosted by Professor Evgeni E. Selkov and coworkers, and is arranged in part by Dr. Ross Overbeek et al. at Argonne National Laboratory, Illinois, U.S.A. We have scheduled the following events: o Overview of EMP (Enzymes and Metabolic Pathways database). EMP contains the encoding of the most important articles (approx. 10,000) describing enzymes, phylogenetically arranged. It also contains in graphical form most of the known metabolic pathways for all organisms. We consider EMP the world's leading database of its kind. All participants will receive a free academic copy of this database (see details below). o For the first time, a presentation of a broad selection of Russian / FSU databases. There will be poster sessions and demonstrations on PC computers. During this winter we have collected brief descriptions and invited representatives from the groups who created (in our judgment) the most interesting of these. In Russia there exist substantial data collections ranging from minor ones done by single experts to very large collections of for example medicinal properties of compounds, 3D structural data, sequence data, culture collections, genetic markers, tumor characteristics, regulatory sequences, and more. o Optional introductory course to general metabolism and related computational issues. This will be given prior to the workshop (June 5-7) by Professor Selkov. There will be no scheduled talks. We instead invite open discussion of topics of common interest, such as metabolism and enzymes, or phylogeny, alignments, compounds, motifs, and maps. If you wish to use or generate such integrated biological data, then please join us. Sincerely, Evgeni Selkov Ross Overbeek Natalia Maltsev Amos Bairoch Nat Goodman George Michaels Harold Morowitz Niels Larsen Anthony Bonner Terry Gaasterland Pat Gillevet Rick Stevens Alexander Zamyatnin Sponsorship ----------- The workshop is so far unsponsored, but we welcome interested sponsors. We need help with computer equipment and coverage of travel expenses for Russian participants. Practical details ----------------- Pushchino is a community of some 30,000 people located 100 km south of Moscow. The main acitivity is research. The area is generally safe. The water is not contaminated; the food is fresh and locally produced. You will be able at least to send electronic mail. The registration fee is US $750 for the workshop if you plan to attend the introductory course, $550 otherwise. The fee covers housing (single hotel rooms), meals, and transportation to and from Moscow International Airport. We accept Visa and MasterCard, or a check made out in US$ and cashable within the United States. Upon payment of the workshop fee, participants will be given a US $400 purchase credit for EMP or an actual CD-ROM copy, if there is enough time before the meeting. EMP will soon be generally available for $400 ($4000 for commercial licenses). Registration after the deadline is possible if you pay extra $100 and if there is enough time. Participants need at least tourist visas, which are issued by the nearest Russian consulate, and for which no invitation is needed. To cover your expenses however, your institution may require a business visa, which does require an invitation from the hosts; in that case, please register as soon as possible. Please fill out the fields below; leave blank the fields that do not apply. Your citizenship, date of birth and passport number is needed only if you apply for a business visa. Please send this information, so that we receive it before May 12, by regular mail, fax, or electronic mail, to: Center for Professional Development Business Office, Mail Stop 3G3 George Mason University Fairfax, VA 22030-4444 Fax: 703-993-2112 Electronic mail: overbeek@juju.mcs.anl.gov Questions can be directed to either Ross Overbeek (overbeek@mcs.anl.gov) or Mary Baroody at George Mason University (703-993-2090). ------------------------------------------------------------------- First name: Last name: Research area: Date of birth: Passport number: Citizenship: Tourist visa: Business visa: Institution: Company: Street address: Postal code: City: State: Country: Telephone: Electronic mail: I pay by check: Visa Card #: MasterCard #: Expiration date: Comments: Comments: Comments: Questions: Questions: Questions: ------------------------------------------------------------------- From owner-acedb@net.bio.net Thu Apr 14 23:00:00 1994 Path: biosci!agate!alfa.berkeley.edu!bks From: bks@alfa.berkeley.edu (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: WWW94 Biology Workshop Date: 15 Apr 1994 23:39:05 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 20 Message-ID: <2on8ip$34k@agate.berkeley.edu> NNTP-Posting-Host: alfa.berkeley.edu If any of the ACEDB extended family are planning on attending WWW94 please drop me a note. Perhaps there is some synergy to be found. I am helping organize the biology workshop. For information about the workshop visit any of: http://beta.embnet.unibas.ch/conference/welcome.html http://www.dl.ac.uk/CBMT/www94.html http://s27w007.pswfs.gov/WWW94bio/index.html For information about the conference: http://www.cern.ch/WWW94/Welcome.html --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 Fri Apr 15 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: add telephone & fax numbers to FAQ? Followup-To: bionet.software.acedb Date: 15 Apr 1994 19:17:50 GMT Organization: Lawrence Berkeley Laboratory Lines: 17 Message-ID: NNTP-Posting-Host: slavsing.lbl.gov The ACEDB FAQ item Q4 is currently the most definitive and helpful list of what ACEDB databases exist and who is responsible for them. I think it might be even more useful if curators were willing to add their telephone and fax numbers. Phone: Fax: -John -- +=====================================================================+ | 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 Sun Apr 17 23:00:00 1994 Path: biosci!mcs.anl.gov!maltsev From: maltsev@mcs.anl.gov (Natalie Maltsev) Newsgroups: bionet.software.acedb Subject: a workshop announcement Date: 18 Apr 1994 12:45:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 161 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199404181843.NAA26038@juju> NNTP-Posting-Host: net.bio.net ------------------------------------------------------------------- Dear reader: Please bring this notice to the attention of persons you think might wish to participate. Workshop on Biological Database Integration June 8 - June 10, 1994 Pushchino, Russia (Registration deadline May 12) We invite all interested researchers to visit this major center of biomedical research in Russia and the former Soviet Union. The workshop will give you the opportunity to informally discuss how to integrate databases relevant to molecular biology and medicine. Several leading biological database experts from outside Russia will be present, and many interesting (and probably unfamiliar) Russian database projects will be demonstrated by their representatives. The workshop will be hosted by Professor Evgeni E. Selkov and coworkers, and is arranged in part by Dr. Ross Overbeek et al. at Argonne National Laboratory, Illinois, U.S.A. We have scheduled the following events: o Overview of EMP (Enzymes and Metabolic Pathways database). EMP contains the encoding of the most important articles (approx. 10,000) describing enzymes, phylogenetically arranged. It also contains in graphical form most of the known metabolic pathways for all organisms. We consider EMP the world's leading database of its kind. All participants will receive a free academic copy of this database (see details below). o For the first time, a presentation of a broad selection of Russian / FSU databases. There will be poster sessions and demonstrations on PC computers. During this winter we have collected brief descriptions and invited representatives from the groups who created (in our judgment) the most interesting of these. In Russia there exist substantial data collections ranging from minor ones done by single experts to very large collections of for example medicinal properties of compounds, 3D structural data, sequence data, culture collections, genetic markers, tumor characteristics, regulatory sequences, and more. o Optional introductory course to general metabolism and related computational issues. This will be given prior to the workshop (June 5-7) by Professor Selkov. There will be no scheduled talks. We instead invite open discussion of topics of common interest, such as metabolism and enzymes, or phylogeny, alignments, compounds, motifs, and maps. If you wish to use or generate such integrated biological data, then please join us. Sincerely, Evgeni Selkov Ross Overbeek Natalia Maltsev Amos Bairoch Nat Goodman George Michaels Harold Morowitz Niels Larsen Anthony Bonner Terry Gaasterland Pat Gillevet Rick Stevens Alexander Zamyatnin Sponsorship ----------- The workshop is so far unsponsored, but we welcome interested sponsors. We need help with computer equipment and coverage of travel expenses for Russian participants. Practical details ----------------- Pushchino is a community of some 30,000 people located 100 km south of Moscow. The main acitivity is research. The area is generally safe. The water is not contaminated; the food is fresh and locally produced. You will be able at least to send electronic mail. The registration fee is US $750 for the workshop if you plan to attend the introductory course, $550 otherwise. The fee covers housing (single hotel rooms), meals, and transportation to and from Moscow International Airport. We accept Visa and MasterCard, or a check made out in US$ and cashable within the United States. Upon payment of the workshop fee, participants will be given a US $400 purchase credit for EMP or an actual CD-ROM copy, if there is enough time before the meeting. EMP will soon be generally available for $400 ($4000 for commercial licenses). Registration after the deadline is possible if you pay extra $100 and if there is enough time. Participants need at least tourist visas, which are issued by the nearest Russian consulate, and for which no invitation is needed. To cover your expenses however, your institution may require a business visa, which does require an invitation from the hosts; in that case, please register as soon as possible. Please fill out the fields below; leave blank the fields that do not apply. Your citizenship, date of birth and passport number is needed only if you apply for a business visa. Please send this information, so that we receive it before May 12, by regular mail, fax, or electronic mail, to: Center for Professional Development Business Office, Mail Stop 3G3 George Mason University Fairfax, VA 22030-4444 Fax: 703-993-2112 Electronic mail: overbeek@juju.mcs.anl.gov Questions can be directed to either Ross Overbeek (overbeek@mcs.anl.gov) or Mary Baroody at George Mason University (703-993-2090). ------------------------------------------------------------------- First name: Last name: Research area: Date of birth: Passport number: Citizenship: Tourist visa: Business visa: Institution: Company: Street address: Postal code: City: State: Country: Telephone: Electronic mail: I pay by check: Visa Card #: MasterCard #: Expiration date: Comments: Comments: Comments: Questions: Questions: Questions: ------------------------------------------------------------------- From owner-acedb@net.bio.net Sun Apr 17 23:00:00 1994 Path: biosci!UX5.LBL.GOV!suzi From: suzi@UX5.LBL.GOV (Suzanna Lewis) Newsgroups: bionet.software.acedb Subject: logfile Date: 18 Apr 1994 14:44:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199404182144.OAA27586@ux5.lbl.gov> NNTP-Posting-Host: net.bio.net Hi Jean, I had a wee problem running a script transparently. By transparently, I mean running it as a cron job in the night. Its one of those things where 2 compounded errors ruins everything. Somehow someone had left the privileges for "logfile" set without group write access (mistake 1). But deep inside messubs there lurks a rather rude and abrupt messcrash. If logfile can't be opened for append or write the entire program dies. This seems rather extreme, especially if its another piece of code on the other end. It's left without a clue that its partner has just met sudden death. I would propose that ace begin an alternative logfile or simply note the fact that it couldn't write to the log (something a bit more resilient). I'd change it, but need to know your philosophy on this first. Suz. From owner-acedb@net.bio.net Mon Apr 18 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: parttionned database Date: 19 Apr 1994 12:50:30 +0100 Lines: 46 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2p0gi6$898@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk We are finishing, with the help of Perre Simondon, a redefinition of the disk handling in acedb this is the first running specification it is called wspec/database.wrm It will in june include raw partion access, with the hope of accelerating the database and correctly handling the large sets needed by the IGD project. In abstentia, the system defaults as usual. *********************** // // initial database structure. // // This file describe the database structure : // - number of partitions // - location, name and maximum size of each partition. // This file must be edited before database creation. It can be modified // for partition incrementation only. // Current version supports only database extension by adding new partitions. // Each line begin with a keyword, a separator ":" . all other informations // on the line in interpreted according to the keyword. // Current Keywords : PART // // note : // - lines beginning by // are comments // - a line don't exeed 512 characters. // // partition definition : // partition types : // UNIX_FILE_SYSTEM = 1 // RAW_FILE_SYSTEM = 2 // hostname : // partition_name : full path or "ACEDB" if relative to ACEDB variable. // file_name : only for unix file system : name of the partition file. // for other types, "NONE" // //Keyword : type hostname partition_name file_name max_size offset PART : 1 local ACEDB database/block1.wrm 5000 0 PART : 1 local ACEDB database/block2.wrm 5000 0 PART : 1 local ACEDB database/block3.wrm 5000 0 PART : 1 local ACEDB database/block4.wrm 5000 0 PART : 1 local ACEDB database/block5.wrm 5000 0 From owner-acedb@net.bio.net Mon Apr 18 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: tace Date: 19 Apr 1994 16:03:13 +0100 Lines: 28 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2p0rrh$lo0@mserv1.dl.ac.uk> Original-To: net@dl.ac.uk Otto says: i use tace for the following way in csh scripts: setenv ACEDB xxx; tace << END y ## parse in.ace find View write out.ace q END - it works obviously for both uninitialized and initialized databases then he adds: I would like to have the following features: (1) destroy all objects in current keyset : like with xace from keyset menu (2) soft parse option : when you don't parse one obj because of constraints then continue parsing the rest of input so i did just that public code soon prerelease on request From owner-acedb@net.bio.net Mon Apr 18 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: logfile diversion Date: 19 Apr 1994 18:28:30 +0100 Lines: 19 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2p14bu$19p@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Following Suzanna's letter, and a brief exchange with Jean, I have changed messubs.c so that if messdump() can not open the requested logfile then it writes to stderr, starting with a message of complaint about failing to open the file. Here is the diff to my previous version of messubs.c: 164,169c164,166 < { dumpfil = stderr ; < fprintf (stderr, "\n** Can't open log file %s - using stderr **\n", < messdumpfilename) ; < } < else < fprintf (dumpfil,"\n%s %s\n", timeStamp(), dateStamp()) ; --- > messcrash ("Can't open dump file %s", messdumpfilename) ; > > fprintf (dumpfil,"\n%s %s\n", timeStamp(), dateStamp()) ; Richard From owner-acedb@net.bio.net Wed Apr 20 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: ace3 Date: 21 Apr 1994 21:10:02 +0100 Lines: 17 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2p6miq$c73@mserv1.dl.ac.uk> Original-To: scartinh@vector.nalusda.gov there should be advantages over 100megs to spread you will then spread preferably over various disks btu also very soon we will handle raw partitions that should be quite fater than unix file systems and meory mapped disks all this is {POSIX compliant. It will particularly enhance th e throughput of acedb for large data servers contemplated for igd we will have raw partitions running before the ace meeting of july and will discuss them then Context: this is a reply to Sam we now have a running multi disk access in ace From owner-acedb@net.bio.net Wed Apr 20 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!gatech!swrinde!sdd.hp.com!nigel.msen.com!zib-berlin.de!news.belwue.de!news.dfn.de!scsing.switch.ch!urz.unibas.ch!bioftp.unibas.ch!genome.vjf.inserm.fr!genome!dessen Newsgroups: bionet.software.acedb Subject: q Message-ID: <2p64b8$ben@genome.vjf.inserm.fr> From: dessen@genome.vjf.inserm.fr (Philippe Dessen) Date: 21 Apr 1994 14:58:48 GMT Organization: Noeud Francais EMBnet NNTP-Posting-Host: genome.vjf.inserm.fr X-Newsreader: TIN [version 1.2 PL2] Lines: 10 -- Philippe Dessen Service de Bioinformatique CNRS INSERM 7 rue Guy Moquet BP8 94801 VILLEJUIF Cedex France e-mail : dessen@genome.vjf.inserm.fr From owner-acedb@net.bio.net Wed Apr 20 23:00:00 1994 Path: biosci!sanger.ac.uk!fw From: fw@sanger.ac.uk Newsgroups: bionet.software.acedb Subject: release V2.0 of IMAGE fingerprint analysis Date: 21 Apr 1994 03:45:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404211044.AA27352@sanger.ac.uk> NNTP-Posting-Host: net.bio.net Image is an integrated program for image analysis of physical mapping fingerprint gels. This runs on Unix workstations using X11 for display. It analyses scanned fingerprint gels, finding lanes, extracting bands from lanes, and correcting for gel distortion by aligning known standard marker lanes. At each stage there are hand editing tools for correcting errors. The output format can be read by the Contig9 fingerprint assembly routines being integrated into ACEDB. The version 2.0 of IMAGE is now available. Every function has been revised and if possible improved, such as the user interface, handling of defaults, image zooming, load/save of various image formats. It also comes with a complete Unix man-page. The package is available by anonymous ftp from rona.sanger.ac.uk (193.60.84.39), in directory /pub/image. Read the files README in /pub/image and the README's in the untarred archive for further information. There are also binaries for these systems - sgi-irix, sun-sparc, solaris, alpha-osf When you get this email you're in my mailing list for image-users. Mail me if other people want to be informed about updates or if you want to be removed from the list. Friedemann Wobus (fw@sanger.ac.uk) From owner-acedb@net.bio.net Thu Apr 21 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: parttionned database Date: 22 Apr 1994 16:43:40 GMT Organization: University of California, Berkeley Lines: 30 Message-ID: References: <2p0gi6$898@mserv1.dl.ac.uk> NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: mieg@kaa.crbm.cnrs-mop.fr's message of 19 Apr 1994 12:50:30 +0100 Sorry, but you're trying to beat the system programmers at their own job and it's not going to work. The overhead the system has in vnodes is more than offset by efficiencies in caching and device management. The raw disk system will be slower than Ace is now with a single reader, and much slower with multiple readers (as they page out each other's read buffers, because the pages have been dirtied with the data read from disk). There are certain gains you could make in writes, but mostly the database just reads. It would be much better to do Read In Place(RIP?), where the database file is mmap()ed in, object references are given as offsets from the base of the file and the data is referenced in place. The system manages your buffer, and it's exactly as big as it can afford, plus all of the readers share the same buffer and normally don't need to duplicate the data in the database into their private pools, as they can refer to it directly. The effect is that zero copies in memory are made, as you're drinking from the system's own buffers and it can simply drop your pages at will, because you haven't changed what it's read. -- Henry J. Cobb hcobb@fly2.berkeley.edu, SFB Tyrant-for-life "Battleships cannot be used as escorts" -SVC (quite a shock for the crew of the Iowa, I'd wager) From owner-acedb@net.bio.net Mon Apr 25 23:00:00 1994 Path: biosci!agate!agate!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: ScriptAce = Ace + Tcl Date: 26 Apr 1994 17:06:01 GMT Organization: University of California, Berkeley Lines: 1512 Message-ID: NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: hcobb@fly2.berkeley.edu's message of 22 Apr 1994 16:43:40 GMT Scriptace was spawned by my difficulties of getting the AceServer to run automatically from a script, and catch every error. As I realized that AceServer was already taking its inputs from and putting its outputs through a narrow pipe, I decided that I would work from this form of Ace. I yanked out the RPC "stimulus-response" mechanism and replaced it with Tcl "thunks". The program still acts as a server, but now it's client is a single Tcl script. Instead of runing through XDR, the strings are simply converted from Ace to Tcl forms (and vice-versa), etc. The remaining problem was that AceServer (and therefore Scriptace) was throwing any errors encountered deep in the processing of a request to stderr (via messout and friends). So the program was registering errors, at a deep level and making complaints, without realizing that it was doing so. (Kind of like electronic Tourette's syndrome) But with Mieg's help, we established a buffer that messout will use, if present, and when the program finds this buffer filled after processing a command, it throws a Tcl error exception. (Study the test.spa script to see how this can be used). One last thing, if ScriptAce is invoked with no parameters, it first "sources" your ~/.acerc file and then enters into an interactive mode. \\\\\\\\\\\\\\\\\\\\Next section from help.wrm\\\\\\\\\\\\\\\\\\\\ ################################################################### **Scriptace Scriptace is the form of Acedb that runs Tcl scripts. This provides a directly scriptable version of Ace for automatic data management or reports. This program is invoked as `scriptace scriptfile`, where scriptfile is a file of Tcl commands. The program registers the single "object-oriented" command "acedb" with the interpreter before parsing the scriptfile. This command takes all of its parameters and hands them back over to Ace to treat in the same manner as Tacedb commands. (Essentially the interpreter is given a single "acedb" database object as part of its environment, see Chapter 28 of Dr Ousterhout's book). In addition to the normal commands of Tacedb (each invoked as: acedb command args), Scriptace has a few new features to take advantage of the embedded interpreter. acedb parse -v TclVar Parses a TclVar, like it was a file. acedb write -v TclVar Acedumps current keyset to TclVar, like it was a file. acedb table -l tablefile With the '-l' parameter, makes the table from the current keyset. acedb getkey TclVar Returns the next element of the current keyset in TclVar (In an Ace-dump format), starting from the first element. Returns '1' if there was an element or '0' if there was no element left in the keyset. acedb reset Restarts a getkey walk through the current keyset. Changing the current keyset will also do this, and `acedb undo` will not recover the lost position acedb_ketsize This Tcl variable tracks the current size of the current keyset, or zero when it's not valid. This variable has the relationship to `acedb getkey` as the total number of valid entries that will be returned in total by that call, but not the number of iterations remaining. Any errors encountered in the processing of a command will cause the `acedb` function to throw an error exception. Tcl's catch command can be used to retrieve the error message. The intent being that usually, most errors will leave the database in a state such that the operation can be restarted. (Perhaps with an `acedb undo` after the catch.) In addition, for various reasons, the Acedb side of the program can crash, with or without any warning. (I sure hope that none of this is ever used in a "life critical" installation...) [From the Tcl FAQ by Larry W. Virden (lwv26@cas.org ) ftp://harbor.ecn.purdue.edu/pub/tcl/docs/tcl-faq.part*] Tcl and Tk originated with Dr. John Ousterhout (Oh'-stir-hout - last syllable rhymes with rout, not root) from the University of California, Berkeley, California. Tcl (current release version 7.3) stands for ``tool command language'' and is pronounced ``tickle.'' The author's home ftp site for the Tcl source code is ftp.cs.berkeley.edu. Tcl is actually two things: a language and a library. First, Tcl is a simple textual language, intended primarily for issuing commands to interactive programs such as text editors, debuggers, illustrators, and shells. It has a simple syntax and is also programmable, so Tcl users can write command procedures to provide more powerful commands than those in the built-in set. Second, Tcl is a library package that can be embedded in application programs. The Tcl library consists of a parser for the Tcl language, routines to implement the Tcl built-in commands, and procedures that allow each application to extend Tcl with additional commands specific to that application. The application program generates Tcl commands and passes them to the Tcl parser for execution. Commands may be generated by reading characters from an input source, or by associating command strings with elements of the application's user interface, such as menu entries, buttons, or keystrokes. When the Tcl library receives commands it parses them into component fields and executes built-in commands directly. For commands implemented by the application, Tcl calls back to the application to execute the commands. In many cases commands will invoke recursive invocations of the Tcl interpreter by passing in additional strings to execute (procedures, looping commands, and conditional commands all work in this way). ###################################################################### **Tacedb ************************************************************** **** acedb: A C. elegans Database **** **** Richard Durbin (MRC, UK) rd@mrc-lmba.cam.ac.uk **** **** Jean Thierry-Mieg (CNRS, France) mieg@kaa.cnrs-mop.fr**** ************************************************************** This help page provides basic information for the line oriented version of the acedb program. Note that both Aceserver and Scriptace embed these commands into their environments. These programs have a single KeySet with a single-step undo buffer (i.e.: undo twice, and you'll have nothing). Queries return their results as the current keyset and most commands work only on this subset of the items in the database. The following commands may be recognized. Quit : Exits the program. Help : for further help. ? : List of commands. Classes : Give a list of all the visible class names and how many objects they each contain. Find class [name]: Creates a new current list with all objects from class, optionally matching name. Model class: Shows the model of the given class, useful before Follow or Where commands. Grep template: Generates a list from a search for *template* everywhere in the database, except longtexts. LongTextGrep template: searches for *template*, everywhere, including longtexts. Undo : returns the current list to its previous state. List [template]: lists names of items in current list [matching template]. Show [tag] : shows the [branch tag of] objects of current list. Is template : keeps in the active list only those objects whose name match the template. Remove template : removes from the active list only those objects whose name match the template. Follow Tag : Replaces all elements in the current list with the elements referenced by Tag. i.e. Tag Author replaces the current list of papers with their authors. (Note that this is setwise replacement so that a list of two papers Paper_A by Bob and Harry and Paper_B by Harry and Smith would result in a list of three elements: Bob, Harry and Smith). (Note also the the Keyset previous to this command is kept in the undo buffer, and so if you are careful, you can take this stuff, do a few things, and then step back.) Where query_string : Trims the current list to the set of only those members that match the query_string (see: Query_syntax). Write filename : acedump current list to file. Biblio : shows the associated bibliography of the items in the current Keyset. Dna filename : Fasta dump of related sequences to filename. Array class:name format : formatted acedump of A class object. Parse [aceFile] : parses an aceFile, or stdin,