From owner-acedb@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: ACEDB vs. RDBMS Date: 2 Apr 1997 09:28:54 +0100 Lines: 97 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5ht5c6$2n6@mserv1.dl.ac.uk> Original-To: fvevert@soils.umn.edu Obviously, i have a biased opinion, but i would say that acedb is to be recommended if the following criteria are met: 1) A very complex schema, that cannot be developped at once, but will need continuous refinement in parallel with the accumulation of the data 2) The type of questions that will be asked are rather complex, with rather fuzy answers, that one tries to refine progressivelly. The acedb browsing capacities are useful in this case and have no equivalent in a relational dbms ______________ I would rather recommand sysbase in the following case 1) Simple schema, that can be designed from the start and does not contain too many n.n relations and does not need recursivity 2) The type of questions that will be asked is: succession of decorelated simple questions with simple answers ____________________ Within this context, i would then list the following goodies of acedb: 1) The ace file format, which is a powerful system to prepare and exchange data between data curators. 2) The existence of an easy graphic browsing interface 3) The availibility of a biology-layer, if the application is about genetics 4) Portability (any unix machine), mac (with some limitations), windows in development) and price (ace is a freeware). This implies that you can actually redistribute the complete system, say on a CD, something impossible with sysbase. 5) Ease of use, i seriously believe that ace is much easier to configurate and use than sybase. _____________________ _____________________ Finally one should consider the following question: concurency. Sybase has a well designed transation system, which will allow roll backs and refined lockings. This is essential for an application like a booking agency, with many users in simultaneous write access. Ace is much simpler minded. The graphic acedb creates a global lock allowing a single user with write access at the time, and the modifs are not echoed to the other "read access" users in real time. The non graphic client server system allows parallel downloading of data by many users, it is intended for example for collection of robots sending their independant data in parallel. This is now well tested. A graphic client system is beeing developped and now runs in our hands, but is not yet released. -- Therefore, if you do need real time simultaneous write access with partial locks, and roll backs, use sybase/oracle ________________ Last issue is speed and quantities of data. In principle, sybase/oracle is unlimited, whereas acedb needs to keep around 5-10% of the data in ram. But this apparent difference is misleading. On a 32 Meg machine, you can run ace with around 300.000 objects with a complex schema at high speed. With say 1M objects, you will need more memory or the performance would totally degrade because of swapping. However, this is really a lot of data. On a similar machine, your sybase oracle will work with that amount or more data only if you do not perform too many joints. This implies that you are asking simple questions from a simple schema which was indeed our first criterion to choose sybase. If you start asking complex questions and make joins, acedb is actually much more powerful. During tests ran on a big dec alpha server by Otto Ritter in decembre 1995 on several million biological objects with a complex schema, acedb was about 10 times faster than sysbase, both to load the data and to answer queries. I would therefore conclude that the quantity of data is not a criterion pushing one way or the other, it is the complexity of the schema that matters. Jean Thierry-Mieg From owner-acedb@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!is.bbsrc.ac.uk!news From: Matt Couchman Newsgroups: bionet.software.acedb Subject: Passing external parameters to TableMaker Date: Wed, 02 Apr 1997 16:10:10 +0100 Organization: The John Innes Centre Lines: 17 Message-ID: <334276D2.41C6@bbsrc.ac.uk> NNTP-Posting-Host: jiio5.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V3.2 alpha) Hello, I've got a couple of queries regarding the new "Parameters" field in TableMaker... 1. From the way the relative documents are written I get the impression that it is possible to specify more than one parameter. How do you do this? Is it a comma/semi-colon delimited list or something? Or is it not possible after all? 2. There seems to be a problem specifying a parameter with white space in it (even when it is in quotes). TableMaker always returns 0 objects that match a parameter with white space. Thanks very much for any help, Matt. From owner-acedb@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: Passing external parameters to TableMaker Date: 2 Apr 1997 19:08:06 +0100 Lines: 80 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5hu7a6$r1n@mserv1.dl.ac.uk> Original-To: Matthew.Couchman@bbsrc.ac.uk multiple parameters are just several words on the same line i beleive you can "" the parameters, can you give me a table example, i ll try but may be you must escape the " on top of that something absurd like: acedb> table -n mytable parm1 \"parm two\" this is all due to the crazy empilement of shells but i beleive it does work in some way ok i have it: acedb> find table t1 // Found 1 objects in this class // 1 Active Objects acedb> show -a Table : "t1" Sortcolumn 1 Parameters "toto" Colonne 1 From 1 Colonne 1 Visible Colonne 1 Width 12 Colonne 1 Optional Colonne 1 Condition "IS \%1" Colonne 1 A_Class "Author" // 1 object dumped // 1 Active Objects acedb> table -n t1 "\\\"a b\\\"" "a b" //# 1 lines in this table // 1 Active Objects acedb> find author // Found 2 objects in this class // 2 Active Objects acedb> list KeySet : Answer_1 Author: a b tyty // 2 object listed // 2 Active Objects acedb> list -a KeySet : Answer_1 Author : "a b" Author : "tyty" // 2 object listed // 2 Active Objects acedb> note also that with query, you should be more pedantic acedb> find author a b // Found 1 objects in this class // 1 Active Objects acedb> query find author "a b" // Found 1 objects // 1 Active Objects acedb> find author "a b" // Found 1 objects in this class // 1 Active Objects acedb> query find author a b // Found 0 objects // 0 Active Objects From owner-acedb@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: schasa@scri.sari.ac.uk (Scott Chasalow) Newsgroups: bionet.software.acedb Subject: acedb HP binary? Date: 4 Apr 1997 11:50:32 +0100 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5i2mdo$h6t@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Hi, Can somebody please tell me if there is an acedb binary available for HP UX-10? If so, how might I get my paws on it? Thanks, Scott ---------------------------------- Scott.Chasalow@users.pv.wau.nl Department of Plant Breeding Wageningen Agricultural University PO Box 386 6700 AJ Wageningen The Netherlands ---------------------------------- From owner-acedb@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: HP Date: 4 Apr 1997 15:34:46 +0100 Lines: 1 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5i33i6$777@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk yap, acedb works fine on HP, just recompile From owner-acedb@net.bio.net Mon Apr 14 23:00:00 1997 Path: biosci!daresbury!uninett.no!news.algonet.se!news-feed.inet.tele.dk!news.he.net!supernews.com!newsfeed.direct.ca!news.uoregon.edu!news.emf.net!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Curator) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 15 Apr 1997 14:59:27 GMT Organization: Dept. Plant Breeding, Cornell University Lines: 1291 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <5j054f$dks@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 genome database software ACEDB. Xref: biosci bionet.software.acedb:1173 news.answers:92889 URL: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html Archive-name: acedb-faq Last-modified: 15 Apr 97 Version: 1.36 ---------------------------------------------------------------------------- ACEDB FAQ ---------------------------------------------------------------------------- Curated by: Dave Matthews ---------------------------------------------------------------------------- Frequently Asked Questions 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 : + How does ACEDB compare to commercial relational DBMS's? * Q5 : Is ACEDB object-oriented? * Q6 : What documentation exists for ACEDB? * Q7 : What other resources are available for ACEDB? * Q8 : How should ACEDB be cited? * Q9 : How does one get on/off the ACEDB announcements mailing list? * Q10 : When and where is the next ACEDB Workshop? * Q11 : What ACEDB databases exist? * Q12 : 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 [Q11 gives contact information]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions ---------------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: (This answer refers to the software, not the C. elegans data.) Current Unix version is 4_3 (as of May 1996) and is identical to the test version test.4_3i. A Macintosh version is available as version 4.1b1. A Windows 95/NT version is available as version beta960927. To retrieve the software see Q3. To be kept informed of new releases see Q9. Return to List of Questions ---------------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. * Unix: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series 4, 5, 6 o IBM RS-6000 o PC 386/486/Pentium with Linux o NEC EWS4800 o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o There exist, or have existed, ports onto Alliant, Hewlett- Packard, Convex. You may have to contact the developer responsible for the port to make these real. * Windows 95/NT * Macintosh (not currently supported) Return to List of Questions ---------------------------------------------------------------------------- Q3: Where can I get ACEDB? A3: Source code and Unix binaries are available in the following anonymous ftp sites: * lirmm.lirmm.fr in pub/acedb * ftp.sanger.ac.uk in pub/acedb * ncbi.nlm.nih.gov in repository/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb Linux binaries in ELF and a.out format, from Jeff Bryer: * ncbi.nlm.nih.gov in repository/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb NEC EWS4800 binaries: * http://www.labs.nec.co.jp/freesoft/freesofte.html Windows 95/NT 3.51, from Richard Bruskiewich: * ftp.sanger.ac.uk in pub/winace * bioinformatics.weizmann.ac.il in pub/databases/acedb MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin: (Note: The authors are not currently able to support MacAce. Latest version was 4.1b1.) * genome.lbl.gov in pub/macace * ncbi.nlm.nih.gov in repository/acedb/macace * bioinformatics.weizmann.ac.il in pub/databases/acedb Return to List of Questions ---------------------------------------------------------------------------- NEW! Q4: How does ACEDB compare to commercial relational DBMS's? A4: From Jean Thierry-Mieg, 4/97: Obviously, i have a biased opinion, but i would say that acedb is to be recommended if the following criteria are met: 1) A very complex schema, that cannot be developed at once, but will need continuous refinement in parallel with the accumulation of the data 2) The type of questions that will be asked are rather complex, with rather fuzzy answers, that one tries to refine progressively. The acedb browsing capacities are useful in this case and have no equivalent in a relational dbms ______________ I would rather recommend sybase in the following case 1) Simple schema, that can be designed from the start and does not contain too many n.n relations and does not need recursivity 2) The type of questions that will be asked is: succession of de-correlated simple questions with simple answers ____________________ Within this context, i would then list the following goodies of acedb: 1) The ace file format, which is a powerful system to prepare and exchange data between data curators. 2) The existence of an easy graphic browsing interface 3) The availability of a biology-layer, if the application is about genetics 4) Portability (any unix machine), mac (with some limitations), windows (in development) and price (ace is a freeware). This implies that you can actually redistribute the complete system, say on a CD, something impossible with sybase. 5) Ease of use, i seriously believe that ace is much easier to configure and use than sybase. _____________________ Finally one should consider the following question: concurrency. Sybase has a well designed transaction system, which will allow roll backs and refined lockings. This is essential for an application like a booking agency, with many users in simultaneous write access. Ace is much simpler minded. The graphic acedb creates a global lock allowing a single user with write access at the time, and the modifications are not echoed to the other "read access" users in real time. The non graphic client server system allows parallel downloading of data by many users, it is intended for example for collection of robots sending their independent data in parallel. This is now well tested. A graphic client system is being developed and now runs in our hands, but is not yet released. -- Therefore, if you do need real time simultaneous write access with partial locks, and roll backs, use sybase/oracle ________________ Last issue is speed and quantities of data. In principle, sybase/oracle is unlimited, whereas acedb needs to keep around 5-10% of the data in ram. But this apparent difference is misleading. On a 32 Meg machine, you can run ace with around 300.000 objects with a complex schema at high speed. With say 1M objects, you will need more memory or the performance would totally degrade because of swapping. However, this is really a lot of data. On a similar machine, your sybase oracle will work with that amount or more data only if you do not perform too many joins. This implies that you are asking simple questions from a simple schema which was indeed our first criterion to choose sybase. If you start asking complex questions and make joins, acedb is actually much more powerful. During tests run on a big dec alpha server by Otto Ritter in decembre 1995 on several million biological objects with a complex schema, acedb was about 10 times faster than sybase, both to load the data and to answer queries. I would therefore conclude that the quantity of data is not a criterion pushing one way or the other, it is the complexity of the schema that matters. Return to List of Questions ---------------------------------------------------------------------------- Q5: Is ACEDB object-oriented? A5: From the ACEDB User's Guide: A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions ---------------------------------------------------------------------------- Q6: What documentation exists for ACEDB? A6: 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 in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z. The files are in TeX (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. ACEDB User's Guide in Japanese, from Tohru Sano, NEC, sano@exp.cl.nec.co.jp http://www.cbi.or.jp/~sano/ . (Postscript at http://www.labs.nec.co.jp/ . Follow the prompts to register and "download the software".) SampleDB, by Dave Matthews, is an ACEDB database constructed to demonstrate features of ACEDB, especially map and sequence displays. Anonymous ftp to probe.nalusda.gov:pub/acedocs/sampledb You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angistute.ps and angistute.hqx available by anonymous ftp at ncbi.nih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). URL : http://genome-www.stanford.edu/docs/aatdb_man.html. A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. URL : http://probe.nalusda.gov:8000/acedocs/overview.html. Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. Return to List of Questions ---------------------------------------------------------------------------- Q7: What other resources are available for ACEDB? A7: Perl and WWW tools The AGIS server at the National Agricultural Library provides tools for integrating version ACEDB with perl and the World-Wide Web. A WWW interface to 4.3 is available as ftp://probe.nal.usda.gov/pub/tools/webace.tar.gz. Instructions for this interface can be found at http://probe.nal.usda.gov:8000/acedocs/webace.html. (An earlier tool set is available as ftp://probe.nalusda.gov/pub/tools/acelib.tar.gz). For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/. Java Interface A Java interface to acedb is under active development. Involved people are Lincoln Stein, Jean Thierry-Mieg, Doug Bigwood, John Barnett, Sam Cartinhour. A test system can be seen at http://alpha.crbm.cnrs-mop.fr If you are interested in this approach, please contact mieg@kaa.crbm.cnrs-mop.fr X-client The 4_3 distribution contains the source code for a new version of the code called xclient. You need to recompile it (make xclient). Then, you create an empty database with the nematode models and strat xclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the montpellier server in the distrib server.wrm). The data will be saved locally and can then be viewed with a normal xace. The control of which data should be imported is very crude. In anay session, every object will be imported once. This should be rationalised, please let us know if this approach seems useful, and how it should be configured. (mieg@kaa.crbm.cnrs-mop.fr) The Developers' Archive Mike Cherry maintains an archive of tools that may be useful in curating ACEDB databases via gopher at ftp://genome-ftp.stanford.edu/pub/acedb_dev/ If you have a contribution send a message to Mike (cherry@genome.stanford.edu). The Biosci conference bionet.software.acedb There is a USENET/Biosci conference titled bionet.software.acedb created expressly for discussion of ACEDB. The best way to interact with the Biosci conferences is via a newsreader like rn, trn, tin or a WWW browser. Consult your system administrator for more information. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. All of the articles in biosci.software.acedb are archived by Biosci at http://www.bio.net/archives.html and by Mike Cherry at http://genome-www.stanford.edu/cgi-bin/biosci_acedb. If your WWW browser is configured properly you may be able to read the newsgroup at news:biosci.software.acedb. And more The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q11] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: * http://moulon.inra.fr/acedb/acedb.html for C. elegans data * http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data * http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html A how-to manual on the Moulon server is available at http://keck.tamu.edu/cgi/staff/ace-mosaic-howto.html The Genome Computing Group, Lawrence Berkeley Laboratory, has an anonymous ftp service at machine genome.lbl.gov which contains: * flydb - LBL's Drosophila Acedb-style database * 21bdb - LBL's Human Chromosome 21 Acedb-style database * querdb - LBL's query-language extensions to Acedb * metadata - LBL's compendium of Acedb database schema variants * macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version * There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to databases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: * 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). * 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier (Jean Thierry-Mieg et al), and the Integrated Genome Database project in Heidelberg (Otto Ritter, Detlef Wolf et al). Return to List of Questions ---------------------------------------------------------------------------- Q8: How should ACEDB be cited? A8: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions ---------------------------------------------------------------------------- Q9: How can I get on/off the ACEDB announcements mailing list? A9: To get on or off the mailing list send mail to rd@sanger.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q7 for details] is on the mailing list. Return to List of Questions ---------------------------------------------------------------------------- Q10: When and where is the Next ACEDB Workshop? A10: The ACE97 Conference and Workshop will be held July 27 - August 9 in Ithaca, New York, USA. See the ACE97 Home Page for details. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/index.html. A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html. Also available online are collections of snapshots taken during the conference by Frank Eeckman and by Dave Matthews. For pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, see the online collections: * by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; * by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; * and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions ---------------------------------------------------------------------------- Q11: What ACEDB databases exist? A11: In alphabetic order by Database name [Curators, please submit changes as new paragraphs, preferably in html.] Database : AaeDB Species : Aedes aegypti (Mosquito) ACEDB_version : 3.0 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Last_update : December 1994 Database : AtDB Species : Arabidopsis thaliana ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4-7 PI : J. Michael Cherry Curator : David Flanders Contact : arab-curator@genome.stanford.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : genome-ftp.stanford.edu in arabidopsis/AtDB FTP : ncbi.nlm.nih.gov in repository/AtDB WWW : http://genome-www.stanford.edu Last_update : December 1996 Database : AboutDB Curator : Staffan Bergh, staffan@biochem.kth.se Subject : ACEDB itself (meta-meta-metadata) ACEDB_version: 3.0 WWW : http://www.biochem.kth.se/AboutDB.html Last_update : July 1995 Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@sanger.ac.uk Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ Last_update : August 1995 Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu ACeDB_version : 3.0 Subject: Contains extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe yeast); interacting loci via defined Interactions for each locus Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html FTP: ftp://keck.tamu.edu/pub/agsdb/agsdb1_0_acedb3_0_solaris2.3.tar.Z Last_update : March 1994 Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_Update : July 1995 Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 4.1 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : September 1995 Database : BrassicaDB Species : Brassica napus (Canola/Oilseed Rape) and its parental diploid species ACEDB_version : 4.3 Description : Genetic maps of Brassica napus, QTL analyses for agronomic traits, literature references and B. napus-specific DNA sequences will be incorporated. We aim to integrate with B. napus genetic maps developed elsewhere and to produce a Java interface that will link BrassicaDB with the AAtDB (Arabidopsis thaliana) database through gene orthologies that are becoming established between these closely related plant genomes. PI : Martin Trick, Martin.Trick@bbsrc.ac.uk Curator/Developer : Mazda Hewitt, Mazda.Hewitt@bbsrc.ac.uk WWW : http://nasc.nottm.ac.uk Last_update : Under development Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : August 1995 Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : September 1995 Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edubr> ACEDB_version : 3.0 Gopher : gopher://probe.nalusda.gov:7000/11/genome.databases/coolgenes/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : January 1996 Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 ACEDB_version : 3.0 Data_version : January 1995 (version 95.1) FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ Last_update : January 1995 Database: Cruzdb Species: Trypanosoma cruzi PI: Wim Degrave ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/cruzi/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Last_updated: In development Database : CSNDB Focus : Cell Signaling Networks Species : human Curator : Takako Igarashi, taka@nihs.go.jp Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Assistant_Curator : Masumi Yukawa, yukawa@nihs.go.jp Assistant_Curator : Shikiko Hasegawa, shasegaw@nihs.go.jp Contact : Takako Igarashi, taka@nihs.go.jp ACeDB_version : 4.1 Data : molecular data of signal molecules, molecular data of signal transductions, signal transduction pathways, domain structure and function of signal molecules, and three dimensional structures of signal molecules. Availability : CSNDB is on WWW. WWW-browser is required to attach molecular viewer RasMol (ftp: colonsay.dcs.ed.ac.uk ) for displaying three dimensional structure of protein. WWW : http://geo.nihs.go.jp/csndb.html Database : Cyanoace Species : Cyanobacterium synechocystis sp. strain PCC6803 Developer : Nobuyuki Miyajima, miyajima@kazusa.or.jp Comment : Converted to ACEDB from Sybase FTP : ftp://ftp.kazusa.or.jp/pub/acedb/cyanoace/ WWW : http://www.kazusa.or.jp/cyanobase/ Remark : WWW interface uses Java enhanced clickable maps. Last_update : December 1996 Database : EthnobotDB (worldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : June 1995 Database: FilDB Species: Filarial nematodes PI: Mark Blaxter ACEDB_version: 4.3 Curator: Martin Aslett Contact: Mark Blaxter, mark.blaxter@ed.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Brugia WWW: http://helios.bto.ed.ac.uk/mbx/fgn/filgen.html WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Last_updated: In development Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : May 1995 Database : GrainGenes Species : Wheat, barley, oats, sugarcane, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu Curator : Gerard R. Lazo, lazo@pw.usda.gov PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_3 (Unix), 4.1b1 (MacAce) Data_version : 1.7, December 1996 Availability : UNIX and Macintosh versions via anonymous ftp Availability : Macintosh version on CD-ROM "RiceMac / MacGrainGenes", from Dr. Baek Hie Nahm, Korea Rice Genome Research Program, Myongji University, Yongin, Korea. FTP : probe.nalusda.gov in pub/graingenes FTP : grain.jouy.inra.fr in pub/database Gopher : greengenes.cit.cornell.edu Gopher : grain.jouy.inra.fr Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://wheat.pw.usda.gov/ WWW : http://grain.jouy.inra.fr Last_update : December 1996 Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr WWW : http://moulon.inra.fr/acedb/igd.html Description : IGD (Integrated Genomic Database) aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : IXDB (Integrated X chromosome DataBase) Species: Homo sapiens Subject: Chromosome X Acedb_version : 4.1 Data: The YAC map constructed by the Max-Planck-Institut fuer Molekulare Genetik in Berlin, with all the attached experimental data necessary to reconstruct the map. Information on each of 9000 YAC clones mapped to the X chromosome, and constituting the YAC collection assembled with clone sets from 14 different laboratories worldwide. Latest_release:March 1996 Curator: Hugues Roest Crollius, roest@mpimg-berlin-dahlem.mpg.de Contact: Ulf Leser, leser@mpimg-berlin-dahlem.mpg.de PI: Hans Lehrach FTP: ftp.mpimg-berlin-dahlem.mpg.de in directory pub/lehrach/x-map WWW: http://www.mpimg-berlin-dahlem.mpg.de/~xteam Database: Leishdb Species: Leishmania major, L. infantum, L. peruviana, L. donovani and others PI: Jennie Blackwell PI: Al Ivens ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Leish WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/leish/leishpage.html (in development) Last_updated: October 1996 Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie-Paule Lefranc Contact : Veronique Giudicelli, LIGM IGMM UMR CNRS 9942, BP 5051 Rte de Mende, 34000 Montpellier, giudi@ligm.crbm.cnrs-mop.fr Database : MaizeDB Species : Zea mays L. ssp. mays and related species Content : Maps, raw map data, loci, probes, genetic stocks, variations, mutant images, agronomic traits, gene products, QTL, bibliography, colleague addresses; hardlinks to sequence and germplasm databases. Latest_release : Oct 1996 Acedb_version : 4.1 Curator : Mary Polacco, maryp@teosinte.agron.missouri PI : Ed Coe, Jr., ed@teosinte.agron.missouri.edu Systems : Denis Hancock, dhancock@teosinte.agron.missouri.edu FTP : probe.nalusda.gov/pub/maizedb/macedist961001.tar.gz WWW : http://www.agron.missouri.edu WEBACE : http://probe.nalusda.gov:8300/ Contact : db_request@teosinte.agron.missouri.edu Comment : Data are periodically extracted into ACEDB format from Sybase Comment : Genera software used to maintain the Sybase database and its gateways, except for ACEDB Comment : ACEDB releases are announced on the MAIZE bulletin board; http://www.bio.net/hypermail/MAIZE/ Comment : WEBACE records are hardlinked to the Sybase server where data are curated Funding : USDA ARS Plant Genome Research Program Last_update : Mar 7, 1997 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : July 1995 Database : Millet Genes Species : Pennisetum glaucum (Pearl Millet) ACEDB_version : 4.3 Curator : Matt Couchman, Matthew.Couchman@bbsrc.ac.uk PI : Katrien Devos, Katrien.Devos@bbsrc.ac.uk FTP: ftp://jiio5.jic.bbsrc.ac.uk/pub/millet WWW : http://nasc.nott.ac.uk:8400/db.html WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.shtml WWW : http://probe.nalusda.gov:8300/plant/ Last_update : March 1997 DataBase : Mousedb Species : Mus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD Last_update : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : June 1995 Database : MsqDB Species : Interspecies Mosquito database ACEDB_version : 4.1 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Contact : aaedbmgr@klab.agsci.colostate.edu Last_update : March 1996 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. Curator : Staffan Bergh, staffan@biochem.kth.se Curator : Stewart Cole, stcole@pasteur.fr ACEDB_version : 4.3 Data_version : 4-22 (December 1996) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ Last_update : December 1996 Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html Last_update : September 1995 Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurrence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : June 1995 Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 FTP : ftp.sanger.ac.uk in pub/PomBase Last_update : September 1995 Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : June 1995 Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susan McCouch ACEDB_version : 4.1 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : November 1996 Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4.6 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB WWW : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Curator : Yankai Jia, jia@genome.stanford.edu Programmer : Gail Juvik, gjuvik@genome.stanford.edu Programmer : Shuai Weng, shuai@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Last_update : September 1996 Database: SchistoDB Species: Schistosoma mansoni (plus other schistosomes) PI: David Johnston ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Schisto/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Last_update: In development Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu PI : Steve Tanksley Release : ACEDB 4.3 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : April 1996 Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : September 1995 Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker, rcsshoe@iastate.edu Curator : David Grant, dgrant@iastate.edu Assistant_curator : Marica Imsamde, mimsande@iastate.edu Contact : David Grant, dgrant@iastate.edu ACEDB-Version : 3.7 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://macgrant.agron.iastate.edu Last_update : October 1995 Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Last_update : October 1994 Database: ToxoDB Species: Toxoplasma gondii PI: David Sibley PI: David Roos PI: Jim Ajioka ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Toxo/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/toxo/toxpage.html Last_update: October 1996 Database : TreeGenes Species : Forest trees ACEDB_version : 4.3 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ Last_update : May 1996 Database: Trypbase Species: Trypanosoma brucei PI: Sara Melville ACEDB_version: 4.3 Curator: Howard Cobb Curator: Martin Aslett Contact: Sara Melville, sm160@mole.bio.cam.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/brucei WWW: http://parsun1.path.cam.ac.uk/newtryp/toppage.htm WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Last_updated: October 1996 Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Last_update : April 1994 Database : 11Db Species : Homo sapiens Subject : Physical and Genetic mapping of Human Chromosome 11 Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk) PI : Peter Little (p.little@bc.ic.ac.uk) ACEDB_version : based on 4_1 with added map displays. ACEDB_version : based on 3_6 with added map displays. Data version : 1.0 Last Update : December 1995 WWW : http://chr11.bc.ic.ac.uk FTP : ftp.cc.ic.ac.uk Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Database : 22ace Species : Homo sapiens Subject : Physical map of human chromosome 22, genomic sequencing and more ACEDB_version : 4.1 Curator : Ian Dunham, id1@sanger.ac.uk Curator : Gareth Maslen, glm@sanger.ac.uk PI : Ian Dunham FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ Last_update : August 1995 Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions ---------------------------------------------------------------------------- Q12:Who prepared this document & where is the current version? A12: 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 WWW version of this document is at: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html A text version is available via anonymous ftp at machine rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. 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 This FAQ was created and maintained from 1993 - 1996 by Bradley K. Sherman. Major contributions in getting it off the ground were made by Mike Cherry, John McCarthy, and Doug Bigwood. Other contributors include: * Lisa Lorenzen * David Matthews * Edie Paul * Donn Davy * Eric De Mund * Sam Cartinhour It is currently maintained by Dave Matthews. Please cite as: Matthews, D.E., and B.K. Sherman, ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993-1996, approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov The GrainGenes Project is funded by the USDA ARS Plant Genome Research Program. Return to List of Questions ---------------------------------------------------------------------------- From owner-acedb@net.bio.net Mon Apr 14 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!fido.news.demon.net!demon!newsgate.unisource.nl!surfnet.nl!news.tue.nl!usenet From: j.w.j.gijsen@stud.tue.nl (Gijsen) Newsgroups: bionet.software.acedb Subject: mailbombers Date: Tue, 15 Apr 1997 19:09:42 GMT Organization: Eindhoven University of Technology, The Netherlands Message-ID: <3353d26d.2769308@news.tue.nl> NNTP-Posting-Host: annex1s37.urc.tue.nl X-Newsreader: Forte Free Agent 1.1/32.230 Lines: 1 Please help me find an email bomber program...mine crashed From owner-acedb@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: getting to Ithaca Date: 15 Apr 1997 18:31:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9704160132.AA08475@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net We've received some questions about how to arrange travel to Ithaca for the ACE97 Conference and Workshop. The quickest way to Ithaca is by air. We're served by Continental (Newark) and USAirways (La Guardia, Boston, Philadelphia, Pittsburgh, White Plains, Syracuse). It's a short taxi from the airport to Cascadilla Hall. If you have an urge to drive and see some countryside, we're about 5 hours from New York City, Philadelphia or Toronto, and 8 hours from Boston, Washington DC or Pittsburgh. Travel by bus takes slightly longer. There are no trains. Looking forward to seeing you at ACE97! - Dave From owner-acedb@net.bio.net Tue Apr 15 23:00:00 1997 Newsgroups: bionet.software.acedb Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ix.netcom.com!bks From: bks@netcom.com (Bradley K. Sherman) Subject: Re: getting to Ithaca Message-ID: Organization: DNA + Sunlight References: <9704160132.AA08475@greengenes.cit.cornell.edu> Date: Wed, 16 Apr 1997 13:18:00 GMT Lines: 15 Sender: bks@netcom20.netcom.com In article <9704160132.AA08475@greengenes.cit.cornell.edu>, Dave Matthews wrote: > >If you have an urge to drive and see some countryside, we're about 5 hours >from New York City, Philadelphia or Toronto, and 8 hours from Boston, >Washington DC or Pittsburgh. Travel by bus takes slightly longer. There >are no trains. International visitors take note: Flying into Toronto or Buffalo and renting a car will allow you to stop at Niagra Falls; be sure to arrange to view the Falls from the Canadian side. --bks From owner-acedb@net.bio.net Thu Apr 17 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!tank.news.pipex.net!pipex!news.hol.gr!not-for-mail From: "Paul Reckas" Newsgroups: bionet.software.acedb Subject: Opinions for new software wanted Date: 18 Apr 1997 07:33:33 GMT Organization: Softrie S.A. Lines: 26 Message-ID: <01bc4bd3$fbd11ea0$1ed01ec2@comp126> NNTP-Posting-Host: port14.ppp10.hol.gr X-Newsreader: Microsoft Internet News 4.70.1155 We are trying to get an honest feedback on our new Business Information Management software we have developed. Please visit us at our site: http://www.softrise.com. There you can find information on our products, Business Coordinator Professional and Light. We have a FULL working demo at http://www.softrise.com/demo_dl.htm for you to download and evaluate. You may send us your opinion from our feedback page at http://www.softrise.com/feedback.htm or e-mail us directly at feedback@softrise.com. As a courtesy for your time and effort we will enter you on our drawing to win one of 19 Business Coordinator packages that we give away every month (total value of packages $7,150.00). We thank you in advance for your interest and your opinions. -- ________________________________________ Paul Reckas International Marketing Executive Softrise S.A. http://www.softrise.com softrise@softrise.com ---------------------------------------------------------------------------- ---- From owner-acedb@net.bio.net Thu Apr 17 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!newsxfer3.itd.umich.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!EU.net!enews.sgi.com!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!not-for-mail From: frist@cc.umanitoba.ca Newsgroups: bionet.software.acedb Subject: Re: getting to Ithaca Date: Fri, 18 Apr 1997 12:43:19 -0500 Organization: University of Manitoba Lines: 39 Message-ID: <3357B2B7.1742@cc.umanitoba.ca> References: <9704160132.AA08475@greengenes.cit.cornell.edu> NNTP-Posting-Host: brassica.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------12081A887035" X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5.1 sun4u) This is a multi-part message in MIME format. --------------12081A887035 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dave Matthews wrote: > > We've received some questions about how to arrange travel to Ithaca .... deleted... > The quickest way to Ithaca is by air. We're served by Continental (Newark) ... deleted > are no trains. Just wanted to add a historical note. It was on the (now extinct) train from New York to Ithaca that Hans Bethe came up with the mechanism for hydrogen fusion in the sun. The train ride may have taken longer, but it gave you time to think! --------------12081A887035 Content-Type: text/plain; charset=us-ascii; name="signature" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="signature" =============================================================================== Brian Fristensky | Department of Plant Science | There are more elk than people in Wallowa University of Manitoba | County. The people like it that way. Winnipeg, MB R3T 2N2 CANADA | So, most likely do the elk. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Jonathan Nicholas, 1989 FAX: 204-261-5732 | Plaque in Oregon Convention Center http://home.cc.umanitoba.ca/~frist/ =============================================================================== --------------12081A887035-- From owner-acedb@net.bio.net Tue Apr 22 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!tank.news.pipex.net!pipex!duke.telepac.pt!news.telepac.pt!usenet From: "SOFERRAGENS" Newsgroups: alt.autos.mitsubishi,alt.binaries.w-software,alt.computer.drivers.wanted,alt.journalism.print,at.tuwien.software,bionet.software,bionet.software.acedb,chile.mercado.software,chinese.comp.software,cis.winnt.drivers,cis.winnt.printing,cix.free_so Subject: dirvers for w95 from a Mitsubishi S3410 30d/30b Date: 23 Apr 1997 23:56:06 GMT Organization: Soc. Ferr. Prog. Albic. Lda Lines: 6 Message-ID: <01bc5031$6398a920$910841c2@Host.telepac.pt> NNTP-Posting-Host: cb1_p15.telepac.pt X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.software:18445 bionet.software.acedb:1184 I have a Mitsubishi Sublimation Full Color Printer, S3410-30D, but I don't have the drivers for Windows95. Do you know where can I get them? If you know or you have it, I would greated if you send them to me to soferragens@grupo.bfe.pt From owner-acedb@net.bio.net Mon Apr 28 23:00:00 1997 From: "Adam Cooper" Subject: LIFETIME REMINDER SERVICE Newsgroups: bionet.software.acedb Message-ID: <01bc53fb$01ec6ea0$37ef10d0@default> X-Newsreader: Microsoft Internet News 4.70.1161 NNTP-Posting-Host: mo-ken-p05.bootheel.net Date: 29 Apr 97 16:24:17 GMT Organization: Primary Network. http://www.primary.net Lines: 40 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news-peer.sprintlink.net!sprint!news-pull.sprintlink.net!news.sprintlink.net!cheech.primary.net!mo-ken-p05.bootheel.net Dear Newsgrouper, DO YOU FORGET? -Friends Birthdays -Anniversaries -Any Important Dates that you want to be reminded of? -Or even reminders to call your friend once a year in Alaska FOR THE REST OF YOUR LIFE WE WILL REMIND YOU!!!!!!! One Time Fee of $39.00 and this lasts for the rest of your life. Also, we can even send Gift Paks to anyone you want automatically. (This is optional) Memberships available in USA ONLY Send Check or Money Order TO: Adam Cooper Email: Rt. 1 Box 63-A acooper@mail.bootheel.net Senath, MO 63876 Please allow 2 weeks for clearance on Checks. Thank You, Adam Cooper BE SURE TO INCLUDE MAILING ADRESS From owner-acedb@net.bio.net Wed Apr 30 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 May 1997 02:00:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199705010900.CAA04394@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-acedb@net.bio.net Wed Apr 30 23:00:00 1997 Path: biosci!pipeline.net!2358945567 From: 2358945567@pipeline.net Newsgroups: bionet.software.acedb Subject: INTERNET CREDIT APPROVAL LETTER Date: 1 May 1997 12:30:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: <199705011820.LAA26822@big.fishnet.net> NNTP-Posting-Host: net.bio.net INTERNET CREDIT CARD APPROVAL LETTER (ACTIVATION NUMBER: 1-702-733-9400) CASH ADVANCE APPROVED:YES APPROVAL NUMBER:000-4777001 CREDIT LIMIT:$2,000.00 APPROVAL EXPIRES:05/31/97 CREDIT PROVIDER:CMM BANK AFFILIATION:NONE CARD ISSUED:MONEYFIRSTCARD MEMBER STATUS:PENDING ANNUAL FEE:NONE APR:17.99% DEAR FUTURE CARDHOLDER, CONGRATULATIONS! YOU HAVE BEEN APPROVED FOR A $2,000.00 UNSECURED CREDIT LINE FROM THE FINANCIAL CARD DIVISION OF CMM BASED ON THE INFORMATION WE HAVE ON FILE REGARDLESS OF PAST CREDIT. YOUR APPROVAL NUMBER IS 000-4777001 AND YOUR APPROVED CREDIT AMOUNT OF $2,000.00 FOR CREDIT PURCHASES AND CASH ADVANCES WILL BE AVAILABLE ONCE YOU RECEIVE YOUR MONEYFIRSTCARD JUST BY CALLING NOW! AS A MEMBERSHIP BENEFIT, YOU WILL BE PROCESSED* AT NO COST FOR AN UNSECURED MAJOR CREDIT CARD WITH A CREDIT LINE OF UP TO $2,000.00 REGARDLESS OF PAST CREDIT. SEND NO MONEY NOW - THERE IS NO SECURITY OR MONEY DEPOSITS REQUIRED! CALL IMMEDIATELY WITH YOUR APPROVAL NUMBER TO ACTIVATE YOUR MEMBERSHIP AND ITS BENEFITS. BY ACTING NOW - WE'LL ASSIGN YOUR MONEYFIRSTCARD WITHIN THE NEXT 48 HOURS AND THEN APPLY YOUR ONE TIME MEMBERSHIP FEE BY THE PAYMENT METHOD YOU PREFER. IN ADDITION, YOU'LL RECEIVE $100.00 OFF YOUR FIRST CREDIT PURCHASE OVER $200.00 WITH THE MONEYFIRSTCARD JUST BY CALLING NOW! GETTING MORE CREDIT IS AS SIMPLE AS CALLING US TODAY TO ACTIVATE YOUR MEMBERSHIP AND TO OBTAIN YOUR PIN CODE FOR CASH ADVANCES BEFORE YOUR APPROVAL EXPIRES. SO CALL NOW AND GET THE CREDIT YOU DESERVE. 100% QUALITY ASSURANCE AND NO LESS! SINCERELY, J. A. MILLER PRESIDENT CALL RIGHT NOW (IF BUSY KEEP TRYING) ***** 1-702-733-9400 ***** FOR IMMEDIATE ACTIVATION AND ESTABLISH YOUR CREDIT TODAY! * YOU MUST CALL TO OBTAIN YOUR PIN CODE FOR CASH ADVANCES AND FOR MEMBERSHIP ACCEPTANCE ALONG WITH OBTAINING COMPLETE DETAILS OUTLINING OUR PROGRAM!