From owner-acedb@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!webtv.net!uunet!in3.uu.net!newsfeed.internetmci.com!204.59.152.222!news-peer.gip.net!news.gsl.net!gip.net!feeder.qis.net!news.umbc.edu!eisenman From: eisenman@umbc.edu (David M. Eisenmann) Newsgroups: bionet.software.acedb Subject: acedb for linux error Date: Tue, 02 Dec 1997 15:14:41 -0500 Organization: UMBC - Biological Sciences Lines: 13 Message-ID: NNTP-Posting-Host: macbio471-2.biosci.umbc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Hello, I have Linux running on a PowerMac (mklinux) and I recently installed Acedb 4.5 from bin.linux.4_5e.tar.Z. The install went OK, but I get the following message when I type 'acedb' /usr/acedb/bin/xace: Exec format error. Wrong Architecture. My default shell is bash, but I got the same error message when I changed it to csh. Can somebody please let me know what is wrong here? Thanks, Dave Eisenmann eisenman@umbc.edu From owner-acedb@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!europa.clark.net!192.174.65.44!newscore.univie.ac.at!03-newsfeed.univie.ac.at!fstgal00.tu-graz.ac.at!spaniel From: smith@umes07.avl.co.at (Search Spaniel) Newsgroups: bionet.software.acedb Subject: Software-search the web quickly with Search Spaniel Date: Wed, 03 Dec 97 17:35:21 GMT Organization: Search Spaniel Lines: 4 Message-ID: <250108697@searchspaniel.com> NNTP-Posting-Host: isdn024.tu-graz.ac.at To Software-search the most search engines in the shortest time, use the internet's newest search engine - Search Spaniel at: http://www.searchspaniel.com/ From owner-acedb@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!uni-muenster.de!pbio16.uni-muenster.de!user From: "Uwe Baumert" Newsgroups: bionet.software.acedb Subject: Re: acedb for linux error Date: Wed, 03 Dec 1997 14:22:56 +0200 Organization: University of Muenster Lines: 30 Sender: "Uwe Baumert" Message-ID: References: NNTP-Posting-Host: pbio16.uni-muenster.de In article , eisenman@umbc.edu (David M. Eisenmann) wrote: > Hello, > > I have Linux running on a PowerMac (mklinux) and I recently installed Acedb > 4.5 from bin.linux.4_5e.tar.Z. The install went OK, but I get the > following message when I type 'acedb' > > /usr/acedb/bin/xace: Exec format error. Wrong Architecture. > > My default shell is bash, but I got the same error message when I changed > it to csh. Can somebody please let me know what is wrong here? Thanks, > > Dave Eisenmann > eisenman@umbc.edu Hi, the binary distribution of AceDB for linux is for intel i386 and higher. I do not know if somebody else has build a mklinux binary for the PowerMac. I think you have to build it on your own. Uwe Baumert -- Institute for General Zoology & Genetics University of Muenster Schlossplatz 5 Tel: +49 251 83-24675 D-48149 Muenster, Germany Fax: +49 251 83-24723 From owner-acedb@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!204.59.152.222!news-peer.gip.net!news.gsl.net!gip.net!news.new-york.net!news.columbia.edu!news-not-for-mail From: Justin Lee Newsgroups: bionet.software.acedb Subject: Mini Analysis Program Date: Wed, 03 Dec 1997 13:35:59 -0500 Organization: Columbia University Lines: 26 Message-ID: <3485A68F.18D993E2@columbia.edu> Reply-To: cjl2@columbia.edu NNTP-Posting-Host: bb110101.cpmc.columbia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (Win95; U) Hi, I have written a mini analysis program to analyse spontaneous miniature EPSCs or IPSCs under Windows environment. It can detect 3pA peaks with 5pA noise. It can also be used for any spontaneous activities, such as spontaneous action potential firing, current recordings for electochemical measurements, etc.. Please visit at http://128.59.170.42 to download the program and try it out. I also have several other programs useful for electophysiology and immunocytochemistry. Justin Lee -- Columbia University Department of Physiology 630 W. 168th Street BB1106 New York, NY 10032 Phone (212) 305-3817 Fax (212) 305-5775 e-mail cjl2@columbia.edu http://128.59.170.42 ftp://128.59.170.42 From owner-acedb@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!NET.BIO.NET!biosci-help From: biosci-help@NET.BIO.NET (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: ATTN: bionet.acedb to be automoderated for spam Date: 3 Dec 1997 15:37:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 165 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: biosci-help@net.bio.net NNTP-Posting-Host: net.bio.net As you may have seen in an earlier posting to bionet.announce, we will soon implement a new policy to control spam in unmoderated groups. The original message is copied directly below. Appended after it is a copy of my proposed new group charter, which is minimally different from the current one. If you have any suggestions for change in the text or in the policy, please let me or the group know within the next few days. Thanks, Serge Taylor Biosci Administrator Stanford University ============== original message ============================== As part of our effort to eliminate "spam" messages which are offensive and distracting to the scientific discussions which the Biosci newsgroups are designed to facilitate, we are creating a new type of moderated newsgroup -- "Moderated (only to filter out spam)". Our rationalie is that only what usenet recognizes as "moderated" newsgroups can filter mail postings, yet it has proven difficult to find volunteer moderators from each newsgroup. Our intention is to use a combination of human and software filters to eliminate the most egregious examples of spam. Since we value diversity of opinion in scientific communications, and recognize that our efforts are unavoidably subject to both Type I and Type II errors, we aim to err on the side of allowing arguably scientifically relevant communications to be posted. We intend to convert all the unmoderated bionet newsgroups to the new status as soon as possible, and forsee two situations: (1) Where a charter exists for an established but unmoderated group, we will take the current charter and add the following language (taken >From the policy statement which we send to anyone who wishes to start a new newsgroup or convert an unmoderated to moderated newsgroup, and suitably customized to the newsgroup where necessary) on "Moderation Policy": "Moderation Policy: Mass-posted commercial messages, chain letters, and similar postings not germane to the stated purpose of the charter will be deleted without comment. Inappropriate messages posted in good faith will be returned to the sender where feasible. Messages not strictly within the charter but likely to be of interest to many subscribers will be accepted. Use of the newsgroup for commercial purposes is prohibited." The proposed new charter will be posted to the newsgroup for a short comment period. (2) Where a charter does not exist for an established unmoderated group, we will solicit the newsgroup's discussion leader(s), where listed, to draft a non-controversial charter and submit it to the newsgroup for a short comment period. If at any time a moderated-for-spam newsgroup wishes to convert to a regular "moderated" group, with its own moderator, we shall be happy to treat such a request just as we do the request to change from unmoderated to moderated status. Finally, if a currently moderated group wishes to take advantage of the spam filtering software to ease the administrative burden on the moderator, we will discuss the logistics and policy guidelines with the group's moderator. (We will notify moderators when we are ready to offer this facility; we are not currently ready.) We hope that these new arrangements will protect the integrity of our newsgroups and allow us to focus on other ways of improving Biosci. Thank you for your patience and understanding as we deal with the spam problem. Serge Taylor Biosci Administrator Stanford University Libraries ========== proposed modified charter ==================== Proposal for ACEDB-SOFT/bionet.software.acedb (moderated-for-spam) USENET newsgroup name: bionet.software.acedb Status: Moderated for spam One line Description: Discussions by users of genome databases using ACEDB Moderation address: acedb@net.bio.net (acedb-moderator@net.bio.net is an alias for acedb@net.bio.net) Moderator: Biosci Staff Mailing list name: ACEDB-SOFT E-mail addresses: acedb@net.bio.net acedb@daresbury.ac.uk Purpose: Discussions by users and developers of genome databases using the ACEDB software. This group includes discussions ranging from construction of new databases using the ACEDB software, curation of genetic and physical map information into Ace format, to questions about the use of any of the species specific databases utilizing the ACEDB software. As part of the C. elegans genome effort Jean Thierry-Mieg and Richard Durbin developed a generalized software solution for genome databases. ACEDB is the name of the software used for the organization, presentation and storage of genome information. It is also the name of the first database to use this software, the the C. elegans genome database. ACEDB includes an X-windows user interface and an object-like database engine developed specifically for storage of biological information. Many groups have begun using ACEDB to create a variety of genome databases. As of April 1993 three of these groups have released their databases to the general public and many others are well along in their development. The number of groups utilizing the ACEDB software to organize, manipulate and disseminate genome information is increasing. An informal community of ACEDB developers has formed to share knowledge and resources. This group allows the community of developers and users to continue sharing and growing. The archives of the group also provide a useful resource to both developers and users. Moderation policy: This newsgroup is moderated by automatic spam filtering software and by Biosci personnel to implement the following policy: Mass-posted commercial messages, chain letters, and similar postings not germane to the stated purpose of the charter will be deleted without comment. Inappropriate messages posted in good faith will be returned to the sender where feasible. Messages not strictly within the charter but likely to be of interest to many subscribers will be accepted. Use of the newsgroup for commercial purposes is prohibited. Discussion leader: Mike Cherry Department of Genetics Stanford University Stanford, CA 94305-5120 Voice: 650-723-7541 FAX: 650-723-7016 Internet: cherry@genome.stanford.edu From owner-acedb@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Amber Technologies@dl.ac.uk, "Inc." Newsgroups: bionet.software.acedb Subject: MegaWeb Date: 5 Dec 1997 05:38:19 -0000 Lines: 60 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <66840b$52u@mserv1.dl.ac.uk> Original-To: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="03242318" X-Encoding: MIME This is a multi-part message in MIME format. --03242318 --03242318 Content-Type: text/html; name="MegaWeb.html" Content-Transfer-Encoding: quoted-printable MegaWeb
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--03242318-- From owner-acedb@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!ais.net!news.idt.net!dispose.news.demon.net!demon!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: Matt Couchman Newsgroups: bionet.software.acedb Subject: Position: Bioinformaticist-co-ordinator Date: Fri, 05 Dec 1997 17:12:19 +0000 Organization: The John Innes Centre Message-ID: <348835F3.41C6@bbsrc.ac.uk> Reply-To: Pauline.Stephenson@bbsrc.ac.uk, Sally.Jeffery@bbsrc.ac.uk NNTP-Posting-Host: jiio5.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.04Gold (X11; I; OSF1 V3.2 alpha) To: grains@greengenes.cit.cornell.edu Lines: 37 JOHN INNES CENTRE BIOINFORMATICIST-CO-ORDINATOR Applications are invited for a Bioinfomaticist-co-ordinator to work jointly on two EU Biotechnology projects on comparative mapping of monocat and dicot plant genomes: EGRAM (European Gramineae Mapping Project) and EuDicot Map (European Dicotyledonous Mapping Project). The post will involve information strategy development with partner colleagues and ensuring that the work of all groups from 9 European countries is databased from the outset in ways compatible with and linked to international plant genome and DNA databases. The postholder will also develop bioinformatic means of information flow between groups including the organisation of meetings as required. The post is funded by AMICA (Advanced Molecular Initiative in Community Agriculture) and will be based at the John Innes Centre at Norwich in the UK. The postholder will interact closely with the several bioinformaticists at JIC already working on comparative, brassica and cereal bioinformatics as well as EuDicot Map staff at Perpignan, France. The successful candidate will have experience in plant genome research and/or bioinformatics. The post will normally be appointed between £13860 and £16500 (Band 7) or £16000 and £22000 (Postdoctoral Research Scientist) level depending on qualifications and experience. For further information contact Pauline Stephenson (Pauline.Stephenson@bbsrc.ac.uk), Mike Gale (Sally.Jeffery@bbsrc.ac.uk) or write to the Personnel Officer, John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH, quoting reference number MDG/315. The closing date for application froms will be 9th January 1998. The John Innes Centre is a registered charity (No. 511709) grant-aided by the Biotechnology and Biological Sciences Research Council and is an Equal Opportunities Employer. From owner-acedb@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!rutgers!uwm.edu!newsfeeds.sol.net!newspump.sol.net!sol.net!news.maxwell.syr.edu!uninett.no!newsfeed.nacamar.de!eerie.fr!jussieu.fr!ext.jussieu.fr!mac2-info.sb-roscoff.fr!user From: crepinau@pas-de-spam.sb-roscoff.fr (Crepineau florent) Newsgroups: bionet.software.acedb Subject: NEWBIE : TIGR assembler and ACEDB? Date: 8 Dec 1997 16:37:22 GMT Organization: Station biologique de Roscoff Lines: 21 Message-ID: NNTP-Posting-Host: mac2-info.sb-roscoff.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear ACEDB users, I am new to this field, I was looking for this type of database and found the one developed by TIGR. However it uses Sybase and we can't afford it. Still they have released a program called 'TIGR Assembler' which assembles contigs. In their last release they say that the program is now supporting .Ace output format to use with consed. I know that AceDB has its own contig assembler : Ace.embly. However I have used the 'TIGRassembler' and I would rather not have done this for nothing :-) Does one know if I can use the .Ace output from the TIGRAssembler with AceDB? And secondly, by reading the FAQ of this list I have realised how AceDB can be used in such diver ways! However, when I downloaded the program, the database was the one of C. elegans. How can I creat my own database? Thanks in advance. Florent Crépineau crepinau@sb-roscoff.fr Please remove pas-de-spam to answer back (thank you) From owner-acedb@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!agate!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: 8 Dec 1997 17:55:58 GMT Organization: Dept. Plant Breeding, Cornell University Lines: 1297 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <66hcbe$noe@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.psw.fs.fed.us Summary: Frequently Asked Questions about finding and getting started with the genome database software ACEDB. URL: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html Archive-name: acedb-faq Last-modified: 8 Dec 97 Version: 1.40 ---------------------------------------------------------------------------- ACEDB FAQ ---------------------------------------------------------------------------- Curated by: Dave Matthews ---------------------------------------------------------------------------- Frequently Asked Questions about ACEDB * Q0 : What is ACEDB? * Q1 : ! What is the current version of ACEDB? * Q1.5 : + What's new in ACEDB 4_5? * Q2 : Where can I get ACEDB? * Q3 : ! What hardware/software do I need to run ACEDB? * Q4 : Can ACEDB be networked? * Q5 : What documentation exists for ACEDB? * Q6 : What newsgroups and mailing lists are available for ACEDB? * Q7 : Is there a repository of software tools for ACEDB curators? * Q8 : When and where is the next ACEDB Workshop? * Q9 : How does ACEDB compare to commercial relational DBMS's? * Q10 : How should ACEDB be cited? * 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. 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 in 1989. 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. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups. 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 the ACEDB software? A1: The current Unix version is ace.4_5d/e, released 28 August 1997. Enhancements added during the ACE97 Workshop will be incorporated in the next release. The very latest development version is always available at ftp://ftp.sanger.ac.uk/pub/acedb_src/. This is unsupported and not to be redistributed. The Windows 95/NT version 4.5.2, 15 August 1997, corresponds to Unix test.ace.4_5c. For current information see the WinAce Web page at http://mendel.medgen.ubc.ca/rbrusk/winace.html. A Macintosh version is available as version 4.1b1, August 1995. Return to List of Questions ---------------------------------------------------------------------------- Q1.5: What's new in ACEDB 4_5? A1.5: At present, all documentation on new ace4_5 features is in the Proceedings of the ACE97 workshop. Return to List of Questions ---------------------------------------------------------------------------- Q2: Where can I get ACEDB? A2: Source code and Unix binaries are available in the following anonymous ftp sites: * ncbi.nlm.nih.gov in repository/acedb * ftp.sanger.ac.uk in pub/acedb * lirmm.lirmm.fr in pub/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 * Documentation: http://mendel.medgen.ubc.ca/rbrusk/winace.html 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 ---------------------------------------------------------------------------- Q3: What hardware/software do I need to run ACEDB? A3: The software is available in binary (pre-compiled) format for a variety of machines. * 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) The software is also available as source code, so you may be able to get it working on any machine. Memory requirements (from Richard Durbin, aug 97) The amount of memory you require for ACEDB depends very much on how big the database is (i.e. the disk space used by the database/ subdirectory). Our rule of thumb is that one typically uses 5-10Mb plus up to 10% of the disk space size of the database. So with a 200Mb database perhaps 25Mb memory, and with a 500Mb database (e.g. the C. elegans one) up to 50-60Mb. In fact for short sessions less memory is used -- it is only when all classes are explored, or for example when parsing big files that these amounts of memory get used. Return to List of Questions ---------------------------------------------------------------------------- Q4: Can ACEDB be networked? A4: ACEDB Client / Server Computing (from Doug Bigwood, aug97) There are several client/server models for ACEDB computing and several more are in development. The start of the ACEDB client/server age began with the inclusion of aceclient and aceserver in version 4.0. These are C - based and use the RPC protocol for communication. These executables can be made from the standard ACEDB distributions. Starting in version 4.5 an xaceclient is also included with ACEDB. Xaceclient provides remote read/write access to an aceserver while providing the user with the same X displays that are found in xace. To use it, you create an empty database with the appropriate models and start xaceclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the Montpellier server in the distribution server.wrm). The data will be saved locally and can then be viewed with a normal xace. A perl extension which provides aceclient functionality to Perl 5.x was developed at ACE95. The files necessary for this perl extension are now (ACEDB 4.5 and later) included in the wrpc directory of the ACEDB directory hierarchy. Documentation about how to extend perl is found at http://probe.nalusda.gov:8000/ace97/perlace/perlacecl.html. WWWAce and its successor webace were developed to provide a World Wide Web interface for ACEDB. Webace instructions can be found at http://probe.nal.usda.gov:8000/acedocs/webace.html, and http://probe.nal.usda.gov:8000/ace97/webace.html and the program itself at ftp://probe.nalusda.gov/pub/tools/webace.tar.gz. A Java-based client called Jade allows communication via sockets to an aceserver. Jade installation instructions and information on downloading can be found at http://probe.nalusda.gov:8000/ace97/Jade.installation.html. There are now development efforts underway to provide additional client/server functionality to ACEDB including a CORBA server and socket-based communications. These will likely be included in future versions of ACEDB. A new C library interface to ACEDB internals will greatly ease the development of new clients and servers that will support additional protocols. ---------------------------------------------------------------------------- Q5: What documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Library 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. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The WWW documentation server is part of the Agricultural Genome Information System, at http://probe.nalusda.gov:8000/acedocs/. Documents in Postscript, wordprocessor, and other non-html formats are available by ftp at ftp://probe.nalusda.gov/pub/acedocs/. Information in the ACEDB Documentation Library includes: * Primary documents from the developers Durbin & Thierry-Mieg, ca. 1992. o acedb -- A C. elegans Database: I. Users' Guide o acedb -- A C. elegans Database: II. Installation Guide o acedb -- A C. elegans Database: III. Configuration Guide o acedb -- A C. elegans Database: Syntactic Definitions for the ACEDB Data Base Manager * Tutorials, general and specific * Documentation written at the ACEDB Workshops * A repository of curator tools * A selection of models.wrm files from various databases * SampleDB, a sample database to demonstrate some ACEDB features, 1995 * This FAQ, in html format Other sources of documentation: * The ACEDB online help, a hypertext reader for the contents of the whelp directory of the ACEDB software distribution. * Contents of the wdoc, wtools, and wscripts directories. * Archives of the bionet.software.acedb newsgroup (both searchable) o http://www.bio.net/hypermail/ACEDB/, from BIOSCI o http://genome-www.stanford.edu/cgi-bin/biosci_acedb, from the Saccharomyces Genome Database site * 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".) * Paper publications o Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992). AAtDB, an Arabidopsis thaliana database. Plant Molecular Biology Reporter 10: 308-309, 409-410. o Cherry, J.M. and Cartinhour, S.W. (1994). ACEDB, A tool for biological information. Pp. 347-356 in: Automated DNA Sequencing and Analysis, M. Adams, C. Fields, and C. Venter (Eds.). Academic Press. Online version: http://probe.nalusda.gov:8000/acedocs/overview.html. o Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994). Physical mapping projects and ACEDB. Pp. 111-158 in: Guide to Human Genome Computing. Bishop, M.J (Ed.). Academic Press. Return to List of Questions ---------------------------------------------------------------------------- Q6: What newsgroups and mailing lists are available for ACEDB? A6: The USENET/BIOSCI conference bionet.software.acedb is dedicated to discussions of ACEDB. The newsgroup can be accessed via a newsreader like rn or tin, a WWW browser (news:bionet.software.acedb), or e-mail. To subscribe to the e-mail version, send the message "subscribe acedb" to biosci-server@net.bio.net. Mail sent to acedb@net.bio.net will be distributed to all subscribers and to the electronic conference. Articles posted to 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. There is also a separate mailing list for announcements of new releases of the ACEDB (worm) database as well as the ACEDB software. To get on or off this mailing list send mail to rd@sanger.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. The BIOSCI newsgroup is on this list. Return to List of Questions ---------------------------------------------------------------------------- Q7 : Is there a repository of software tools for ACEDB curators? A7: Not really, but there are several partial ones. The main tools available are for converting data from other formats to .ace format. The Agricultural Genome Information System has a growing stock of useful tools at http://probe.nalusda.gov:8000/acedocs/conversion.html. Some additional ones were contributed at the ACE97 Workshop and can be found in the Proceedings, http://probe.nalusda.gov:8000/ace97/tools/. Mike Cherry maintains an archive of tools at ftp://genome-ftp.stanford.edu/pub/acedb_dev/utilities/ 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/. Return to List of Questions ---------------------------------------------------------------------------- Q8: When and where is the next ACEDB Workshop? A8: The next ACEDB meeting is planned for summer 1998 in England. The ACE97 Conference and Workshop was held July 27 - August 9 at Cornell University, Ithaca, New York, USA. See the ACE97 Proceedings Page, http://probe.nalusda.gov:8000/ace97/proceedings.html for the results. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/. 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 ---------------------------------------------------------------------------- Q9: How does ACEDB compare to commercial relational DBMS's? A9: 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 ---------------------------------------------------------------------------- Q10: How should ACEDB be cited? A10: 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 ---------------------------------------------------------------------------- Q11: What ACEDB databases exist? A11: In alphabetic order by Database name [Curators, please submit changes as new paragraphs. You may include html links.] A repository of many of these databases is maintained by the Agricultural Genome Information System, both for anonymous ftp at ftp://probe.nalusda.gov/pub and for WWW access via Webace at http://probe.nalusda.gov:8000/alldbs.html. Database : AaeDB Species : Aedes aegypti (yellow fever mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@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 Data_updated : regularly FAQ_updated : April 1997 Database : AalDB Species : Aedes albopictus (Asian tiger (forest day) mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@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 Data_updated : regularly FAQ_updated : April 1997 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/ FAQ_updated : August 1995 Database : aCHEdb Species : wide range of species Subject : alpha/beta fold family of proteins database ESTHER. Sequences phylogenetically related to cholinesterases (alpha/beta hydrolase, carboxylesterases, lipases, adhesion molecules.) Comment : Converted to ACEDB from the original ESTHER database. ACEDB_version : UNIX 4.5, MacAce 4.0b4 Data_version : August 1997 Curator : Xavier Cousin - cousin@ensam.inra.fr Curator : Thierry Hotelier - hotelier@ensam.inra.fr Curator : Arnaud Chatonnet - chatonne@ensam.inra.fr Contact : chedb@ensam.inra.fr Availability: Unix and Macintosh versions via anonymous ftp FTP: ftp://ftp.toulouse.inra.fr in pub/esther WWW : http://www.ensam.inra.fr/cholinesterase FAQ_updated : September 1997 Database : AgaDB Species : Anopheles gambiae (malaria mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@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 Data_updated : regularly FAQ_updated : April 1997 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 FAQ_updated : 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/ FAQ_updated : July 1995 Database : AnoDB Species : Anopheles sp. ACEDB_version : 4.5 WWW : http://konops.imbb.forth.gr/AnoDB/ Curator : Christos Louis, louis@konops.imbb.forth.gr Co-Curator : Pantelis Topalis, topalis@konops.imbb.forth.gr Contact : AnoDB-comments@konops.imbb.forth.gr Data_updated : regularly FAQ_updated : August 1997 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 FAQ_updated : December 1996 Database : AtrDB Species : Aedes triseriatus (Eastern tree hole mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@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 Data_updated : regularly FAQ_updated : April 1997 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/ FAQ_updated : 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://synteny.nott.ac.uk/brassica.html Data_updated : Under development FAQ_updated : August 1997 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/ FAQ_updated : 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/ FAQ_updated : September 1995 Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edu 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/ FAQ_updated : 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/ FAQ_updated : 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 Data_updated : In development FAQ_updated : November 1996 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 : CupDB Species : Culex pipiens ACEDB_version : 4.3 WWW : currently unavailable via www Curator : Dennis Knudson, dknudson@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 Data_updated : regularly FAQ_updated : April 1997 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. FAQ_updated : 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/ FAQ_updated : 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 Data_updated: In development FAQ_updated : November 1996 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/ FAQ_updated : 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 Data_updated : December 1996 FAQ_updated : 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 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) Data_updated: October 1996 FAQ_updated : November 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 FAQ_updated : 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/ FAQ_updated : 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://synteny.nott.ac.uk/millet.html WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.shtml WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : 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 FAQ_updated : 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/ FAQ_updated : June 1995 Database : MsqDB Species : Interspecies Mosquito database ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@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 Data_updated : regularly FAQ_updated : April 1997 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/ FAQ_updated : 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 FAQ_updated : 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/ FAQ_updated : 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 FAQ_updated : 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/ FAQ_updated : June 1995 Database : Receptor Database Species : all Curator : Kotoko Nakata, nakata@nihs.go.jp Co-Curator : Takako Igarashi, taka@nihs.go.jp Co-Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Contact : Kotoko Nakata, nakata@nihs.go.jp ACeDB_version : 4.1 WWW : http://impact.nihs.go.jp/RDB.html Data_updated : regularly FAQ_updated : October 1997 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/ FAQ_updated : 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 FAQ_updated : 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 Data_updated: In development FAQ_updated : November 1996 Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Sam Beer, sbeer@nightshade.cit.cornell.edu PI : none currently 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/ Data_updated : May 1997 FAQ_updated : May 1997 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/ FAQ_updated : 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 FAQ_updated : 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 FAQ_updated : 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 Data_updated: October 1996 FAQ_updated: November 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/ FAQ_updated : 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 Data_updated: October 1996 FAQ_updated: November 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 FAQ_updated : 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/ FAQ_updated : 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 is 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, 1993-1997, approx. 70K 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 Dec 08 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: Martin Trick Newsgroups: bionet.software.acedb,bionet.software Subject: Position: Brassica genome bioinformatics Date: Tue, 09 Dec 1997 16:57:02 -0800 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 72 Message-ID: <348DE8DE.AED326C4@bbsrc.ac.uk> NNTP-Posting-Host: pc0419.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------E2C9E5A0449FBD9592236D6D" X-Mailer: Mozilla 4.03 [en] (Win16; I) Xref: biosci bionet.software.acedb:1543 bionet.software:20112 --------------E2C9E5A0449FBD9592236D6D Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Position: Brassica genome bioinformatics As advertised in New Scientist (6/12/97, p78), applications are invited for a position immediately available at the John Innes Centre, Norwich UK in Brassica Bioinformatics. The successful candidate will curate and further develop a Brassica genome database funded by the UK BBSRC UKCropNet initiative (http://synteny.nott.ac.uk). A key aim is to integrate genetic data from Brassica which can be integrated with that from the closely related Arabidopsis genome. A degree in a biological subject with a strong background in genetics is required, together with an interest and aptitude in applying database methods to facilitate genome research. Experience of any of UNIX, Perl or Java would be an advantage. The post is available for approximately two years and will be appointed between £13860 and £16500 (Band 7), at a level depending on qualifications and experience. For further information please contact Martin Trick (tel: +44 1603 452571 or martin.trick@bbsrc.ac.uk) or see www.uea.ac.uk/nrp/jic/b90trick.htm. For written particulars and an application form, please contact the Personnel Officer (jicpers@bbsrc.ac.uk), John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH, quoting reference number BR/330. The closing date for application forms will be 5th January 1998. Interviews are expected to be held February 4-5 1998. The John Innes Centre is a registered charity (No. 511709) grant-aided by the Biotechnology and Biological Sciences Research Council and is an Equal Opportunities Employer. --------------E2C9E5A0449FBD9592236D6D Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit             Position: Brassica genome bioinformatics

As advertised in New Scientist (6/12/97, p78), applications are invited for a position  immediately available at the John Innes Centre, Norwich UK in Brassica Bioinformatics.
The successful candidate will curate and further develop a Brassica genome database funded by the UK BBSRC UKCropNet initiative (http://synteny.nott.ac.uk). A key aim is to integrate genetic data from Brassica which can be integrated with that from the closely related Arabidopsis genome. A degree in a biological subject with a strong background in genetics is required, together with an interest and aptitude in applying database methods to facilitate genome research. Experience of any of UNIX, Perl or Java would be an advantage.

The post is available for approximately two years and will be appointed between £13860 and £16500 (Band 7), at a level depending on qualifications and experience. For further information please contact Martin Trick (tel: +44 1603 452571 or martin.trick@bbsrc.ac.uk) or see www.uea.ac.uk/nrp/jic/b90trick.htm. For written particulars and an application form, please contact the Personnel Officer (jicpers@bbsrc.ac.uk), John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH, quoting reference number BR/330. The closing date for application forms will be 5th January 1998. Interviews are expected to be held February 4-5 1998.

The John Innes Centre is a registered charity (No. 511709) grant-aided  by the Biotechnology and Biological Sciences Research Council and is an Equal Opportunities Employer. --------------E2C9E5A0449FBD9592236D6D-- From owner-acedb@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!webtv.net!uunet!in5.uu.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!205.252.116.205!howland.erols.net!usc!newshub.cts.com!relief.cts.com!not-for-mail From: jason@genosbio.com (Jason R. Martin) Newsgroups: bionet.software.acedb Subject: Setting up Printers in 4.5 Date: Wed, 10 Dec 1997 10:08:43 -0800 Organization: Genos Biosciences, Inc. Lines: 13 Message-ID: NNTP-Posting-Host: wagasa.cts.com X-Newsreader: Anawave Gravity v1.10 Cache-Post-Path: wagasa.cts.com!unknown@204.216.217.215 Could someone point me to some documentation on setting up printers in Acedb4.5 (solaris 2.5.1)? I've set the ACEDB_LPR variable, and that works fine, but noticed that there is support in the source code for /etc/printcap (for setting up multiple printers mabey??). Please cc me in your reply...our news server has been flakey. Thanks, Jason Martin jason@genosbio.com Genos Biosciences, Inc. From owner-acedb@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!marketcom.com!HappyAgent From: HappyAgent@marketcom.com Newsgroups: bionet.software.acedb Subject: Exciting Web Sales Engine!! Date: 10 Dec 1997 20:43:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello! Have a Nice Day! ************************************************************** This message brought to you by the all new MktAgent, the World's Premier Web Site Promotion Engine! http://209.54.41.90/MktAgent/MktAgent.htm ************************************************************** You are not part of a mailing list. You were selected to receive this message because your email address was publicly posted on a web page. You will not receive this message more than once - so there is no need to reply in order to be removed. However, for those that want to reply anyway: "To be removed from our list, just hit Reply and type remove." From owner-acedb@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!newsrelay.netins.net!newsfeed.dacom.co.kr!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: printer support in 4.5 Date: 11 Dec 1997 13:35:57 -0000 Lines: 21 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <66oq7t$2bt@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk acedb 4.5 has automatic analysis of /etc/princap normally, any printer available in printcap appears as a button and i no longer use ACEDB_LPR, just unsetenv it. the printer chooser allows resizing and a choice between mail, print, save on disk and a separate choice between ps, color-ps and text text print of diagrams is quite unreliable, but works well for all text windows selecting mail sets you in text mode, selecting print in PS and you can then rechange the ps/text switch the reason is that biologist often do not know what PS means and it is nearly always not what you want to mail a ps file or to print the non-ps Please let me know of any further problem From owner-acedb@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.algonet.se!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!eerie.fr!jussieu.fr!ext.jussieu.fr!mac2-info.sb-roscoff.fr!user From: crepinau@pas-de-spam.sb-roscoff.fr (Crepineau florent) Newsgroups: bionet.software.acedb Subject: looking for the model from the IMAGE ACEDB database Date: 12 Dec 1997 11:01:31 GMT Organization: Station biologique de Roscoff Lines: 16 Message-ID: NNTP-Posting-Host: mac2-info.sb-roscoff.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear ACEDB users Thank you for answering my previous question. I have another problem. Recently, there has been a paper published describing an ACEDB database for the IMAGE EST library. In the paper (Genome research Miller et al. 1997) they give 2 adresses from where the model for the database is dowloadable (ftp @ ncbi.nlm.nih.gov/repository/EST_INFORMER and ftp.ebi.ac.uk/pub/databases/est_informer). In one case the folder is empty and in the second case it does not exist. Does any of you know where I could get the model? If one has managed to dowload it, would that personne agree to share the model with me. Thanks in advance Florent Crépineau From owner-acedb@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!141.211.144.13!newsxfer3.itd.umich.edu!oleane!jussieu.fr!ext.jussieu.fr!mac2-info.sb-roscoff.fr!user From: crepinau@pas-de-spam.sb-roscoff.fr (Crepineau florent) Newsgroups: bionet.software.acedb Subject: NEWBIE : instaling Acembly? Date: 12 Dec 1997 13:12:47 GMT Organization: Station biologique de Roscoff Lines: 22 Message-ID: NNTP-Posting-Host: mac2-info.sb-roscoff.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear ACeDB users, As acembly is an extention for ACEDB, I thought that it would be the best place to ask. I am instaling Acembly 4.5. When I do instal.acembly, everything goes well except that it can't do a chmod on SGI_4 and whelp because it can't recognise them (actually, when you look at these files they have a question mark on them) Is that OK? And then when I run Acembly for the first time doing : acembly -Create clone_name it answers that it can't find the bin.SOLARIS_4_OPT. I have tried to download the missing file, I found several bin.--- but no bin.SOLARIS_4_OPT. Does it exist and where can I get it from? Thanks in advance. Florent Crépineau crepinau@sb-roscoff.fr From owner-acedb@net.bio.net Tue Dec 16 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!news.he.net!news.pbi.net!206.170.114.8.MISMATCH!news.infonex.net!alpha.jpunix.com!m2n Date: Wed, 17 Dec 1997 04:39:34 -0600 (CST) From: m2n-19971217-bionet.software.acedb+bionet.software.acedb@alpha.jpunix.com Message-ID: <199712171039.EAA06867@alpha.jpunix.com> Subject: Publicity agent will work for you! Mail-To-News-Contact: postmaster@alpha.jpunix.com Organization: m2n@alpha.jpunix.com Newsgroups: bionet.software.acedb,bionet.software.acedb Lines: 22 Xref: biosci bionet.software.acedb:1551 Wishing you (and yours) a joyous holiday season, and the most prosperous New Year. ----------------------------------------- This was posted by MarketCom's MktAgent, the interNet's premier publicity engine. Got something to say, a cause to promote, or a product/service to sell? Then it's time to get the word out to thousands of interested individuals. Locate 100,000 targetted leads, potential clients, and/or penpals, in only five days by utilizing our FREE demo model. http://www.MarketCom.com/MktAgent/ ----------------------------------------- glirmmvb lgn qfigwukvxtexaxjib xgpr gnsusafcplaqhqbnrwta From owner-acedb@net.bio.net Thu Dec 18 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!eerie.fr!jussieu.fr!ext.jussieu.fr!mac2-info.sb-roscoff.fr!user From: crepinau@pas-de-spam.sb-roscoff.fr (Crepineau florent) Newsgroups: bionet.software.acedb Subject: Acembly and // !! KEYWORD name_of_command does not match Date: 19 Dec 1997 13:23:58 GMT Organization: Station biologique de Roscoff Lines: 41 Message-ID: NNTP-Posting-Host: mac2-info.sb-roscoff.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Acedb users, As I was told I could ask question on Acembly in this newsgroup, that is what I am doing. I have been trying to use Acembly for the last three weeks without success. First I did not realise that Acembly was not the software so I downloaded (from the NCBI ftp server) the sources to recompile them for SOLARIS_4 but the script for cc does not work so I had to use the gcc. Eventually I managed to compile the sources but I did not find, in the bin.SOLARIS_4, the files I was supposed to find (ie : acembly and tacembly and makeSCF). For make SCF it is quite normal I did not recompile the sources I downloaded :-) but for the other one??? What I found was 'tace' and 'xace'. After making the commande acembly it was clear that 'tace' should have been 'tacembly'. I changed the name and at the same time I changed 'xace' to 'xacembly'. Actually, I copied the two files and changed the names so that 'xace' and 'xacembly' are both present in the bin.SOLARIS_4 ! Well everything went smoothly when I typed the command : %acembly I created a new project using the name of the folder containing my scf files and the software carried on. It found the scf file, did a scf2ace but when it tried to do the quality clipping it did // !! KEYWORD Acembly does not match // !! KEYWORD newSCF does not match Why? And when it does a AddNewRead, all the KEYWORD do not match. Why? Has anybody been faced by this problem? Wich you a merry christmas and happy new year florent Crepineau crepinau@sb-roscoff.fr From owner-acedb@net.bio.net Tue Dec 23 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!news-peer.sprintlink.net!news-peer-east.sprintlink.net!news.sprintlink.net!Sprint!sunqbc.risq.qc.ca!news.uquebec.ca!not-for-mail From: "Druzil" Newsgroups: alt.binaries.dominion.warez,alt.binaries.dominion.warez.decrypted,alt.japanese.neojapan.warez.ibmpc,alt.japanese.neojapan.warez.ibm-pc,alt.warez.godz,alt.warez.ibm-pc.games,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software Subject: cool warez... todays update and fresh link... Date: 24 Dec 1997 05:07:27 GMT Organization: Universite du Quebec Lines: 7 Message-ID: <01bd102a$77aded80$e179d484@eric> NNTP-Posting-Host: ppp225.uqac.uquebec.ca Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Microsoft Internet News 4.70.1161 Xref: biosci bionet.software:20211 bionet.software.acedb:1554 bionet.software.gcg:2927 this site contain a lot of cool warez... http://www.chez.com/druzil2 ce site contient beaucoup de warez... http://www.chez.com/druzil2 From owner-acedb@net.bio.net Mon Dec 29 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: professorship Date: 30 Dec 1997 18:03:32 -0000 Lines: 188 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <68bd1k$h8c@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk From jmc@euler.cnrs-mrs.fr Tue Dec 23 16:57:34 1997 Return-Path: Received: from davinci.cnrs-mrs.fr ([193.50.234.243]) by kaa (4.1/SMI-4.1) id AA01560; Tue, 23 Dec 97 16:57:33 +0100 Received: from euler.cnrs-mrs.fr (euler.cnrs-mrs.fr [193.50.234.241]) by davinci.cnrs-mrs.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id QAA09809; Tue, 23 Dec 1997 16:57:27 -0800 Received: by euler.cnrs-mrs.fr (951211.SGI.8.6.12.PATCH1502/911001.SGI) id QAA06464; Tue, 23 Dec 1997 16:54:51 +0100 Date: Tue, 23 Dec 1997 16:54:51 +0100 From: jmc@euler.cnrs-mrs.fr (Jean-Michel Claverie) Message-Id: <199712231554.QAA06464@euler.cnrs-mrs.fr> To: galibert@univ-rennes1.fr, dessen@genome.vjf.inserm.fr, rlegouis@pasteur.fr, cpetit@pasteur.fr, cedergren@bch.umontreal.ca, pbucher@isrec-sun2.unil.ch, aisrael@pasteur.fr, mieg@kaa.crbm.cnrs-mop.fr, bairoch@cmu.unige.ch Subject: APPEL A CANDIDATURES/POSTES Status: RO Cher collegue: L'Universite AIX-MARSEILLE-2, a laquelle notre laboratoire est associe, mettra bientot en concours plusieurs postes d'enseignants-chercheurs (3 postes de Maitre de conference, 1 poste de professeur) dans les domaines de la bioinformatique et/ou de la genomique fonctionnelle. Ces thematiques (y compris au plan experimental) sont centrales a notre activite de recherche, et notre laboratoire (http://igs-server.cnrs-mrs.fr) pourra accueillir les candidats retenus. Je vous remercie de bien vouloir porter cette information a la connaissance des jeunes chercheurs qui vous entourent, afin que ces postes puissent etre attribues dans la plus grande transparence, et sur la base du seul merite des candidats. En vous remerciant d'avance, ================================================================ Jean-Michel Claverie jmc@igs.cnrs-mrs.fr Tel: +33 4 91 16 45 48 Fax: +33 4 91 16 45 49 Laboratoire "Information Genetique & Structurale" (EP 91 - CNRS) internet: http://igs-server.cnrs-mrs.fr 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, FRANCE ================================================================ ANNEXE I -------- QUOI FAIRE: professeur/Maitre de conferences - textes officiels Toutes les modalites de la premiere phase du concours, l'inscription sur les listes de qualification AVANT le 12 Janvier 1998, sont disponible sur le serveur web de la Direction des personnels de l'enseignement superieur et de la recherche: http://dpesr.mesr.fr/news.htm Les coordonnees des rectorats pour envoyer les dossiers sont a l'adresse: http://www.education.gouv.fr/syst/acad.htm Voir aussi les textes relatifs a la qualification des Professeurs (5 ans d'activites professionnelles peuvent etre pris en equivalence d'un habilitation a diriger les recherches ["HDR"]) Le serveur de l'ABG continue d'assurer la veille du concours et de se tenir a l'ecoute de vos questions: http://www.abg.asso.fr/concours/universites.html +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ANNEXE II : profils --------- Poste de Professeur ******************* 1. Biochimie generale et metabolique (64 eme section) Profil pedagogique ------------------ Le candidat devra pouvoir prendre en charge dans les 3 cycles universitaires plusieurs modules dans les domaines de - la biologie structurale - l'enzymologie - le metabolisme et la bioenergetique Profil de recherche ------------------- Le candidat devra s'integrer dans l'un des laboratoires de recherche associes a l'universite de la Mediterranee. Il developpera une activite de recherche en relation avec les thematiques et les techniques deja presentes dans les laboratoires. Un projet presentant une synergie avec le profil pedagogique, par exemple prenant en compte les projets proteomes, la spectrometrie de masse ou l'analyse fonctionnelle des genomes, serait appreciee. --------------------- ----------- Postes de Maitre de conference ****************************** 2. Genetique procaryote ou genetique eucaryote L'enseignement de la genetique procaryote et eucaryote tient une tres grande place dans le cursus des licences et maitrises de Biochimie et biologie cellulaire enseignees a la faculte des Sciences de Luminy: modules de genetique procaryote, genetique eucaryote, biologie moleculaire procaryote et eucaryote dans chacune des licences et maitrise, et les M4 de genetique et M4 de microbiologie dans chacune des maitrises. Tous ces enseignements forment un ensemble integre. L'enseignant concerne devra etre capable d'assurer des travaux diriges et des travaux pratiques dans l'une de ces displines. Par ailleurs, la genetique est un des axes forts de recherche de la faculte, dans des unites soutenues par le CNRS. Le candidat retenu devra effectuer sa recherche dans l'un des laboratoires ou sont developpees ces thematiques. 3. BioInformatique ( 64 et 65 eme sections) Profil pedagogique ------------------ Enseignements theoriques et pratiques en bioinformatique dans les differentes filieres de la biologie, avec une majorite de service effectues ay DEUG B. En premiere annee, il s'agit d'une initiation a l'outil informatique, l'esprit etant de montrer les possibilites existantes en traitement de texte (WORD), tableur (EXCEL), et gestion de base de donnees (ACCESS). En deuxieme annee (mise en place 1997-1998), il est prevu une partie langage de programmation structuree, une partie utilisation des serveurs Web, l'initiation comportant la realisation d'un mini-projet. Em maitrise (avec glissement progressif vers la licence), les enseignement porteront sur le traiteement de l'information en biologie, centre sur l'analyse de sequences genomiques: - recherche de similarite dans les banques - alignement deux a deux et alignement multiples - connaissance des matrices de substitutions (PAM, Blosum) Profil Recherche ---------------- Le candidat s'integrera dans l'un des laboratoires associe a l'universite de la Mediterranee (IBSM, IBDM ou CIML). Le travail de recherche se situera a l'interface du traitement des donnees biologiques et de la validation experimentale des predictions obtenues a partir de l'analyse des donnees. De ce fait, le candidat sera aussi un experimentateur, ce implique qu'il possede une double formation allie a un doctorat et/ou un post-doctorat tourne vers l'experimentation biologique. Un projet de recherche dans le domaine de l'analyse fonctionnelle et informatique des genomes (eucaryotes ou procaryotes) serait apprecie. Le projet s'integrera dans les thematiques deja presentes dans le laboratoire d'accueil. 4. BioInformatique (64 et 65 eme sections) Profil pedagogique ------------------ Le titulaire de ce poste aura un role determinant dans la mise en place d'un nouvel enseignement d'ingenierie bioinformatique axe sur l'analyse des sequences genomiques. Une familiarite avec le monde de la recherche industrielle en biotechnologie est desirable. Le candidat aura la charge de l'enseignement des techniques de bio-mathematique, de biostatistique et d'informatique particulieres a ce domaine: - approche bayesienne et modele de Markov - Programmation dynamique et methodes de phylogenie moleculaire - algorithme d'exploration des bases de donnees - identification des motifs fonctionnels et structuraux Profil Recherche ---------------- Elle se developpera au sein du laboratoire "information structurale et genetique" (http//:igs-server.cnrs-mrs.fr) dans un domaine directement lie aux themes d'enseignement cites plus haut, afin d'en garantir la qualite et de l'adapter aux evolutions rapides du domaine. Le candidat trouvera dans le laboratoire IGS l'infrastructure et les moyens qui lui seront necessaires. From owner-acedb@net.bio.net Tue Dec 30 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!195.99.66.215!news-feed1.eu.concert.net!btnet-peer!btnet!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: Martin Trick Newsgroups: bionet.software.acedb Subject: Bioinformatics Position at John Innes Centre Date: Wed, 31 Dec 1997 16:14:04 -0800 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 33 Message-ID: <34AADFCC.10FDA41D@bbsrc.ac.uk> NNTP-Posting-Host: pc0419.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.03 [en] (Win16; I) John Innes Centre Brassica Genome Bioinformatics As advertised in New Scientist (6/12/97, p78), applications are invited for a position immediately available at the John Innes Centre, Norwich UK in Brassica Bioinformatics. The successful candidate will curate and further develop a Brassica genome database, funded by the UK BBSRC UKCropNet initiative (http://synteny.nott.ac.uk). The database is currently using ACEDB 4.5. A key aim is to integrate genetic data from Brassica which can be integrated with that from the closely related Arabidopsis genome. A degree in a biological subject with a strong background in genetics is required, together with an interest and aptitude in applying database methods to facilitate genome research. Experience of any of UNIX, ACEDB, Perl or Java would be an advantage. The post is available for approximately two years and will be appointed between £13,860 and £16,500 (Band 7), at a level depending on qualifications and experience. For further information please contact Martin Trick (tel: +44 1603 452571 or e-mail: martin.trick@bbsrc.ac.uk) or see www.uea.ac.uk/nrp/jic/b90trick.htm. For written particulars and an application form, please contact the Personnel Officer (jicpers@bbsrc.ac.uk), John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH, quoting reference number BR/330. The closing date for application forms will be 5th January 1998. Interviews are expected to be held February 5-6, 1998. The John Innes Centre is a registered charity (No. 511709) grant-aided by the Biotechnology and Biological Sciences Research Council and is an Equal Opportunities Employer. From owner-acedb@net.bio.net Wed Dec 31 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Jan 1998 02:00:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801011000.CAA19542@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.