From owner-acedb@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 1 Dec 1994 02:00:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 337 Sender: daemon@net.bio.net Distribution: world Message-ID: <199412011000.CAA27756@net.bio.net> Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions on how to subscribe/unsubscribe will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. Any text placed on the Subject: line of your message will be ignored, so be sure to put the "help" command in the body of the message. If you need personal assistance, a BIOSCI staff member can be contacted at either of the following addresses. Please contact the address designated for your location. Support Address Location --------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim **** SEARCHING BIOSCI ARCHIVES **** The easiest way to search the BIOSCI archives is to use gopher software and connect over the Internet to net.bio.net, the U.S. BIOSCI computer. We maintain three indexes which are searchable from the main gopher menu on net.bio.net: (1) an index of all BIOSCI postings; (2) an index of individual journal article references from the Table of Contents postings on the BIO-JOURNALS newsgroup; and (3) an index of BIOSCI users including regular mail and e-mail addresses, phone/FAX numbers, research interests, and newsgroup participation. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). Finally, the BIOSCI archive files are accessible by anonymous FTP to net.bio.net [134.172.2.69] in the directory pub/BIOSCI. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS, waismail, and gopher access. If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 15-05-93 for 15 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 15-05-93, not 15-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-acedb@net.bio.net Sun Dec 04 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!futures.wharton.upenn.edu!cook33 From: cook33@futures.wharton.upenn.edu (DARA A. COOK) Newsgroups: bionet.software.acedb Subject: Electronic Books Date: 5 Dec 1994 21:37:10 GMT Organization: University of Pennsylvania Lines: 61 Message-ID: <3c0166$6ti@netnews.upenn.edu> NNTP-Posting-Host: futures.wharton.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] We are University of Pennsylvania students doing a marketing project for electronic books and would appreciate if you would take a few minutes to read the following short description and answer the following questions. POCKET-SIZED ELECTRONIC BOOK A pocket-sized electronic book allows you to search and retrieve instant information. It is available in two different versions: Merriam-Webster Dictionary and Holy Bible King James Version. On the back of each electronic dictionary or Bible, there is an open slot to insert an additional cartridge. Adding an additional cartridge allows you to search and retrieve instant information from two books at the same time. For example, If you are reading a passage from the electronic Bible and you found a word confusing, you can find the meaning of that word by inserting the dictionary cartridge into the back of the electronic Bible. There are many cartridge titles to choose from, including food guides, games, encyclopedias, medical manuals as well as a host of other titles. The prices of the cartridges range from $20 to $60 each. The pocket-sized electronic book is portable, convenient and easy to use. What do you think about this concept? How much do you think it costs? Would you purchase it this price? Where would you find it? How would you use it in your everyday life? Think about the last time you needed to correctly spell a word, find a definition or synonym, or pronounce a word. How did you get the information? What, if any, are other products that you would use instead of this electronic book ? THANK YOU!!!!!!!! From owner-acedb@net.bio.net Mon Dec 05 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!yuma!usenet From: mferguso@agsci.colostate.edu (Martin Ferguson) Newsgroups: bionet.software.acedb Subject: new acedb server Date: 6 Dec 1994 22:41:53 GMT Organization: csu Lines: 77 Distribution: world Message-ID: <3c2pbh$2cbf@yuma.ACNS.ColoState.EDU> Reply-To: mferguso@agsci.colostate.edu NNTP-Posting-Host: klab.agsci.colostate.edu From dknudson Tue Dec 6 14:46 MST 1994 Date: Tue, 6 Dec 1994 14:45:44 -0700 (MST) From: "Dennis L. Knudson" Subject: Mosquito Genomics WWW To: Michael Gottlieb , Stephanie James , "Major Scott W. Gordon" , Anthony James , Administration , laugh@lamar.ColoState.EDU, rsmith@vines.ColoState.EDU, AIDL Faculty , brm4@cidvbi1.em.cdc.gov, jcarlson@ops.AgSci.ColoState.EDU, tabachni@uwyo.edu, wcb4@lamar.colostate.edu Cc: Martin Ferguson Mime-Version: 1.0 ********************* Announcment ***************************** Mosquito Genomics WWW Server URL http://klab.agsci.colostate.edu/ ********************* Announcment ***************************** This server is under continuing construction. The Mosquito Genomics WWW Server provides access to mosquito genomics and links to other genomics WWW servers, to the National Center for Biotechnology Information, and to other WWW servers around the world. Mosquito Genomics Aedes aegypti Anopheles gambiae Aedes aegypti Genome Database (AaeDB) About AaeDB: The purpose of this database is to collate both the genetic and physical chromosome mapping data available for the Aedes aegypti mosquito. The information therein is made available to the Internet community through this World Wide Web (WWW) Server. The database is running on ACeDB v3.0, a relational database developed by the C. elegans community. The nph-acedb software is being used as the gateway to our WWW server. You may browse or query the database, but you will need a Mosaic reader (X version 2 or higher) that is capable of forms fill in and spawning external viewers such as ghostview for full functionality. This work and WWW are sponsored by the MacArthur Foundation Researcg Network on the Biology of Parasite Vectors, National Institutues of Health - National Institute for Allergy and Infectious Diseases, and others. About the AaeDB Curators: The Aedes aegypti database is maintained in the laboratory of Dennis Knudson, Department of Entomology at Colorado State University, Ft. Collins, CO, USA 80523. This lab is member of CSU's Arthropod-borne Infectious Disease Laboratory (AIDL), a MacArthur Foundation Network on the Biology of Parasite Vectors member. In due course, the AIDL faculty will be found by clicking here. The database curators are Dennis Knudson and Martin Ferguson. Who can be reached via e-mail at aaedbmgr@klab.AgSci.ColoState.EDU. In addition, Dave Severson (dave@aedes.VetSci.Wisc.EDU) is a co-curator of the genetic mapping data. This WWW server is maintained by Dennis L. Knudson (dknudson@klab.AgSci.ColoState.EDU) From owner-acedb@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!newsxfer.itd.umich.edu!gatech!news-feed-1.peachnet.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: Macace again Date: 8 Dec 1994 09:27:38 GMT Organization: University of Georgia, Athens Lines: 34 Message-ID: <3c6jia$6t7@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi all again: We're working on an acedb for peanuts. Not in production yet. While UNIX is our production environment, we're trying to get a macace version running too. To this end, I got the 21bDB macace from genome.lbl.gov, which uses a 3.0 version of the code. I added classes, models and tags for our data, and when it read in my models.wrm it complained of "unknown item xxxxxx", referring to one of my tags. Altering the order of some of the contents of models.wrm and tags.wrm made it seem as though my tags were not known to the database, although I had reinitialised it. But I thought "better start from scratch". So I did. This time, all I did was add my tags to tags.wrm (starting at 3001), and didn't touch anything else. This time, whether or not I removed the distribution ACEDB.wrm from the database folder, I got a startup error something like "tag 3001 (_Archived) tried to overwrite tag 3001 (NULL key)". "Archived" is the name of my tag. Earlier, in the folly of my youth, I asked about recompiling macace, and was gently reminded that one of the strengths of acedb is precisely that you *don't* need to recompile if you're only adding data and models. But now I have no guesses as to what is causing the above behaviour. Any ideas? As usual, thanks for your time. The acedb community is quite self-supportive! -- Paul Brunk, ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Fri Dec 09 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uunet!utcsri!utnut!torn!uunet.ca!uunet.ca!interlog.com!ivor.interlog.com!ivor From: ivor@interlog.com Newsgroups: bionet.software.acedb Subject: The SIMTEL for Sale - 2 CDs with the BEST Shareware. Date: Fri, 9 Dec 1994 22:39:10 EST Organization: Interlog Internet Services -Voice (416) 975-2655 -Data 515-1414 Lines: 24 Message-ID: NNTP-Posting-Host: ivor.interlog.com X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] The SIMTEL Archive for Sale - 2 CD-ROM disks of Shareware The Largest Shareware Archive - released September 1994 Only $39.95 US or $49.95 CAN - 10,000 MS-DOS and Windows shareware programs on 2 disks. - Disks contain utilities, communication programs, BBS's editors, documentarion, programs for the handicapped, genealogy, database software, animation software, BBS programs, books and documentation, communication packages, etc. - Many programs contain source code. - A wealth of programming tools for many languages including C, Assembly and Basic (there's a great 32 bit C++ compiler). - There is a huge number of programs for Windows including the Telix version for Windows. - There are no games. - User friendly browser. - BBS Discription files included. If you are interested, please E-Mail: ivor@interlog.com for ordering information. From owner-acedb@net.bio.net Sun Dec 11 22:00:00 1994 Newsgroups: bionet.software.acedb Path: biosci!agate!howland.reston.ans.net!pipex!uunet!olivea!charnel.ecst.csuchico.edu!csusac!csus.edu!netcom.com!karis From: karis@netcom.com (Robert Karis) Subject: Re: Electronic Books Message-ID: Organization: NETCOM On-line Communication Services (408 261-4700 guest) X-Newsreader: TIN [version 1.2 PL1] References: <3c0166$6ti@netnews.upenn.edu> Date: Sun, 11 Dec 1994 07:13:30 GMT Lines: 48 DARA A. COOK (cook33@futures.wharton.upenn.edu) wrote: : We are University of Pennsylvania students : doing a marketing project for electronic books and : would appreciate if you would take a few minutes : to read the following short description : and answer the following questions. : POCKET-SIZED ELECTRONIC BOOK (description deleted) : There are many cartridge titles to choose from, including food guides, : games, encyclopedias, medical manuals as well as : a host of other titles. The prices of the cartridges range from $20 : to $60 each. The pocket-sized electronic book is portable, : convenient and easy to use. : What do you think about this concept? I would like it if the books were available on PCMCIA cards, so we could use them on palmtops or noteboooks. : How much do you think it costs? $200? How about $100 and make your money on the software? The price of the cartridges sounds ok. Could read-only PCMCIA cards be made for the same price? : Would you purchase it this price? No, I don't want to carry around both a notebook and another electronic gadget. : Where would you find it? Campus bookstore...Whole Earth Access : How would you use it in your everyday life? I would want reference books. : Think about the last time you needed to correctly : spell a word, find a definition or synonym, or pronounce : a word. How did you get the information? Paper dictionary, even though I have the American Heritage dictionary in my desktop computer. : What, if any, are other products that you would : use instead of this : electronic book ? Actually, what I need is a PCMCIA CDROM drive! : THANK YOU!!!!!!!! From owner-acedb@net.bio.net Mon Dec 12 22:00:00 1994 Path: biosci!GENOME.LBL.GOV!workshop From: workshop@GENOME.LBL.GOV (john mccarthy) Newsgroups: bionet.software.acedb Subject: ACEDB 1995 Conference and Workshop Date: 13 Dec 1994 09:59:20 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 237 Sender: daemon@net.bio.net Distribution: world Message-ID: <9412131759.AA11549@genome.lbl.gov> NNTP-Posting-Host: net.bio.net ACEDB 1995 CONFERENCE & WORKSHOP The 1995 ACEDB Conference and Workshop will be held May 14-27, 1995, at the Isis Oasis, a small retreat center in Geyserville, about 80 miles north of SanFrancisco in Sonoma County, California. We will have exclusive use of the entire retreat center, including the theater (for workstations and primary sessions), dining room, lodge, and other residential facilities. The main goal of the three day ACEDB Conference (May 14-17) is information exchange. It will feature tutorials (May 15), oral presentations, posters, on- line demonstrations, and discussions. The further goals of the ten day ACEDB Workshop following the conference (May 18-27) are code development and consolidation, database building, documentation writing, special interest group discussions, and long range planning. Since its introduction in 1991 for the C. elegans research community, ACEDB has been adopted by a number of diverse organizations and individuals to maintain and distribute data on over forty different genomes, including human, bovine, Drosophila, yeast, mycobacteria, Arabidopsis, grains, trees, and fungi. ACEDB has become one of the most successful examples of collaborative software for genome research. Annual meetings have been a key ingredient in building and maintaining this growing international community of ACEDB users, curators, and developers. PARTICIPANTS & SELECTION PROCEDURES Everyone who wants to attend the Conference or Workshop should submit a a pre-registration form (included at the end of this announcement) and a brief (one page) description of how they would like to participate. We may need to limit the number of participants from each organization, particularly for the Workshop. Contributions may include presentations (oral, poster, or computer demos), giving tutorials, developing new databases, upgrading existing databases, programming, writing documentation, or simply discussing your own work as it relates to ACEDB. The program committee will select 35 workshop participants plus an additional 30 or 40 conference participants on the basis of these descriptions, trying to balance different types of contributions and representation from different organizations. IMPORTANT DATES February 1 Pre-registration & final version of participation descriptions due March 1 Participants notified about which parts they will be able to attend, how much financial support they can expect, and room forms April 1 Final WWW versions of abstracts due for posters, presentations, etc. Short descriptive self-introductions due for all participants Final registration, housing and room requests due COSTS AND FINANCIAL SUPPORT Like previous ACEDB workshops, we have selected a site that will keep our costs low, and we are trying to secure computer equipment from vendors that we can use for the conference and workshop without charge. Local genome research organizations (including Stanford, LBL, UCB, and USFS) are contributing staff time and equipment as well as helping with local arrangements. We hope to secure funding from the Department of Energy's Human Genome Program, the National Center for Human Genome Research at NIH, the National Science Foundation, and the Department of Agriculture's Plant Genome Program to support some of our basic costs plus support for some people who might not otherwise be able to participate -- especially graduate students and post-docs. Otto Ritter also hopes to secure European Community funding for some European participant scholarships. If we can secure funding to underwrite our infrastructure costs, the basic costs for participants may be as low as $30 per day for meals and $25 to $50 per day for triple, double, or single rooms. ACEDB CONFERENCE, May 14-16 --------------------------- Our agenda is still evolving. We welcome your suggestions. The current version is as follows: Sun 14, 4-9pm Arrival, Reception Mon 15 TUTORIALS (potential topics) GENERAL Introduction to ACEDB Query Tools and Language Map Displays Sequence Displays & Analysis CURATORS Database Definition (models) Data Loading & Maintenance (.ace files & tools) Customizing User Help Lab Notebook Databases PROGRAMMERS Connections to External Software Client-server Front Ends Graphics Library Query and Database Subroutines ACEDB 95 CONFERENCE, Tues-Wed, May 16-17 ------------------------------------------------ These two days will be primarily devoted to formal presentations, a poster session, and special interest groups. Topics may include the following: Map Display tools Sequence Display and analysis Laboratory Information Management Community archival databases Data distribution and exchange Database interoperability ACEDB and the World Wide Web Sharable Software Components Connecting ACEDB to other software Non-biological ACEDB databases New Features and Future Plans ACEDB WORKSHOP, May 18-27 -------------------------- Like last year's successful workshop, each day will be organized around a particular topic, with plenary presentations in the morning and working groups in the afternoon or evening. Some days will have afternoons off with evening sessions, while others will have afternoon rather than evening sessions. We will continue to meet on Saturday, May 20, but take off Sunday, May 21 for rest and recreation. We will conclude with a wrap-up session Saturday morning, May 27. Possible daily workshop themes include the following: Thu: Models & Data Definition Fri: Data Import & Export (.ace files, TACE, etc.) Sat: Query Language and Tools (including Table-Maker) Sun: Off Mon: Map Displays Tue: Sequence Displays Wed: Communicating with External Software Thu: Client-Server Architecture Fri: Project Coordination Sat: Assessment, Open Questions, Future Plans POTENTIAL SPECIAL INTEREST GROUPS Client-Server Archtecture(s) Map Displays Sequence Tools Lab Databases Archival Databases Query Language and Tools Documentation 1995 CONFERENCE AND WORKSHOP COMMITTEES The local organizing committee includes the following individuals: John McCarthy (LBL) Frank Eeckman (LBL, author of MacACE) Suzanna Lewis (U.C. Berkeley, author of flydb) Mike Cherry ((Saccharomyces Genome Database, Stanford)) Brad Sherman (U.S. Forest Service Tree Genome Database Project, Albany) The Program Committee currently includes the above, plus the following: Richard Durbin (Sanger Centre, ACEDB author) Jean Thierry-Mieg (CNRS, Montpellier, ACEDB author) Sam Cartinhour (USDA National Agricultural Library) Jaime Prilusky (Weizmann Institute) Otto Ritter (DKFZ, Heidelberg. IGD project) INTERNET AND WORLD WIDE WEB OUTREACH Prior to the Conference and Workshop, we plan to use WWW documents to publicize our plans, share statements of interest from individual participants, distribute various materials, and solicit input for the final agenda. During and after the Workshop, we plan to use WWW to summarize presentations and discussions, provide access to demonstrations, and share written results. A growing number of conferences are finding this to be a very effective mechanism. Our web home page is currently http://genome.lbl.gov/ace95.html. INFORMATION We are distributing this announcement to individuals who have already expressed an interest in the workshop and the ACEDB newsgroup (acedb@net.bio.net) [and conferences]. We will also send shorter announcements to the DoE Human Genome Newsletter and CABios. Suggestions for other places to announce the conference and workshop would be welcome. For further information, send email to ace95@genome.lbl.gov PRE-REGISTRATION In order to give our program committee a rough idea of how many people may wish to attend the tutorials, conference, and workshop, please fill out information following colons (:) and other items below, and return by February 1 to ace95@genome.lbl.gov. ====================== cut here ======================================= ACEDB 95 Conference and Workshop -- Pre-registration Form Name: Organization: Email Address (if not return address): Put "X" in brackets [ ] for each part in which you wish to participate: [ ] Reception and tutorial sessions (May 14-15) [ ] Two day ACEDB 95 Conference (May 16-17) [ ] Ten day ACEDB 95 Workshop (May 18-27) [ ] Not sure whether I can participate [ ] Cannot participate, but please keep me on the ACE95 mailing list Please use the space below to describe what contributions you would like to make to one or more parts of this year's ACEDB 95 Conference and Workshop. We would like someone from each participating organization to prepare one poster that summarizes its work. We also want to post abstracts and and as many posters as possible on the World Wide Web prior to the conference. You may resubmit this section any time prior to February 1, but please return the above information as soon as possible. From owner-acedb@net.bio.net Mon Dec 12 22:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: "name read" Date: 13 Dec 1994 11:48:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <199412131805.AA13462@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net a suggestion from a discussion in one of the IGD courses: if one ACEDB is shared by (several) people not having write access to the database they cannot store a keyset (the result of possibly longer work) and continue on it in the next session. suggestion: in the KeySet menu, analgous to "name dump" there should be a function "name read". It reads the contents of the .ace file ~/myKeySet and makes it the active KeySet. It skips objects that do not exist in the database. The file ~/myKeySet can be generated by the "name dump" function. What do you think about that? Detlef ---------------------------------------------- Appendix: this code works, but is not nice. it should use ACEDB parsing routines and could work on lexiques directly to be faster. The KEYSET readKeySet(FILE* ksf) { KEYSET ks=0,kstmp; char classname[128]; char objname[256]; char queryt[384]; int i; kstmp=keySetCreate(); classname[0]='\0'; /* ignore first line */ while ((i=fscanf(ksf,"%s : %s",classname,objname))!=2 && i!=EOF); if (strcmp(classname,"KeySet")) { printf("expected class KeySet, but found %s. Abort reading\n",classname); return(0); }; while (fscanf(ksf,"%s : %s",classname,objname)==2) { sprintf(queryt,"FIND %s %s",classname,objname); kstmp=query(0,queryt); ks=keySetOR(kstmp,ks); }; keySetDestroy(kstmp); return(ks); } From owner-acedb@net.bio.net Tue Dec 13 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!news.bu.edu!olivea!charnel.ecst.csuchico.edu!waldorf.csc.calpoly.edu!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!unixg.ubc.ca!unixg.ubc.ca!swood From: swood@unixg.ubc.ca (Stephen Wood) Newsgroups: bionet.software.acedb Subject: Clone_Grid Date: 14 Dec 94 16:33:37 GMT Organization: The University of British Columbia Lines: 13 Message-ID: NNTP-Posting-Host: unixg.ubc.ca The Clone Grid tool is limited to 10 characters for the names of clones, while this limitation does not exist for naming a new clone using Alias-Rename-Delete. Thus clone names can be entered exceeding 10 characters (which may a convenient name) and then the data cannot be mapped onto a Clone_Grid. Can the size of the clone field be easily changed to exceed this 10 character limitation? Thanks, Stephen From owner-acedb@net.bio.net Tue Dec 13 22:00:00 1994 Path: biosci!GENOME.STANFORD.EDU!cherry From: cherry@GENOME.STANFORD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: Ace GUIs -- model and data files Date: 14 Dec 1994 10:41:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <199412141843.KAA21854@fafner.Stanford.EDU> References: NNTP-Posting-Host: net.bio.net Susan, You might want to check out the ACEDB FAQ: Please cite as: Sherman,B.K., ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993,1994, approx. 50K bytes. There are over 40 different database groups now using ACEDB for there information some are already doing conversions from ace to whatever. There are many "tags" of the models that can not be changed and that data must be associated before the displays will work. For example Map must be set for a Locus for the genetic maps to display that locus. A list of these "magic" tags was prepared at the last ACEDB workshop, some one on the list probably has it. Some of the references in the FAQ will explain this more. There is also a "programmers" type guide available, and mentioned in the FAQ. ACEDB is built on top of a graphics and database library so it is straight forward to extend ACEDB or produce new applications that read and write into an ACEDB database. Mike From owner-acedb@net.bio.net Tue Dec 13 22:00:00 1994 Path: biosci!rutgers!uwm.edu!msunews!netnews.upenn.edu!netnews!susan From: susan@central.cis.upenn.edu (Susan Davidson) Newsgroups: bionet.software.acedb Subject: Ace GUIs -- model and data files Date: 14 Dec 94 13:11:32 Organization: /home/susan/.organization Lines: 43 Distribution: bionet Message-ID: NNTP-Posting-Host: central.cis.upenn.edu I have some questions about how closely AceDb graphical user interfaces are tied to the data and model files. For example, we have downloaded the sample Acedb at ncbi.nlm.nih.gov, which comes with a lovely gui that lets you point and click on regions of chromosomes. Suppose I am not really interested in the sample data this comes with, and instead want to view my own data with that interface. My questions are: 1. I presume that I can delete the existing data, and load in my own data as long as it conforms to the existing model definitions (schema). Correct? 2. How *closely* does the model definition of my new data have to conform? That is, I presume that the existing schema could be modified somewhat without having to alter the code for the gui's (otherwise the gui's are very brittle). Is there some way of knowing what part of the model definitions must remain stable? 3. Is there a "library" of such gui's and the requirements they place on the model definition files? I am interested in this because we are looking at translating data "into" and "out of Ace" format. Getting data "out of" Ace format is useful for integrating data from Acedb databases with data from other sources, such as relational and ASN.1. Getting data "into" Ace format will allow us to use the great user interfaces that have been developed in connection with Ace and still maintain the data in our own local databases. If you are familiar with this part of Ace, or know of a document and its source that would be helpful, please let me know. Thanks, Susan Davidson From owner-acedb@net.bio.net Tue Dec 13 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!trane.uninett.no!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: "name read" Date: 14 Dec 1994 09:54:09 -0000 Lines: 8 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3cmfc1$28b@mserv1.dl.ac.uk> Original-To: D.Wolf@dkfz-heidelberg.de We have already introduced exactly this idea into our working code. There is a menu item "Import Keyset" in the keyset display window menu that lets you read in a keyset from a file without write access. If the file contains references to objects that do not exist in the database then it tells you how many of these there were. As Detlef says, it is a useful function. Richard From owner-acedb@net.bio.net Wed Dec 14 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!news.kth.se!kiev.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: Ace GUIs -- model and data files Followup-To: bionet.software.acedb Date: 15 Dec 1994 08:11:09 +0100 Organization: Biochemistry, KTH, Stockholm Lines: 25 Sender: staffan@biochem.kth.se Distribution: world Message-ID: <3coq6d$g1g@kiev.physchem.kth.se> References: <199412141843.KAA21854@fafner.stanford.edu> NNTP-Posting-Host: kiev.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Keywords: magic tags, AboutDB In article <199412141843.KAA21854@fafner.stanford.edu> cherry@GENOME.STANFORD.EDU (Mike Cherry) writes: [in reply to article from Susan Davidson] > .. some stuff deleted .. >There are many "tags" of the models that can not be changed and that >data must be associated before the displays will work. For example Map >must be set for a Locus for the genetic maps to display that locus. A >list of these "magic" tags was prepared at the last ACEDB workshop, >some one on the list probably has it. Some of this is available in AboutDB, the ACEDB database: Check out the class TagInfo for information on specific tags. The help is a bit scanty (non-existent, really) but changing tags that are used in the code (have the tag SourceCode in AboutDB) should maybe be avoided. Lots of experimentation recommended! Unfortunately querying in TagInfo class doesn't work (and also you cannot display the model), probably because of a lingering bug in the web server. AboutDB is available through the web at URL: http://kiev.physchem.kth.se/AboutDB.html /staffan From owner-acedb@net.bio.net Thu Dec 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!hookup!swrinde!howland.reston.ans.net!spool.mu.edu!uwm.edu!lll-winken.llnl.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 16 Dec 1994 00:07:33 GMT Organization: Dendrome, A genome database for forest trees Lines: 1141 Approved: news-answers-request@MIT.Edu Message-ID: <3cqlo5$eut@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.pswfs.gov Summary: Frequently Asked Questions about finding and getting started with the database system ACEDB. ACEDB is used to collect information regarding the molecular biology of the genome. Xref: biosci bionet.software.acedb:510 news.answers:28711 Archive-name: acedb-faq Last-modified: 12/15/94 Version: 1.17 Common Questions, with Answers, about ACEDB. ---------------------------------------------------------------------- Q0: What is ACEDB? Q1: What is the current version of ACEDB? Q2: What hardware/software do I need to run ACEDB? Q3: Where can I get ACEDB? !Q4: What ACEDB databases exist? Q5: What written documentation exists for ACEDB? Q6: Where can I find further information about ACEDB? Q7: How should ACEDB be cited? Q8: Is ACEDB object-oriented? Q9: What's all this about Gopher|WAIS|ftp|WWW|URL ... Q10: How can I get on/off the ACEDB announcements mailing list? !Q11: When and where is the next ACEDB Workshop? Q411: Who prepared this document & where is the current version? Questions marked with + are new, those with ! have substantially changed answers. ---------------------------------------------------------------------- Q0: What is ACEDB? A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [see Q4]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage -missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions ---------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: [This answer refers to the software not the C. elegans data.] Currently there are two threads of the ACEDB kernel: the 2.x series which represents the C. elegans project under the tutelage of Richard Durbin, and the 3.x series from Jean Thierry-Mieg. However, the differences in the code are slight and the two authors committed to a single kernel at the ACEDB workshop in July, 1994. The most recent release is an experimental version 3.3 which is available from the repositories. A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q10. Return to List of Questions ---------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: Unix and X11: Sun/SunOS 4.x Sun/Solaris DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series PC 386/486 with Linux (free Unix) [note from Jeff Bryer, jbryer@darwin.mbb.sfu.ca] I just installed up Linux yesterday and today spent the many hours to compile in the C. elegans data for ACEDB v2.0 So to save other people the trouble of doing the same the entire package ACEDB for Linux 2-10 is available on trog.mbb.sfu.ca in /pub/acedb as linux.2_10.tar.Z The data was compiled in on a 486DX-33 with 16MBs of RAM running Linux 1.1.18 (Slackware 2.0.0 distribution) and a 32MB swap device (and it chugged away for a couple hours chewing up all 16MBs and half the swap space). File size is about 73MBs uncompressed, 26MBs compressed. This is based on the ACEDB v2.0 port for Linux that Ken Clark (ken@darwin.mbb.sfu.ca) did. There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu MSDOS/Windows/NT: A port to NT is rumored to be in the works. Macintosh: [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a decent color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. To retrieve the software see Q3. For cost savings, a combination of a high-end Intel platform with Linux appears very attractive. [Though the port does not seem robust, yet --bks] Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems SPARCstation II, and users can interact using Macintoshes and PC-clones by using X11 implementations for the personal computers and a LAN. X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions ---------------------------------------------------------------------- Q3: Where can I get ACEDB? A3: All the files are available in the following public access accounts (anonymous ftp sites) accessible via Internet: lirmm.lirmm.fr (193.49.104.10) in pub/acedb cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb. MacAce is available from: genome.lbl.gov (131.243.224.80) in pub/macace cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb/macace Linux; ACEDB version 2.0 for Linux 2-10: trog.mbb.sfu.ca /pub/acedb as linux.2_10.tar.Z A typical session would be: ftp ncbi.nlm.nih.gov login: anonymous password: your email address cd repository/acedb/ace3 binary ls get README_3 get NOTES get INSTALL get bin.sparc.3.0.tar.Z quit Return to List of Questions ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alphabetic order by Database name. Curators, submit changes as new paragraphs.--bks] Database : AaeDB Species : Aedes aegypti Last_update : December 1994 ACEDB_version : 3.0 http://klab.agsci.colostate.edu/index.html PI : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Contact : aaedbmgr@klab.agsci.colostate.edu Database : AAnDB-1.0 Species : Aspergillus nidulans PI : Leland Ellis Last_update : February 1994 ACEDB_version : 3.0 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : AAtDB Species : Arabidopsis thaliana Current version : 3-4 Last_update : November 1994 Curator : John Morris Contact : curator@frodo.mgh.harvard.edu Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x Availability : Macintosh version in /aatdb/MacAAtDB directory URL : gopher://weeds.mgh.harvard.edu/ URL : http://weeds.mgh.harvard.edu:80/index.html URL : http://probe.nalusda.gov:8300/ Database : ABtDB-1.0 Species : Bovine, Bos taurus ACEDB_version : 3.0 extended PI : Leland Ellis Last_update : February 1994 Contact : leland@stralight.tamu.edu URL : http://keck.tamu.edu/ibt.html Comment : defunct, See AGsDB Database : AboutDB Curator : Staffan Bergh PI : Staffan Bergh Subject : ACEDB itself (Is this meta-meta-metadata) ACEDB 3.0 Contact : staffan@biochem.kth.se URL http://kiev.physchem.kth.se/AboutDB.html Database : ACeDB Species : Caenorhabditis elegans Current version: 2-10 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@mrc-lmb.cam.ac.uk Contact : mieg@kaa.crbm.cnrs-mop.fr Last_update : May 1994 DataBase : AceMap Species : Homo sapiens (Mus musculus under development) Focus : Physical mapping of human chromsome X and 21 ACEDB_version : 3.0 Curator : Hugues Roest Crollius PI : Hans Lehrach Availability : beta release of the X chr. data/models by anonymous ftp to ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap. Get the README file in the directory above. Contact : hrc@gea.lif.icnet.uk (Hugues Roest Crollius) ICRF, Lincoln's Inn Fields London, UK. Last_update : August 94 Database : AGsDB A Genus species Database Species : Aspergillus nidulans Species : Neurospora crassa Species : cow w/ human anchor loci Species : cotton (demo) Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast PI : Leland Ellis Curator : Leland Ellis Last_update : March 1994 ACeDB_version : 3.0 (beta still), with extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe) yeast); interacting loci via defined Interactions for each locus Models : as of 3.13.94 Data : as of 3.13.94 Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux (ducoux@moulon.inra.fr). URL : http://keck.tamu.edu/ibt.html Contact : leland@straylight.tamu.edu Database : ChlamyDB Species : Chlamydomonas PI : Elizabeth Harris Contact : chlamy@acpub.duke.edu Availability : ChlamyDB 1.0, using ACEDB 3.0, is now on WWW and gopher (probe.nalusda.gov). Complete version using ACECB 3.3 will be available soon by ftp. URL : http://probe.nalusda.gov:8300 Last_update : 25 Oct, 1994 Database : CottonDB Species : Gossypium hirsutum (cotton) PI : Russell J. Kohel USDA-ARS Southern Crops Research Laboratory Route 5, Box 805, College Station, Texas 77845 Curator : Gerard R. Lazo Curator : Sridhar Madhavan Last_update : July, 1994 ACEDB_version : 3.0 Contact : rjk0339@zeus.tamu.edu (Russell Kohel) Contact : lazo@genome.tamu.edu (Gerard Lazo) Availability : still under construction Phone : 409-260-9311 Fax : 409-260-9333 Database : CSNDB Focus : Cell Signalling Molecules and Interactions Contact : Takako Igarashi National Insitute of Health Sciences Division of Chem-Bio Informatics Setagaya-ku, Tokyo, Japan 158 taka@nihs.go.jp Database : EcoDB Species : E. coli PI : Staffan Bergh Contact : staffan@biochem.kth.se Availability : Proposed Last_update : Aug. 1994 Database : 11DB Species : Homo sapiens Focus : Physical mapping of chromosome 11 Availability : under development Curator : Benedict Arnold PI : Peter Little Contact : Benedict Arnold Dept. Biochemistry, Imperial College, London, SW7 2AZ b.arnold@ic.ac.uk Database : The Encyclopaedia of the Drosophila Genome. Acronym : (none) Species : Drosophilidae (primarily D. melanogaster) Availability : MacFly/FlyDB-based distribution by ftp and CD-ROM due early 1995 Developer : Suzanna Lewis Contact : suzi@fly2.berkeley.edu Developer : Cyrus Harmon Contact : sly@fly2.berkeley.edu Developer : Edward Welbourne Contact : eddy@gen.cam.ac.uk Curation : Data is provided by the collaborating organisations: Collaborator : The FlyBase Consortium, flybase@morgan.harvard.edu Collaborator : The Berkeley Drosophila Genome Project URL : gopher://fly.bio.indiana.edu:70+/11/Flybase Database : Flydb Species : Drosophila melanogaster Curator : Suzanna Lewis Contact : suzi@fly2.berkeley.edu Database : GrainGenes Species : Wheat, barley, oats, relatives Availability : Anonymous ftp from probe.nalusda.gov:pub/grains Availability : Gopher greengenes.cit.cornell.edu port 70 Availability : Gopher probe.nalusda.gov port 7002 Curator : David E. Matthews PI : Olin D. Anderson Contact : matthews@greengenes.cit.cornell.edu Contact : oandersn@wheat.usda.gov URL : gopher://greengenes.cit.cornell.edu/1/ Data_version : 1.3 Released : 12 Jan 1994 Based_on : acedb.1-10 Availability : See following WWW URL URL : http://probe.nalusda.gov:8300 Last_update : Feb. 1994 Database : human.c17 Species : Homo sapiens Availability : the database is under development Contact : lsprilus@weizmann.weizmann.ac.il Focus : mapping & sequencing of Human Chromosome 17 Based_on: acedb.3-0 Last_update : Jan. 1994 Database : IGD - the Integrated Genomic Database Species : Homo sapiens (later mouse and other mammalian species) Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter [ o.ritter@dkfz-heidelberg.de ] Curator : tba Description : IGD - the 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. 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 : Maize Species : Zea mays L. ssp. mays Focus : Maize genome Acedb_version : 1.9 FTP : probe.nalusda.gov, pub directory; anonymous ftp Comment : Maize is an acedb front end for the Maize Genome Database, MaizeDB, a SYBASE database. Comment : MaizeDB is updated daily and has WWW connectivity to external databases: GenBank (loci, alleles and probes), SwissProt (gene products) and the E. coli Stock Center (loci). Data : Major data categories: 4522 mapped loci (located to chromosome or better) including 684 mapped genes and 1423 mapped probed sites (gene candidates); 982 probes; 1850 map scores; 1533 gel patterns (Probe/Enzyme/Stock); 4231 stocks; 5105 Variations (alleles, DNA polymorphisms, rearrangements, etc); 465 phenotypes; 223 traits; 547 gene products; 5314 bibliographic references; 1979 persons with addresses. Gopher : host = teosinte.agron.missouri.edu, port = 70 Telnet : telnet teosinte.agron.missouri.edu login as guest, use password 'corncob' HTTP : http://teosinte.agron.missouri/top.html HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant Genome Database Comment : Genera is a software toolkit for creating and extracting data from Sybase databases; used to create MaizeDB and Worldwide Web connectivity. HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu Curator : Pat Byrne byrne@teosinte.agron.missouri.edu Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu Curator : Mary Polacco maryp@teosinte.agron.missouri.edu Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Curator : Christiane Fauron FAURON@GENE1.med.utah.edu Curator : Carolyn Wetzel cmwetzel@iastate.edu Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU Design : Stan Letovsky letovsky-stan@CS.YALE.EDU Design : Mary Berlyn mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 25 April 1994 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. PI : Staffan Bergh PI : Stewart Cole PI : Doug Smith Curator : Staffan Bergh Contact : staffan@biochem.kth.se Last_update : Apr. 1994 WWW : http://kiev.physchem.kth.se/MycDB.html ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb Database : PomBase Curator : Sean Walsh Curator : Marie-Adele Rajendream PI : Bart Barrell Species : Schizosaccharomyces pombe Contact : svw@sanger.ac.uk Contact : barrell@sanger.ac.uk Comment : Not yet available for distribution DataBase : Mousedb Species : Musculus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Michelle Kirby Curator : Rachael Selley 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 For other information contact Michelle Kirby. Contact : kirbym@har-rbu.mrc.ac.uk (or mkirby@hgmp.mrc.ac.uk) rselley@har-rbu.mrc.ac.uk MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD Last_update : October 1994 Database : RiceGenes Species : Rice (O. sativa) Availability : Anonymous ftp from probe.nalusda.gov:pub/rice Availability : Gopher nightshade.cit.cornell.edu port 70 Availability : Gopher probe.nalusda.gov port 7007 Curator : Edie Paul PI : Susah McCouch Contact : epaul@nightshade.cit.cornell.edu Release : ACEDB 1-10 Last_update : May 1994 Database : SacchDB Species : Saccharomyces cerevisiae Focus : Budding Yeast Genome Acedb_version : 2.0, MacAce FTP : genome-ftp.stanford.edu, not available yet. Comment : The database is in beta test by a small number of yeast labs. The WWW-ACEDB gateway version is currently available, see HTTP below. The Gopher server contains only the Olson restriction map information and views of the resulting Clone (Physical) Map. Data : Olson/Riles Physical Map, Mortimer Genetic Maps and Information, Sequences from GenBank, Gene/Clone associations using the Wash Univ. prime clone filters. Gopher : host = genome-gopher.stanford.edu, port = 70 HTTP : URL 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 : Fred Dietrich, dietrich@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Systems : Dan Mosedale, mosedale@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Last_update : 9 August 1994 Database : SolGenes Coverage: Solanaceae - tomato, potato, pepper Availability : Anonymous ftp from probe.nalusda.gov:pub/solgenes Availability : Gopher nightshade.cit.cornell.edu port 71 Availability : Gopher probe.nalusda.gov port 7006 Curator : Edie Paul PI : Steve Tanksley Contact : epaul@nightshade.cit.cornell.edu Release : ACEDB 3.0 Last_update : May 1994 Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz USDA-ARS Dept. of Soil & Crop Sciences Texas A&M University College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 E_mail : schertz@tamvm1.tamu.edu Curator : Najeeb U. Siddiqui Southern Crop Improvement Facility Crop Biotechnology Center Texas A&M University College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 E_mail : nus6389@tamsun.tamu.edu Last_update : July 1994 ACEDB_version : 3.0 Availability : Under Development Database : SoyBase Species : Soybeans Curator : Lisa Lorenzen PI : Randy Shoemaker Contact : lorenzen@mendel.agron.iastate.edu Phone : 515-294-0421 Fax : 515-294-2299 Last_update : Sept. 1993 Database : Sybace Species : Homo sapiens Creator : Detlef Wolf Comment : Custom software --ACEDB front-end to SYBASE data Contact : D.Wolf@dfkz-heidelberg.de See_also : IGD Database : TreeGenes Species : Forest trees Availability : alpha, contact curator ACEDB_version : 1-10 Curator : Bradley K. Sherman PI : David B. Neale Contact : Dendrome@s27w007.pswfs.gov Contact : bks@s27w007.pswfs.gov Contact : dbn@s27w007.pswfs.gov Last_update : March 1994 URL : gopher://s27w007.pswfs.gov/ URL : http://s27w007.pswfs.gov/ URL : ftp://probe.nalusda.gov/pub/trees Database : 21Bdb Species : Homo sapiens Focus : STS content mapping & sequencing of Human Chromosome 21 Availability : by request, via ftp, world-wide-web Based_on : acedb.1-10 plus moulon server URL : ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z URL : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy Contact : DFDavy@lbl.gov Contact : aggarwal@genome.lbl.gov Focus : STS content mapping & sequencing of Human Chromosome 21 PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng Last_update : Apr. 1994 Database : 22ace Species : Homo sapiens Curator : Ian Dunham Focus : Physical mapping of chromosome 22 PI : Ian Dunham Contact : Ian Dunham Sanger Centre Hinxton Hall, Cambs. UK. id1@sanger.ac.uk Database : VoxPop Species : Populus spp. Availability : contact curator Curator : Carl G. Riches PI : Reinhard F. Stettler Contact : cgr@poplar1.cfr.washington.edu Contact : STETTLER@coyote.cfr.washington.edu Last_update : Sept. 1993 Database : Xace Species : Homo sapiens Curator : Gareth Maslen Focus : Physical mapping of chromosome X PI : David Bentley Contact : Gareth Maslen Sanger Centre Hinxton Hall, Cambs. UK. glm@sanger.ac.uk Database : ? Species : Homo sapiens Focus : Physical mapping of human chromosome 6. Curator : Ioannis Ragoussis Availability : Unknown Contact : Guy's hospital Database : ? PI : Scott Chasalow Species : Potato Contact : Scottish Crop Institute, Dundee Last_update : Sept. 1993 Database : ? PI : George Murphy PI : David Flanders Species : Arabidopsis thaliana Contact : John Innes Center, Norwich, England Last_update : Sept. 1993 Database : ? Species : Homo Sapiens Focus : Physical and linkage mapping of chromosome 8 Availability : Curator : Stephen Wood PI : Stephen Wood Contact : Stephen Wood Dept. Medical Genetics University of B. C. Vancouver, B. C. Canada swood@unixg.ubc.cq Return to List of Questions ---------------------------------------------------------------------- Q5: What written documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000. Primary documents from the developers are: acedb -- A C. elegans Database: I. Users' Guide. acedb -- A C. elegans Database: II. Installation Guide. acedb -- A C. elegans Database: III. Configuration Guide. Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z And ftp://weeds.mgh.harvard.edu/acedb_doc The files are in tex and postscript. [I have had some difficulty printing these. Jean Thierry-Mieg suggests latex xxxx.tex, dvi2ps xxxx.dvi > xxxx.ps, lpr xxxx.ps.] You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angisturte.ps and angistute.hqx available by anonymous ftp at ncbi.hih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Return to List of Questions ---------------------------------------------------------------------- Q6: Where can I find further information about ACEDB? A6: There is a Usenet/Biosci conference titled bionet.software.acedb. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. All of the articles are archived on the gopher at net.bio.net. Mike Cherry has set up an ACEDB Developer's archive. For anonymous ftp use the hostname weeds.mgh.harvard.edu and look in the acedb_dev directory. If you wish to contribute you can put files in the incoming directory. Send a message to Mike (cherry@genome.stanford.edu) that you have put something in that directory then Mike will move it out for general access. For gopher you can connect to weeds.mgh.harvard.edu (132.183.190.21) and ... --> N. FTP Archives for Molecular Biology/ then --> M. ACEDB Developer's archive/ [N and M are integers which are subject to change.] The bionet.software. acedb.conference is archived and can be searched using WAIS. Here is a Gopher-style link to the WAIS archive. (This is also courtesy of Mike Cherry.): # Type=7 Name=ACEDB BioSci Electronic Conference Path=7/.index/acedb-biosci Host=genome-gopher.stanford.edu Port=70 The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: http://moulon.inra.fr/acedb/acedb.html for C. elegans data http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html http://moulon.inra.fr/acedb_conf.html (en francais) The Genome Computing Group, Lawrence Berkeley Laboratory has an anonymous ftp service at machine genome.lbl.gov (131.243.224.80) which contains: flydb - LBL's Drosophila Acedb-style database 21bdb - LBL's Human Chromosome 21 Acedb-style database querdb - LBL's query-language extensions to Acedb metadata - LBL's compendium of Acedb database schema variants macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to dataabases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier Jean Thierry-Mieg et al), and the Interated Genome Database project in Heidelburg (Otto Ritter, Detlef Wolf et al). Return to List of Questions ---------------------------------------------------------------------- Q7: How should ACEDB be cited? A7: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit, available by Anonymous FTP from ... Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions ---------------------------------------------------------------------- Q8: Is ACEDB object-oriented? A8: From the ACEDB User's Guide. A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions ---------------------------------------------------------------------- Q9: What's all this about Gopher/WAIS/ftp/WWW ... A9: These terms all refer to Internet protocols. An excellent introduction to the Internet is: _The Whole Internet User's Guide & Catalog_, by Ed Krol, O'Reilly & Associates, 1992. Or ask your system administrator to provide you with a gopher client or mosaic client and begin navigating on your own. URL is a Universal Resource Locator on the World-Wide Web (WWW). There are many free Internet browsers available that allow you to use an Internet connection and a URL to access services. Mosaic may be the most popular and it is available for Mac, PC or Unix via anonymous ftp from ftp.ncsa.uiuc.edu. Return to List of Questions ---------------------------------------------------------------------- Q10: How can I get on/off the ACEDB announcements mailing list? A10: To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb is on the mailing list. Return to List of Questions ---------------------------------------------------------------------- Q11: When and where is the Next ACEDB Workshop? The 1995 ACEDB Conference and Workshop will be held May 14-27, 1995, at the Isis Oasis, a small retreat center in Geyserville, about 80 miles north of SanFrancisco in Sonoma County, California. We will have exclusive use of the entire retreat center, including the theater (for workstations and primary sessions), dining room, lodge, and other residential facilities. For more information send email to ace95@genome.lbl.gov or vist URL http://genome.lbl.gov/ace95.html on the WWW. If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers taken by Mike Cherry with the camera on an SGI workstation, the URL is: http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html. John Morris has provided some more at URL: http://weeds.mgh.harvard.edu/ace94/ace94.image.html. Return to List of Questions ---------------------------------------------------------------------- Q411:Who prepared this document & where is the current version? [Note to international readers: 411 is the phone number for information in the USA. --bks] This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. Answer 3 demonstrates a sample FTP session. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html http://s27w007.pswfs.gov/Homepage/acedbfaq.html Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov Major contributions in getting this FAQ off the ground were made by John McCarthy and Mike Cherry. Other contributors include: Lisa Lorenzen David Matthews Edie Paul Donn Davy Eric De Mund Sam Cartinhour Please cite as: Sherman,B.K., ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993,1994, approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome Research Program. --bks Return to List of Questions ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Fri Dec 16 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!cs.utk.edu!stc06.CTD.ORNL.GOV!druid!ptv From: ptv@druid.epm.ornl.gov (Sergey Petrov) Newsgroups: bionet.software.acedb Subject: Re: Ace GUIs -- model and data files Date: 16 Dec 1994 19:51:20 GMT Organization: Oak Ridge National Lab/CESAR Lines: 29 Distribution: world Message-ID: <3csr3o$3im@stc06.CTD.ORNL.GOV> References: Reply-To: ptv@druid.epm.ornl.gov NNTP-Posting-Host: druid.epm.ornl.gov In article 94Dec14131132@central.cis.upenn.edu, susan@central.cis.upenn.edu (Susan Davidson) writes: > >I am interested in this because we are looking at translating data >"into" and "out of Ace" format. Getting data "out of" Ace format is >useful for integrating data from Acedb databases with data from other >sources, such as relational and ASN.1. Getting data "into" Ace format >will allow us to use the great user interfaces that have been >developed in connection with Ace and still maintain the data in our >own local databases. > >If you are familiar with this part of Ace, or know of a document and >its source that would be helpful, please let me know. > >Thanks, >Susan Davidson > We did it to for a Sybase database: a script produces a report in .ace format. Weak point: you need to reload ACE any time data changed. Please, let me know if you (or anybody) are interested in this stuff: Ill be glad to send all information I have To export data from ACE, one needs to process .ace file (e.g., simple awk) and bcp it into Sybase. A simple but cumbersome process. The tricky point is to design compatible ACE and Sybase DBs.... Sergey Petrov From owner-acedb@net.bio.net Mon Dec 19 22:00:00 1994 Path: biosci!rutgers!gatech!news-feed-1.peachnet.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: database size? Date: 20 Dec 1994 19:55:07 GMT Organization: University of Georgia, Athens Lines: 18 Message-ID: <3d7cqr$4v5@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi all: I'm working on getting a huge chunk of data into .ace format. The ace file is likely to be at least 20 MB, and there's plenty more data where that came from. Does the acedb code imply a theoretical limit to the size of the databae (blocks1.wrm)? (I imagine changing a few variable values would fix this.) Perhaps more relevantly, have people encountered practical limits on database size when it comes to actually running the thing? We have a SPARCstation 20 with 32 MB RAM, but everything has its limits. Thanks. -- Paul Brunk, ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Tue Dec 20 22:00:00 1994 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: database size? Date: 21 Dec 1994 02:40:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: <199412211040.AA23242@cvx12.inet.dkfz-heidelberg.de> References: <3d7cqr$4v5@hobbes.cc.uga.edu> NNTP-Posting-Host: net.bio.net > I'm working on getting a huge chunk of data into .ace format. The > ace file is likely to be at least 20 MB, and there's plenty more data > where that came from. Does the acedb code imply a theoretical limit > to the size of the databae (blocks1.wrm)? (I imagine changing a few > variable values would fix this.) Perhaps more relevantly, have people > encountered practical limits on database size when it comes to > actually running the thing? We have a SPARCstation 20 with 32 MB RAM, > but everything has its limits. we run ACEDB on a 1GB database and it works well. loading the whole data form .ace files takes 4.5 hours. we use a Silicon Graphics challenge computer with 128MB RAM. with that database size acedb needs about 60MB main memory when running. this depends much on the length of the object names used. also you have to add some more lines for files to wspec/database.map. depending on your data you should be carefull with using ?Text in models.wrm, since those entries are automatically crossref'ed. So, if a ?Text value occurs frequently, inserting new values is slow since the backreferences are maintainded as a linked list. best regards Detlef ----------------------------------------------------------------------------- Detlef Wolf, European Data Resource for Human Genome Research eMail: D.Wolf@dkfz-heidelberg.de phone: +49 6221 42 -2331 fax: -2333 sMail: DKFZ (German Cancer Research Centre), Abt. Molekulare Biophysik (0810) Im Neuenheimer Feld 280, 69120 Heidelberg, Germany finger: dok256@mbp-sun2.inet.dkfz-heidelberg.de mbp-sgi5 21% cat database.map 17 13 1 local ACEDB block1.wrm 5000 0 0 1 local ACEDB block2.wrm 20000 19968 0 1 local ACEDB block3.wrm 50000 49920 0 1 local ACEDB block4.wrm 50000 49920 0 1 local ACEDB block5.wrm 80000 79872 0 1 local ACEDB block6.wrm 100000 99840 0 1 local ACEDB block7.wrm 100000 99840 0 1 local ACEDB block8.wrm 100000 99840 0 1 local ACEDB block9.wrm 100000 99840 0 1 local ACEDB block10.wrm 100000 99840 0 1 local ACEDB block11.wrm 100000 99840 0 1 local ACEDB block12.wrm 100000 99840 0 1 local ACEDB block13.wrm 100000 99840 0 1 local ACEDB block14.wrm 100000 69888 0 1 local ACEDB block15.wrm 100000 0 0 1 local ACEDB block16.wrm 100000 0 0 1 local ACEDB block17.wrm 100000 0 0 From owner-acedb@net.bio.net Wed Dec 28 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!yuma!usenet From: "Martin L. Ferguson" Newsgroups: bionet.software.acedb Subject: How do you enter protein sequences Date: 29 Dec 1994 19:30:56 GMT Organization: Colorado State University, Fort Collins, CO 80523 Lines: 8 Message-ID: <3dv2pg$31il@yuma.ACNS.ColoState.EDU> NNTP-Posting-Host: klab.agsci.colostate.edu Greetings all, If you are using a ?Sequence model that includes Peptide, how do you enter the protein sequence? I tried 'AA : "name"' like one would do 'DNA : "name"' for a DNA sequence. It returns a parse error. Thanks, Martin mferguso@klab.agsci.colostate.edu From owner-acedb@net.bio.net Thu Dec 29 22:00:00 1994 Path: biosci!agate!sunsite.doc.ic.ac.uk!uknet!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: protein sequence Date: 30 Dec 1994 11:07:23 -0000 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3e0plb$en0@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk The public release version 2 of ACEDB will not accept protein sequence. He have, however, added that feature some time ago, and the more recent version 3 releases should accept protein sequence in class Peptide, not AA, in the same type of format as DNA, e.g. Peptide HBA_HUMAN VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA VHASLDKFLASVSTVLTSKYR The new version 4 (coming soon) will contain this code to parse and dump amino acid sequences, and there will also be a protein display package like the DNA display -- probably very basic in the first release. Note that if protein sequences are present, they are used by the blixem multiple alignment viewer, in place of external fetched sequences. This is simpler to maintain, and substantially faster. Richard