From owner-acedb@net.bio.net Tue Jun 01 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!sdd.hp.com!saimiri.primate.wisc.edu!usenet.coe.montana.edu!netnews.nwnet.net!news.u.washington.edu!poplar1!cgr From: cgr@poplar1.cfr.washington.edu (carl g. riches, 114 winkenwerder, 3-2764) Newsgroups: bionet.software.acedb Subject: importing mapmaker output into acedb Keywords: mapmaker import acedb rawdata Message-ID: <1uijviINNp6t@news.u.washington.edu> Date: 2 Jun 93 16:20:02 GMT Reply-To: cgr@poplar1.cfr.washington.edu Followup-To: bionet.software.acedb Organization: University of Washington Lines: 14 NNTP-Posting-Host: poplar1.cfr.washington.edu i'm just getting started with acedb, bringing it up on a sparcstation lx under solaris 2.1. i have compiled acedb and have it running. now i need to start bringing in our poplar data to create our poplar database, voxpop. i can see how to bring in our existing bibliographies and am working on that. i don't see how to bring in our mapmaker output. can anyone provide some advice on this? thanks much! --- carl g. riches college of forest resources internet: cgr@poplar1.cfr.washington.edu university of washington ar-10 voice: 206-543-2764 seattle, wa 98195 fax: 206-543-3254 From owner-acedb@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!agate!dog.ee.lbl.gov!csrgate12.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: "C" Programmer for Bioinformatics Graphical Database System Message-ID: Date: 3 Jun 93 15:59:08 GMT Organization: Lawrence Berkeley Laboratory Lines: 43 NNTP-Posting-Host: 128.3.140.104 POSITION: "C" Programmer for Bioinformatics Graphical Database System ORGANIZATION: Lawrence Berkeley Laboratory (LBL), Genome Computing Group PROJECT: LBL is part of an international InterNet collaboration to extend ACEDB software. ACEDB is a publicly distributed database and graphic display system used by biologists in independent laboratories around the world to store, retrieve, display, and manipulate genome research data. It is written in ANSI C and uses a set of widgets built on X-Windows for portability across different hardware platforms. DUTIES: * Install, maintain and enhance ACEDB graphical database software; * Work with LBL staff and ACEDB developers in England and France to design and implement enhancements and connections to other software; * Help develop ACEDB programmer documentation; * Teach others how to write code contributions for ACEDB. QUALIFICATIONS (Essential): * Demonstrated experience and proficiency in "C" programming language; * Practical experience with Unix operating system and tools; * Good oral communications and writing skills; * Experience with computer graphics and X-Windows; * Working knowledge of data structures and database management; * User-oriented approach to programming and interface development; * Ability to work independently, exercising judgement and initiative; QUALIFICATIONS (Desirable): * B.A., M.S., or equivalent experience in computer science; * Experience in user interface design; * Knowledge of genetics and molecular biology. LOCATION: Lawrence Berkeley Laboratory is a DOE-funded facility in the Berkeley Hills above the University of California. PROJECT: LBL's Human Genome Center is part of a large international effort to map and sequence the DNA from various human, animal, and plant genomes. Its Genome Computing Group works with biologists, instrumentation engineers, and other computer scientists at LBL and around the world to develop and support tools for genome research. CONTACT: please send resume to John McCarthy, jlmccarthy@lbl.gov FAX: 510/486-4004; Mailstop 50B, room 3238, LBL, Berkeley 94720 From owner-acedb@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: importing mapmaker output into acedb Keywords: mapmaker import acedb rawdata Message-ID: <1ulsac$67s@overload.lbl.gov> Date: 3 Jun 93 22:00:44 GMT References: <1uijviINNp6t@news.u.washington.edu> Organization: Dendrome, A Genome Database for Forest Trees Lines: 28 NNTP-Posting-Host: s27w007.pswfs.gov > ... > i don't see how to bring in our mapmaker output. > can anyone provide some advice on this? > The best way to proceed is to take one of the available ACEDB databases and do an ACE dump of a similar class. In, say, AAtDB you will find that the F2_data class contains mapmaker style data. You will need to look at the models.wrm file in the wspec subdirectory and do an "Ace Dump" from the Selection List menu. The file produced from an Ace Dump and the object model found in models.wrm can be mimicked; hopefully after you have transformed the data. There will be, presumably, genomic differences between Populus and Arabadopsis. --bks -- Bradley K. Sherman, Dendrome Project, Institute of Forest Genetics USDA Forest Service, P.O. Box 245, Berkeley, CA, 94701, USA Phone: (510)559-6437 FAX: -6440 Internet: bks@s27w007.pswfs.gov Dendrome Gopher Server: s27w007.pswfs.gov port 70 From owner-acedb@net.bio.net Fri Jun 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!wupost!emory!sol.ctr.columbia.edu!news.kei.com!newsstand.cit.cornell.edu!cornell!matthews From: matthews@cs.cornell.edu (David E. Matthews) Newsgroups: bionet.software.acedb Subject: Re: importing mapmaker output into acedb Keywords: mapmaker import acedb rawdata Message-ID: <1993Jun5.185947.4339@cs.cornell.edu> Date: 5 Jun 93 18:59:47 GMT References: <1uijviINNp6t@news.u.washington.edu> Organization: Dept. Plant Breeding, Cornell University Lines: 66 In article <1uijviINNp6t@news.u.washington.edu> cgr@poplar1.cfr.washington.edu writes: > i'm just getting started with acedb, bringing it up on a sparcstation lx > under solaris 2.1. i have compiled acedb and have it running. now i need to > start bringing in our poplar data to create our poplar database, voxpop. > > i can see how to bring in our existing bibliographies and am working on that. > i don't see how to bring in our mapmaker output. can anyone provide some > advice on this? >thanks much! > >--- >carl g. riches >college of forest resources internet: cgr@poplar1.cfr.washington.edu >university of washington ar-10 voice: 206-543-2764 >seattle, wa 98195 fax: 206-543-3254 Mapmaker output (ie linkage groups) is loaded into acedb as a list of Locus records, each with a value for the tag "gMap". The value is a pair: ?Chromosome Float giving the name of the Chromosome object and the position in centimorgans or whatever your units are. An easy way to see some examples would be to look at the Gopher server "GrainGenes, the Triticeae Genome Database". It's on the list of All the Gopher Servers in the World. Pick menu choice 2, "Search the GrainGenes Database", and search for "gmap". This will list several interesting kinds of objects including Locus's. E.g. Locus : CDO64 RFLP Chromosome_arm 2 gMap Avena-F 44.299999 gMap NABGMP-2H 58.900002 gMap Ta-Anderson-2 18.700001 Probe pCDO64 Linked_QTL Sprouting 4 Data Diploid Oat, Cornell Data Barley, SxM Data Wheat sprouting markers This Locus is mapped on three different chromosomes, Avena-F etc. In GrainGenes the Mapmaker input data (which Brad mentioned as being included in the "F2_data" class) are in a class called "Map"; these are listed in this locus record under the tag "Data": "Diploid Oat, Cornell" etc. You'll find them on that same list of hits from the Gopher search. The load-file (.ace) entry to load the part of this information for one of the maps would be, Locus : "CDO64" RFLP gMap Avena-F 44.3 Probe pCDO64 Data "Diploid Oat, Cornell" Hope this helps, - Dave Matthews matthews@greengenes.cit.cornell.edu P.S. By the way, many of us have had no experience with Solaris 2.x, but we'd been under the impression that acedb would have problems with it. Any comments about special obstacles you had to deal with? - Dave From owner-acedb@net.bio.net Fri Jun 04 23:00:00 1993 Path: biosci!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: importing mapmaker output into acedb Keywords: mapmaker import acedb rawdata Message-ID: <1ur7ls$k8c@overload.lbl.gov> Date: 5 Jun 93 22:45:15 GMT References: <1uijviINNp6t@news.u.washington.edu> <1993Jun5.185947.4339@cs.cornell.edu> Organization: Dendrome, A Genome Database for Forest Trees Lines: 17 NNTP-Posting-Host: s27w007.pswfs.gov In article <1993Jun5.185947.4339@cs.cornell.edu> matthews@cs.cornell.edu (David E. Matthews) writes: [A correct description of putting Mapmaker *output* data into ACEDB]. I earlier described how to deal with mapmaker *input* data. Sorry to introduce confusion into the group so soon. Mea Culpa, --bks -- Bradley K. Sherman, Dendrome Project, Institute of Forest Genetics USDA Forest Service, P.O. Box 245, Berkeley, CA, 94701, USA Phone: (510)559-6437 FAX: -6440 Internet: bks@s27w007.pswfs.gov Dendrome Gopher Server: s27w007.pswfs.gov port 70 From owner-acedb@net.bio.net Fri Jun 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!sol.ctr.columbia.edu!news.kei.com!newsstand.cit.cornell.edu!cornell!matthews From: matthews@cs.cornell.edu (David E. Matthews) Newsgroups: bionet.software.acedb Subject: MultiMap suggestions Message-ID: <1993Jun5.192624.5241@cs.cornell.edu> Date: 5 Jun 93 19:26:24 GMT Organization: Dept. Plant Breeding, Cornell University Lines: 145 [cc of message to jlmccarthy@lbl.gov] John, some time back you asked for some feedback on the MultiMap. Yesterday I finally got an imaginative and demanding user (Steve Tanksley) to sit down and go through it with me. Our reactions below are based on his first-time interaction, with me as operator, after my having used MultiMap several times and read the docs but not actually run Jean's g2pmap.def example. My table definition multimap-dem.def is given at the end of this message. First, he/we were very happy with some aspects of the current version. ("current": Actually this is still xace 1.8.) Specifically, - the tie-lines between the loci on the two maps, and between them and the name - the connection back to the Tablemaker window so that clicking a locus on the MultiMap highlights it in the table - the pickability of the locus name in the table, so that double-clicking it pulls up one of the gMaps it exists on. Problems, suggestions, fantasies: - The default scales, with each map being independently scaled to full size, are a good choice. But Steve also felt it would be good to have a way to easily show both maps on the same scale. Maybe a button labeled "Same scale" or "Proportional"? - We were able to zoom the two maps independently with the "Zoom Active" setting, but we never did figure out how to select which map was "active". - We wanted to be able to display all loci that were on either map, with only those common to both maps connected by tie-lines. So far the best I've been able to get is this: By changing the query condition on Colonne 1 from Mandatory to Optional, I get all the loci that are on the other map listed in the table and shown on the multimap; but the position of the non-common loci is shown as 0.0 in Colonne 2 and that's where they're all plotted on the multimap. A mess. - The main suggestions were about how to friendlify the query mechanism. These were guided by Steve's conviction that in crop plants we will never need to compare anything but gMaps. From that perspective it seems unnecessarily complicated to have the Tablemaker table involved at all, if one could double-click on a locus name in the multimap to jump directly to the gMap. = Aside: Steve wondered why the multimap can't be just two gMap windows fused, with tie-lines added. This would have the advantage that the full power of the main query mechanism could be used to build a keyset of loci to be shown/hidden/highlighted with the Show Selected Objects etc. buttons. In any case, it would be good to have two handy buttons for Show Common Loci, and Show All Loci. The basic query is just to pick two Linkage_Groups ("Chromosomes" in some people's models) to be compared. Very simple question, should be executable very simply. = I suppose the most easily implemented approach would be to have the user filter out a keyset containing the Linkage_Groups to be compared using the Template, or maybe a query, then choose "Compare maps" from the menu. = Easier to use would be for a command (e.g. "Compare maps") to call up a "Map Chooser" window listing all the available Linkage_Groups and allowing two or more of them to be selected. = Steve's vision was a window that would list chooseable Linkage_Groups in an array by homeologous sets. e.g: Tomato Potato PepperMap1 PepperMap2 1 1 1 1 2 2 5 5 ... (or whatever the homeologues actually are) Since of course we don't yet know what the homeologues are in all species, this would have to be an array generated by loadable data. For example there might be a new class ?Homeologue_set: ?Homeologue_set Map_Chromosome ?Map ?Linkage_Group example: Homeologue_set : "2" Map_Chromosome Tomato 2 Map_Chromosome Potato 2 Map_Chromosome PepperMap1 5 Map_Chromosome PepperMap2 5 I hope this is helpful, or at least comprehensible. - Dave :::::::: xgraingenes/wquery/multimap-dem.def: // Spread sheet definition for the ACeDB software // User: matthews // Date: Thu_22_Apr_1993, Time: 15_18_54 Colonne 0 Width 12 Optional Visible Class Class "Locus" From 0 Tag "(null)" Colonne 1 Width 12 Mandatory Visible Class Class "(null)" From 1 Tag "gMap" Condition "NABGMP-6H" Colonne 2 Width 12 Optional Visible Float From 1 Tag "gMap = NABGMP-6H NEXT" Colonne 3 Width 12 Mandatory Visible Class Class "(null)" From 1 Tag "gMap" Condition "Tt-Gill-6D" Colonne 4 Width 12 Optional Visible Float From 1 Tag "gMap = Tt-Gill-6D NEXT" // End of these definitions From owner-acedb@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!concert!duke!news.duke.edu!chlamy.botany.duke.edu!user From: chlamy@acpub.duke.edu (Elizabeth Harris) Newsgroups: bionet.software.acedb Subject: circular chloroplast genome map Message-ID: Date: 7 Jun 93 19:11:05 GMT Sender: news@news.duke.edu Followup-To: bionet.software.acedb Organization: Duke University Lines: 5 Nntp-Posting-Host: chlamy.botany.duke.edu Has anyone put a circular map of a chloroplast genome into an ACeDB database? Elizabeth Harris chlamy@acpub.duke.edu From owner-acedb@net.bio.net Sun Jun 13 23:00:00 1993 Path: biosci!uwm.edu!daffy!uwvax!spool.cs.wisc.edu!todd From: todd@behemoth.genetics.wisc.edu (Todd Richmond) Newsgroups: bionet.software.acedb Subject: Running on IBM RS6000? Message-ID: Date: 14 Jun 93 18:26:18 GMT Sender: news@cs.wisc.edu (The News) Distribution: bionet Organization: UW Genetix Lines: 15 Netlanders, Is anyone out there running the ACeDB software on an IBM RS6000 workstation? If not, is there any reason why it wouldn't run on that platform? Thanks, Todd Richmond -- ********************************************************* Todd Richmond UW-Madison Dept of Genetics todd@genetics.wisc.edu From owner-acedb@net.bio.net Sun Jun 13 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!swrinde!gatech!concert!duke!news.duke.edu!bio3.acpub.duke.edu!glh From: glh@bio3.acpub.duke.edu (Geoff Hughes) Newsgroups: bionet.software.acedb Subject: highlights Message-ID: <16300@news.duke.edu> Date: 14 Jun 93 20:37:33 GMT Sender: news@news.duke.edu Reply-To: glh@bio3.acpub.duke.edu (Geoff Hughes) Lines: 15 Nntp-Posting-Host: bio3.acpub.duke.edu -- _______________________________________________________ Geoff Hughes Duke University Email : glh@acpub.duke.edu Home phone : 919-286-1387 _______________________________________________________ Has anyone out there modified ACeDB or know how to modify ACeDB to highlight entries in the chromosome class to stand out?(Similar to the clone highlight) From owner-acedb@net.bio.net Mon Jun 14 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!psgrain!library.ucla.edu!ucla-mic!unixg.ubc.ca!cs.ubc.ca!newsserver.sfu.ca!sfu.ca!baillie From: baillie@beaufort.sfu.ca (Dave Leonard Baillie) Newsgroups: bionet.software.acedb Subject: Re: Running on IBM RS6000? Message-ID: Date: 15 Jun 93 14:45:41 GMT References: Sender: news@sfu.ca Distribution: bionet Organization: Simon Fraser University, Burnaby, B.C., Canada Lines: 16 todd@behemoth.genetics.wisc.edu (Todd Richmond) writes: >Netlanders, >Is anyone out there running the ACeDB software on >an IBM RS6000 workstation? If not, is there any >reason why it wouldn't run on that platform? >Thanks, >Todd Richmond Jean Thierry-Mieg has compiled aCedb on a IBM RS6000 and has provided the binaries for this machine at the NCBI site. I have not looked to see if it is there for the 1-9 release but it was there previously. dave baillie baillie@sfu.ca From owner-acedb@net.bio.net Mon Jun 14 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!concert!duke!news.duke.edu!bio3.acpub.duke.edu!glh From: glh@bio3.acpub.duke.edu (Geoff Hughes) Newsgroups: bionet.software.acedb Subject: ACeDB Message-ID: <16359@news.duke.edu> Date: 15 Jun 93 15:27:32 GMT Sender: news@news.duke.edu Reply-To: glh@bio3.acpub.duke.edu (Geoff Hughes) Lines: 27 Nntp-Posting-Host: bio3.acpub.duke.edu Hello out there! I would like to invite everyone on the net who reads this, especially those who are involved in developing new ACeDB projects or those who are curious as to what ACeDB does, to start posting regularly in order to create a forum for ACeDB developers to compare notes, troubleshoot software, help new developers along, and discuss improvements( maybe a wish list for future versions of the software, Richard and Jean willing). It would really be something if we could provide everybody out there (especially Jean and Richard) with some feedback/questions on the software without having to fill up their mailboxes; if enough people were interested, and enough information passed through this newsgroup, an archive of FAQs could be designed for the new user. Here are a few questions that I have: How is query useful in an X environment? Does anybody out there know if highlights can be introduced in gMap without altering the source code(i.e. something that can be done from wspec) Geoff Hughes From owner-acedb@net.bio.net Tue Jun 15 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!agate!overload.lbl.gov!gnu.lbl.gov!aochi From: aochi@gnu.lbl.gov (Gary Aochi) Newsgroups: bionet.software.acedb Subject: Re: ACeDB (from Geoff Hughes) Keywords: query Message-ID: <1vlpki$dpn@overload.lbl.gov> Date: 16 Jun 93 00:31:14 GMT References: <16359@news.duke.edu> Organization: Lawrence Berkeley Laboratory Lines: 37 NNTP-Posting-Host: gnu.lbl.gov >In article <16359@news.duke.edu>, glh@bio3.acpub.duke.edu (Geoff Hughes) writes: > Here are a few questions that I have: > > How is query useful in an X environment? > > Geoff Hughes The query() function call, for those who are familiar with the source code, is one of the essential methods for sorting and manipulating data in the database. But, to address your question, I must admit to being puzzled by it. The fact that the external environment is X Windows does not necessarily have much to do with the query system inside ACEDB. If, perhaps, you mean that with BOLD text, you can hyper-browse and move your windows around (in X), yes that is possible. But by using carefully (and not so carefully (1)) constructed queries, you can easily construct useful data keysets of objects which interest you. For example, you could get all the papers written by Jean Thierry-Mieg in the year 1992 or, as another example, all the people who work at LBL and who have written exactly three papers which were accepted into a journal. Of course, these examples are rather useless and probably not at all applicable to the type of data in most genome databases, but I hope it gives you an idea of the potential that lies within the query system. (1) Having talked to Jean Thierry-Mieg recently, I was told that in most common cases, using the general text search box (on the main window of ACEDB) is faster than using a rather complex query command due to the order of evaluation of the general text search which can reduce the searched dataset faster than a complex and very specific query. I hope this helps Gary Aochi ghaochi@lbl.gov From owner-acedb@net.bio.net Tue Jun 15 23:00:00 1993 Path: biosci!enterpoop.mit.edu!gatech!emory!nigel.msen.com!sdd.hp.com!cs.utexas.edu!swrinde!elroy.jpl.nasa.gov!usc!howland.reston.ans.net!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!gilbertd From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.acedb Subject: Macintosh version? Message-ID: Date: 16 Jun 93 12:00:50 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 12 Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] Will there be a Macintosh version of acedb software? When? Will it cost money? Will it be able to use the same data as a Unix acedb (assuming NSF or Unix-Appletalk file system links exist)? I find that X-Window software is not all that suitable for the biologists at IU who mostly use Macs for several reasons (among them when I upgraded Openwindows, the Mac-Sun X-WIndows fails to get the Sun Xwindow manager running; also it is generally an awkward mix). -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-acedb@net.bio.net Tue Jun 15 23:00:00 1993 Path: biosci!MENDEL.AGRON.IASTATE.EDU!lorenzen From: lorenzen@MENDEL.AGRON.IASTATE.EDU (Lisa Lorenzen) Newsgroups: bionet.software.acedb Subject: Re: What data sets are available? Message-ID: <9306161947.AA01518@mendel.agron.iastate.edu> Date: 16 Jun 93 19:47:14 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 46 The USDA-ARS is currently funding three ACE-type databases, Soybean, Wheat/small grains, and Forest Crops. I am currently working on the soybean database, and can only say that it will be 'released' someday. The USDA is putting together a public database, called PGD, which is a relational database encompassing 'all' crop species. The initial species involved in this are maize, soybean, wheat, forest trees, and arabidopsis. Lisa Lorenzen lorenzen@iastate.edu ----- Begin Included Message ----- From BIOSCI-REQUEST@net.bio.net Wed Jun 16 07:04:52 1993 Received: from net.bio.net by mendel.agron.iastate.edu (4.1/UW-NDC Revision: 2.21 ) id AA00592; Wed, 16 Jun 93 07:04:49 CDT Received: by net.bio.net (5.65/IG-2.0) id AA04560; Wed, 16 Jun 93 05:03:05 -0700 Received: by net.bio.net (5.65/IG-2.0) id AA04554; Wed, 16 Jun 93 05:03:02 -0700 Message-Id: <9306161203.AA04554@net.bio.net> To: acedb@net.bio.net From: gilbertd@bio.indiana.edu (Don Gilbert) Subject: What data sets are available? Date: 16 Jun 93 11:58:09 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] Status: RO What data sets are now available publicly for use with acedb software, and from where? I only know about the c.elegans and arabidopsis sets which can be gotten from ncbi.nlm.nih.gov:/repository among other places. Which data sets might we expect to have publicly available in the not-to-distant future? -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 ----- End Included Message ----- From owner-acedb@net.bio.net Tue Jun 15 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!europa.eng.gtefsd.com!emory!news-feed-1.peachnet.edu!concert!duke!news.duke.edu!bio5.acpub.duke.edu!glh From: glh@bio5.acpub.duke.edu (Geoff Hughes) Newsgroups: bionet.software.acedb Subject: Re: What data sets are available? Message-ID: <16409@news.duke.edu> Date: 16 Jun 93 17:03:03 GMT References: Sender: news@news.duke.edu Reply-To: glh@bio5.acpub.duke.edu (Geoff Hughes) Lines: 12 Nntp-Posting-Host: bio5.acpub.duke.edu Currently, there are only the Arabidopsis(AAtDB) and ACeDB data sets available, as far as I know, but there are at least ten projects that are in the making; I am working on one of them. To get an idea of what's to come, take a look at ACeDB's latest release and look at the file tags.wrm in the wspec directory; this is where registered developers tag number allotments can be seen- I think Drosophila, human genome, and mice are among the databases being developed, and I am currently designing a new database from AAtDB for Chlamydomonas. Geoff Hughes From owner-acedb@net.bio.net Tue Jun 15 23:00:00 1993 Path: biosci!enterpoop.mit.edu!gatech!howland.reston.ans.net!usc!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!gilbertd From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.acedb Subject: Easier data installation? Message-ID: Date: 16 Jun 93 12:02:16 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 10 Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] Is anyone giving thought to making data distribution and installation of multiple data sets with acedb software easier on unix sys admins? I would like to keep acedb/aatdb/other data sets updated here, but my time is spread thin and it takes time to fetch distribution sets, read instructions, figure out proper symlinks and such to keep a couple of acedb/aatdb sets running properly w/o lots of duplicated software. -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-acedb@net.bio.net Tue Jun 15 23:00:00 1993 Path: biosci!enterpoop.mit.edu!gatech!usenet.ins.cwru.edu!howland.reston.ans.net!usc!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!gilbertd From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.acedb Subject: What data sets are available? Message-ID: Date: 16 Jun 93 11:58:09 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 10 Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] What data sets are now available publicly for use with acedb software, and from where? I only know about the c.elegans and arabidopsis sets which can be gotten from ncbi.nlm.nih.gov:/repository among other places. Which data sets might we expect to have publicly available in the not-to-distant future? -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-acedb@net.bio.net Wed Jun 16 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!news-feed-1.peachnet.edu!concert!xanth.cs.odu.edu!news.cs.odu.edu!bianco From: bianco@aelle.cs.odu.edu (David J. Bianco) Newsgroups: bionet.software.acedb Subject: Re: ACeDB Message-ID: Date: 17 Jun 93 16:21:37 GMT References: <16359@news.duke.edu> Organization: Old Dominion University, Norfolk, VA, USA Lines: 17 NNTP-Posting-Host: aelle.cs.odu.edu In-reply-to: glh@bio3.acpub.duke.edu's message of 15 Jun 93 15:27:32 GMT I'm sure this is a newbie question, but could someone fill me in on what this software does? Or at least point me to a FAQ. I didn't see one in any of the news.* groups, but we don't keep news around very long... Thanks -- =============================================================================== David J. Bianco "All the computers. All the data. Old Dominion University All the programs. ALL THE POWER!" Dept of Computer Science Norfolk VA 23529 /\ | /_/ /\ \/ | [| =============================================================================== "If we had a budget big enough for drugs and sexual favors, we sure wouldn't waste them on members of Congress..." -John Perry Barlow From owner-acedb@net.bio.net Sun Jun 20 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!gatech!concert!duke!news.duke.edu!bio3.acpub.duke.edu!glh From: glh@bio3.acpub.duke.edu (Geoff Hughes) Newsgroups: bionet.software.acedb Subject: ACeDB for Solaris Message-ID: <16608@news.duke.edu> Date: 21 Jun 93 15:29:53 GMT Sender: news@news.duke.edu Reply-To: glh@bio3.acpub.duke.edu (Geoff Hughes) Lines: 13 Nntp-Posting-Host: bio3.acpub.duke.edu Hello all- I am working on an SGI, and am in the process of making versions of a Chlamydomonas database for SunOS and mips(DEC), but was wondering if anyone out there has a Solaris version already compiled so that I could get a guide to configuring the source code for Solaris or a working copy of ACeDB for Solaris. Thanks, Geoff From owner-acedb@net.bio.net Mon Jun 21 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!decwrl!decwrl!pdq.coe.montana.edu!netnews.nwnet.net!news.u.washington.edu!poplar1!cgr From: cgr@poplar1.cfr.washington.edu (carl g. riches, 114 winkenwerder, 3-2764) Newsgroups: bionet.software.acedb Subject: Re: ACeDB for Solaris Message-ID: <207a74INNt12@news.u.washington.edu> Date: 22 Jun 93 15:58:28 GMT References: <16608@news.duke.edu> Reply-To: cgr@poplar1.cfr.washington.edu Organization: University of Washington Lines: 12 NNTP-Posting-Host: poplar1.cfr.washington.edu i have managed to get acedb (version 1-9) running on a sparcstation lx running solaris 2.1. it's not a clean port, as the compiler emits many "unused variable" messages, "implicit declaration" messages, and "defined but not used" messages. i will make the sources and binaries available via anon ftp at poplar1.cfr.washington.edu in the next day or so. it seems to run with no problems, but any help cleaning this up will be appreciated! --- carl g. riches college of forest resources internet: cgr@poplar1.cfr.washington.edu university of washington ar-10 voice: 206-543-2764 seattle, wa 98195 fax: 206-543-3254 From owner-acedb@net.bio.net Tue Jun 22 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!pdq.coe.montana.edu!netnews.nwnet.net!news.u.washington.edu!poplar1!cgr From: cgr@poplar1.cfr.washington.edu (carl g. riches, 114 winkenwerder, 3-2764) Newsgroups: bionet.software.acedb Subject: Re: ACeDB for Solaris Message-ID: <209th6INN72@news.u.washington.edu> Date: 23 Jun 93 15:40:22 GMT References: <207a74INNt12@news.u.washington.edu> Reply-To: cgr@poplar1.cfr.washington.edu Organization: University of Washington Lines: 18 NNTP-Posting-Host: poplar1.cfr.washington.edu i have now uploaded a version (sources and binaries) of acedb for solaris 2.1 to the anonymous ftp site at poplar1.cfr.washington.edu. these files are located in the directory pub/acedb: total 6792 -rw-r--r-- 1 ftp public 710 Jun 22 16:48 00-INDEX -rw-rw-rw- 1 ftp public 7241 Jun 22 16:30 NOTES -rw-rw-rw- 1 ftp public 629 Jun 22 16:30 README.CGC_DATA -rw-rw-rw- 1 ftp public 2067 Jun 22 16:30 README -rw-rw-rw- 1 ftp public 7079 Jun 22 16:30 INSTALL -rw-rw-rw- 1 ftp public 1525715 Jun 22 16:28 source.1_9_1.sol2.tar.Z -rw-rw-rw- 1 ftp public 1908041 Jun 22 16:28 bin.1_9_1.sol2.tar.Z --- carl g. riches college of forest resources internet: cgr@poplar1.cfr.washington.edu university of washington ar-10 voice: 206-543-2764 seattle, wa 98195 fax: 206-543-3254 From owner-acedb@net.bio.net Tue Jun 22 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!concert!duke!news.duke.edu!bio3.acpub.duke.edu!glh From: glh@bio3.acpub.duke.edu (Geoff Hughes) Newsgroups: bionet.software.acedb Subject: Re: ACeDB for Solaris Message-ID: <16719@news.duke.edu> Date: 23 Jun 93 17:18:58 GMT References: <207a74INNt12@news.u.washington.edu> <209th6INN72@news.u.washington.edu> Sender: news@news.duke.edu Reply-To: glh@bio3.acpub.duke.edu (Geoff Hughes) Lines: 7 Nntp-Posting-Host: bio3.acpub.duke.edu Thanks for the information about solaris 2.1 to everyone who responded to my post; I have the version from poplar1.cfr.washington.edu, but have not yet had a chance to compile it. Thanks, Carl! Geoff Hughes From owner-acedb@net.bio.net Wed Jun 23 23:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!howland.reston.ans.net!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!gilbertd From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.acedb Subject: Summary: What data sets are available? Message-ID: Date: 24 Jun 93 14:07:25 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 74 Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] My question: What data sets are/will be soon available for use with ACeDB software? Currently available: acedb for C.elegans, ftp/gopher to ncbi.nlm.nih.gov:/repository/aatdb aatdb for Arabidopsis, ftp/gopher to ncbi.nlm.nih.gov:/repository/acedb mycdb for Mycobacterium, ftp/gopher to ftp.pasteur.fr:/pub/MycDB graingenes for Triticeae, gopher to greengenes.cit.cornell.edu for info Plans: > From: Mike Cherry > > Besides worms and weeds I believe the only other publically released > ACEDB db is MycDB by Staffan Bergh (staffan@pasteur.fr) of the Pasteur > Institute on mycobacterium. There was an announcement a couple months > ago in bionet.announce. MycDB is available via anonymous ftp from > ftp.pasteur.fr or via Gopher from ftp.pasteur.fr. > > There are many others in the works. I shouldn't publically list all > that I have heard about, each group should make their own > announcements. But generally almost every genomic database you can > think of is looking into using ACEDB as a method of distribution. Plus > there are >10 other species databases from the plant and animal > kingdoms that are developing an ACEDB database. > From: bks@s27w007.pswfs.gov (Bradley K. Sherman) > > We will be making APtDB (A Pinus taeda Database) available soon. > This will have all of our data for the construction of a > loblolly pine genetic map as well as a cross-index to a > complete set of online autorads. > > p.s. by soon, I mean maybe September/October > From: Lisa Lorenzen > > The USDA-ARS is currently funding three ACE-type databases, Soybean, Wheat/small grains, and Forest Crops. I am currently working on the > soybean database, and can only say that it will be 'released' someday. > The USDA is putting together a public database, called PGD, which is a > relational database encompassing 'all' crop species. The initial > species involved in this are maize, soybean, wheat, forest trees, and > arabidopsis. > From: reisner@angis.su.OZ.AU (Alex Reisner) > > we run four 'acedb' types ACeDB and AAtDB of course and > GranGenes (David Mathews, cornell (mostly wheat and barley) MycDB > for Mycobacteria from the Pasteur. I know of no others though am told > Michael Ashburner is working on Dros., as is possibly a US group. > From: glh@bio5.acpub.duke.edu (Geoff Hughes) > > > Currently, there are only the Arabidopsis(AAtDB) and ACeDB data sets available, > as far as I know, but there are at least ten projects that are in the making; > I am working on one of them. To get an idea of what's to come, take a look at > ACeDB's latest release and look at the file tags.wrm in the wspec directory; > this is where registered developers tag number allotments can be seen- I think > Drosophila, human genome, and mice are among the databases being developed, and > I am currently designing a new database from AAtDB for Chlamydomonas. > -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-acedb@net.bio.net Wed Jun 23 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!gilbertd From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.acedb Subject: Summary: Easier data installation? Message-ID: Date: 24 Jun 93 14:10:21 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 71 Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] > In article , gilbertd@bio.indiana.edu (Don Gilbert) writes: > >Is anyone giving thought to making data distribution and installation of > >multiple data sets with acedb software easier on unix sys admins? I would > >like to keep acedb/aatdb/other data sets updated here, but my time is > >spread thin and it takes time to fetch distribution sets, read instructions, > >figure out proper symlinks and such to keep a couple of acedb/aatdb > >sets running properly w/o lots of duplicated software. The general answer here is that updating acedb data sets & software is not hard nor time consuming. I more or less knew that, but haven't updated local ace data yet because as I said I haven't enough time to do everything that people want me to. Let me expand my belly-ache about time spent maintaining/updating biology data (ace & non-ace) at local biocomputing centers & by biologists without much computer expertise. Would it be feasible for acedb software to incorportate a homeserver-localserver-client scheme of automatic network data retreival? This is something perhaps like Worm Community System envisioned (aside: I haven't seen any updates in WCS for > a year -- am I looking in wrong place? place being csl.biosci.arizona.edu). It would make the life of overworked sys admins and undertrained biologists simpler if acedb software could incorportate network links to a home server which would update local data automatically, more or less. I'd hope to see this scheme considered for many biology databases, esp. if they include tailored software like acedb does. Responses: > From: Mike Cherry > > Just put the ACEDB executable in a common place like /usr/local and > have /usr/local in your users path. Thats all it takes to use common > executables. As for the other files associated with an ACEDB database > you need to keep them separate. So that way they are independant. > > Links are not needed. > > However installed completely separate copies of the entire database only > duplicates about 500K. The ACEDB executable, xace. > > From: glh@acpub.duke.edu (Geoff Hughes) > > As far as easier data installation goes, other than just taking the time to get > the data sets via ftp, you use update to read in the update files- it is just > a special .ace file with a header. Let me know if this answers your question; > I'll help if I can. > From: baillie@sfu.ca > > Don, me again. Do you know you can run both aCedb and aAtdb under the same > acedb installation? Up dates only require the import of the new data set. > This takes about 10 min, once every 3-4 months. The new software installation > is most simple if done from binaries (I know not very Unix) and only take > minutes. The new binaries only come out ablout once every 6 months or more. > Jean or Richard can give explicit instructions as to how to run multiple > data sets under on acedb installation. Ooops, on re reading your note, I > guess that is what you are doing, if so please ignore the multiple data > installation comments. > > dave baillie -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-acedb@net.bio.net Wed Jun 23 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!usc!howland.reston.ans.net!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!gilbertd From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.acedb Subject: Summary: Macintosh version? Message-ID: Date: 24 Jun 93 14:08:32 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 47 Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] My question: Will there be a Mac version of ACeDB software? Answers: > From: Mike Cherry > > Probably. There is a lack of funding but a Macintosh version is wanted by > everyone involved. > > No more specifics are available at this time. > From: tim@eeg.com (Tim Stearns) > You might want to contact the yeast people at Stanford (Dr. David Botstein, > Dir); they're trying out various packages on various platforms; one of > their thoughts was to build a Mac version of acedb, though they weren't > overly enthusiastic about the idea, last I knew. > From: baillie@sfu.ca > > Don there is a good cheap PC version, it runs under Linux and it's price > is good (free). It is available at ncbi. The MAC version has specific > code written for it and will always lag behind the Unix/PC version as > the port is not direct. The MAC version is also slow, as compared to the > sparc or 33 mhz 486 PC version. Running a MAC as an x-server seems to be > a viable alternative, but MAC-x is slow, but it works fine. The PC linux > machines will also serve well as X-servers. I think the problem with the > Mac-X Openwindowss combination is best avoided by NOT upgrading the graphical > system, except under threat of death! > I have found that most MAC uses acquire aCedb skills in about a day > or two, if the database has information that they want retrieve. Maybe you > will find it easier to introduce when the fly version is available. > Have you considered using a different graphical front end, TWM or > motif, some of those are faster and more plesent that Openwindows. They > work fine with aCedb and require no tweaking to make them run with it. > I would stick with the generic Unix based aCedb version, as it is much > closer to the developers and thus will recieve bug fixes, add-ons, and updates > more easily. > > dave baillie -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-acedb@net.bio.net Wed Jun 23 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!usc!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!gilbertd From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.acedb Subject: What ACeDB is (?) Message-ID: Date: 24 Jun 93 21:03:43 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 96 Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] I've had a request to explain what ACeDB is. I'm not a developer nor primary user of ACeDB, so my explanation here is limited to copying a segment of the documents that come with the software. Someone else may want to better answer this. --- from acedb/wdoc/users_guide.tex ---------------------------- \title{acedb --- A C.\ elegans Database \\I. Users' guide} \author{Richard Durbin\thanks{MRC Laboratory for Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK. Email: rd@lmba.cam.ac.uk} and Jean Thierry-Mieg\thanks{CNRS--CRBM, Route de Mende, BP 5051, 34033 Montpellier, France. Email: mieg@frmop11.bitnet}} Acedb is the database system that we are writing to meet the needs of the nematode genome project. It is graphic, flexible and portable. As of february 1992, it has been tested on various Unix workstations (SUN, DEC, NEXT, SGI ...), on all sorts of X terminals and under several different windowing systems (X11, Sunview, Mac). The system contains its own portable graphic library, an original object oriented database manager, a series of applications and a set of configuration file corresponding to the nematode data. ---- this is from AAtDB_1-1.Announcement ---------------------- AAtDB, An Arabidopsis thaliana Data Base, uses the excellent database software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg (CNRS, France). AAtDB is funded by the U. S. Department of Agriculture Plant Genome Research Program through the National Agricultural Library and is maintained by a group at the Massachusetts General Hospital and Harvard Medical School. AAtDB is available free of charge via Internet network transfer. A complete description of the procedure to retrieve the software and database is included in a separate message. The ACeDB software allows the user to browse information by simply pointing and clicking with the workstation mouse. A powerful query facility is also available. However, our experience is that most users choose the mouse interface to find the information they are interested in. Currently AAtDB contains: - The Hauge/Goodman cosmid/YAC physical map including >14,000 cosmid clones. - Genetic markers, both RFLP and classical markers. - Unified Genetic Map. Including both the Goodman and Meyerowitz RFLP markers and classical genetic markers. - Primary F2 mapping database from the Goodman and Meyerowitz RFLP mapping projects. - Primary two point recombination data from M. Koornneef. - A strain catalog including all strains and clones available from the Nottingham Stock Centre and the ABRC at Ohio State University. - Bibliographic citations from 1964 to present, currently numbering over 2,600. - List of Arabidopsis researchers including mail address, phone number, FAX number and electronic mail address. Currently information on over 500 colleagues is included. - Green Book. The Green Book by Meyerowitz and Pruitt has been updated and integrated into many parts of the database, including phenotype and allele descriptions. - All Arabidopsis DNA sequences from GenBank, currently there are over 300 sequences. - BLASTX defined amino acid sequence similarities for all Arabidopsis sequences against the SwissProt, PIR and GenPept protein sequence databases. - REBASE restriction enzyme database maintained by R. Roberts, CSHL. - Graphical displays of all Genetic Maps, Physical Maps, and DNA Sequence features and similarities. - Scanned images of photographs showing mutant phenotypes. As much as possible all information is connected to other information in the database. The database presents the information in separate windows that allow many parts of the database to be viewed at one time. There are also many paths to any piece of information, allowing the user to easily navigate the connections between the various types of information. This is just the starting point. Just as the known Arabidopsis genome information is always being expanded AAtDB is also being extended and enhanced via periodic updates. There is much more information that we are working to include in subsequent updates of AAtDB. The database currently requires a Unix workstation running X-Windows. Versions of the ACeDB database software are available for Sun Microsystems SPARCstations, Digital Equipment's DECstation, Silicon Graphics Iris series and NeXT workstations. -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-acedb@net.bio.net Fri Jun 25 23:00:00 1993 Path: biosci!agate!headwall.Stanford.EDU!nntp.Stanford.EDU!genome.Stanford.EDU!cherry From: cherry@genome.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: Summary: Easier data installation? Message-ID: <1993Jun26.155829.16467@leland.Stanford.EDU> Date: 26 Jun 93 15:58:29 GMT References: Sender: news@leland.Stanford.EDU (Mr News) Organization: Stanford Yeast Genome Project Lines: 58 In article gilbertd@bio.indiana.edu (Don Gilbert) writes: > >The general answer here is that updating acedb data sets & software >is not hard nor time consuming. I more or less knew that, but haven't >updated local ace data yet because as I said I haven't enough time >to do everything that people want me to. Its really very easy. Since you say you haven't tried it I can assure you that there is nothing technical about the updates that ACEDB uses. 1) ftp the update file. 2) run a canned csh script to extract the files 3) start the database and choose the Add Update option. >Let me expand my belly-ache about time spent maintaining/updating >biology data (ace & non-ace) at local biocomputing centers & by >biologists without much computer expertise. Would it be feasible for >acedb software to incorportate a homeserver-localserver-client scheme of >automatic network data retreival? This is something perhaps like >Worm Community System envisioned (aside: I haven't seen any updates >in WCS for > a year -- am I looking in wrong place? place being >csl.biosci.arizona.edu). WCS used rdist to update their files, and I believe WCS hasn't had an update since Feb 1992. Which does mean the local WCS admin doesn't do anything except initially setup the software and leave access to your machine open to the database administrators. Thats fine if all the local copies of your database are on the network and available. We'll still need to use other methods of updating. The update procedure used by ACEDB databases (note the correct spelling is all caps) allows local users to add there own private data into the database. If no local data is being added then other methods would be possible. For example we could create a compressed tar file of changed files, including the blocks.wrm the binary database file which for AAtDB is around 50MB, for many other ACEDB based database its much larger. This would remove step 3 from the list above and require more temporary free space during an update. >It would make the life of overworked sys admins and undertrained biologists >simpler if acedb software could incorportate network links to >a home server which would update local data automatically, more or less. >I'd hope to see this scheme considered for many biology databases, esp. >if they include tailored software like acedb does. We, the AAtDB Project, haven't heard many (if any) complains about the update process. We have biologists without any experience with computers doing the AAtDB updates around the world. Do others have suggestions for making the process easier than it already is? Is this a problem that others are concerned about? I should also note that work is underway for a network client/server version of ACEDB. We'll all know more after the ACEDB workshop next month in Boston. Mike -- J. Michael Cherry Project Manager, Yeast Genome Database Stanford Genome Sequencing Center, Department of Genetics Stanford University School of Medicine, Stanford, CA 94305-5120 Voice: 415-723-7541 FAX: 415-723-7016 Internet: cherry@genome.stanford.edu From owner-acedb@net.bio.net Fri Jun 25 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!agate!headwall.Stanford.EDU!nntp.Stanford.EDU!genome.Stanford.EDU!cherry From: cherry@genome.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: Summary: Easier data installation? Message-ID: <1993Jun26.195213.20725@leland.Stanford.EDU> Date: 26 Jun 93 19:52:13 GMT References: <1993Jun26.155829.16467@leland.Stanford.EDU> <1993Jun26.164810.13008@comp.bioz.unibas.ch> Sender: news@leland.Stanford.EDU (Mr News) Organization: Stanford Yeast Genome Project Lines: 48 In article <1993Jun26.164810.13008@comp.bioz.unibas.ch> doelz@urz.unibas.ch writes: >I would very much enjoy more discussion on this topic. Can someone comment >on the availability of WCS in Europe, and its implementation (hardware, >software, reliability)? I have limited information about WCS as we run it in Boston. However the biologist like it alot as it gives a good presentation. This is my view of WCS. It is used as an extension to ACEDB (the worm database) but it works fine on its own. ACEDB (the software) and WCS communicate so that WCS can cause ACEDB windows to appear. WCS is a hypertext like presentation of bibliographic literature but most interestingly it also provides a facility were anyone can comment on a piece of information in the database. So you can see that someone has stated a fact and then make a comment--you disagree or you independently showed the same thing, etc... WCS includes a text formatting and presentation feature that makes the bibliographic information and comments look very nice using fonts and size well. I understand WCS is being completely rewritten and that the group in Arizona has stopped updating the currently released version until the new version is done. The last update to WCS was Feb of 1992. Maybe someone that was at the worm meeting in Wisconsin a few weeks ago can add to the current state of WCS. The current WCS is written in C++, the source is not available. Executables are available for SPARCs only. MOTIF is the X environment. The current version loads slowly because all the data files are stored in compressed form and uncompressed and read into memory at startup. The files on the disk take up about 34MB. WCS is only used for worm information, that is I have not seen anyone else using it. Here are the first two paragraphs from the WCS copyright: This is release 1.0 of the Worm Community System, July 1991. This software is copyright 1991 by the Arizona Board of Regents. The Worm Community System is designed and implemented by the Community Systems Laboratory at the University of Arizona, Tucson. Click on the logo within the system for full credits. We are actively interested in your comments and suggestions. These can be sent electronically to wcs@cs.arizona.edu . Mike -- J. Michael Cherry Project Manager, Yeast Genome Database Stanford Genome Sequencing Center, Department of Genetics Stanford University School of Medicine, Stanford, CA 94305-5120 Voice: 415-723-7541 FAX: 415-723-7016 Internet: cherry@genome.stanford.edu From owner-acedb@net.bio.net Fri Jun 25 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software.acedb Subject: Re: Summary: Easier data installation? Message-ID: <1993Jun26.164810.13008@comp.bioz.unibas.ch> Date: 26 Jun 93 16:48:10 GMT References: <1993Jun26.155829.16467@leland.Stanford.EDU> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 67 Nntp-Posting-Host: biox.embnet.unibas.ch In article <1993Jun26.155829.16467@leland.Stanford.EDU>, cherry@genome.Stanford.EDU (Mike Cherry) writes: ... |> WCS used rdist to update their files, and I believe WCS hasn't had an |> update since Feb 1992. Which does mean the local WCS admin doesn't do ... |> quoting Don Gilbert saying, |> >It would make the life of overworked sys admins and undertrained biologists |> >simpler if acedb software could incorportate network links to |> >a home server which would update local data automatically, more or less. |> >I'd hope to see this scheme considered for many biology databases, esp. |> >if they include tailored software like acedb does. |> |> We, the AAtDB Project, haven't heard many (if any) complains about the |> update process. We have biologists without any experience with |> computers doing the AAtDB updates around the world. Do others have |> suggestions for making the process easier than it already is? Is this |> a problem that others are concerned about? |> I am working with a general-purpose client/server architecture which allows for easy data update/transfer. The software runs under the Hierarchical Access System for Sequence Libraries in Europe (HASSLE protocol) and updates data with a merging process. Tailored procedures for EMBL and other sequence databases makes life quite easy. Test bed installations run successful already for over a year, wider applications are envisaged this fall. Another superior approach for sequence databases is Peter Gad's (Uppsala) EMBL Network Data Transfer protocol (EMBL NDT), which is used in EMBLnet international links. The general question, however, is what the users want. Bluntly, biologists are not informed what they can miss if they don't do the updates right. Two alternatives: PUSH paradigm: A big 'papa' sits somewhere on the network and puts data to all nodes which subscribed to the service. The customer runs a server process (most trivially, a FTP server) and the provider runs a client process which connects to this server in order to push all data needed. EMBL NDT works this way, too. The drawback is that the data service provider might need to access the machine to be updated at times of inconvenience and/or require privileges to run. POLL paradigm: A customer runs a client process and polls for new data at the provider's service process. As this is like the current NCBI setup of Genbank data, the easiest implementation would be an ftp client at the customer's site and a FTP server at the provider. It is, however, desirable that the customer gets all data which are not at the customer's site (and only these). Therefore, some computation at the server's site is desirable. HASSLE's dbtools software works this way. I would very much enjoy more discussion on this topic. Can someone comment on the availability of WCS in Europe, and its implementation (hardware, software, reliability)? Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-acedb@net.bio.net Mon Jun 28 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!swrinde!cs.utexas.edu!news.uta.edu!news From: patrick@wbar.uta.edu (Patrick Phillips) Newsgroups: bionet.software.acedb Subject: ACEDB for NeXT Message-ID: <1993Jun29.165526.26040@news.uta.edu> Date: 29 Jun 93 16:55:26 GMT Sender: news@news.uta.edu (USENET News System) Organization: University of Texas at Arlington Lines: 18 Nntp-Posting-Host: wbar.uta.edu If anyone cares, I have ACEDB vers 1.9 running on my NeXTstation TurboColor under coXist (these capitalization schemes are getting too complex). Jean Thierry-Mieg told me at the worm meetings that he simply forgot to post the latest version for NeXT, but it is still not there. If anyone needs it, let me know. On similar note, NeXT has ported their operating system to IBM compatible 486 machines (these need to be pretty high end in terms of memory and graphics capability). This provides a nice platform for running ACEDB on a PC, *if* you want to have the other nice features of NEXTSTEP. Otherwise, there is always the free LINUX version. You'll never get my NeXT away from me, however. Patrick Phillips Biology Department University of Texas at Arlington patrick@wbar.uta.edu phil@decster.uta.edu From owner-acedb@net.bio.net Mon Jun 28 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!elroy.jpl.nasa.gov!swrinde!network.ucsd.edu!munnari.oz.au!constellation!rex!cpu2.omrf.uokhsc.edu!barsteadr From: barsteadr@omrf.uokhsc.edu Newsgroups: bionet.software.acedb Subject: solaris acedb Message-ID: <1993Jun29.110507.1@omrf.uokhsc.edu> Date: 29 Jun 93 17:05:07 GMT Sender: news@rex.uokhsc.edu (News Admin) Organization: Oklahoma Medical Research Foundation Lines: 11 Nntp-Posting-Host: cpu2.omrf.uokhsc.edu I recently read a note here saying the Carl Riches had a Solaris version of acedb. The note has subsequently disappeared, so I can't reply to it directly. I also saw Dr. Riches name in a README file at the NCBI. When I tried to retrieve it from 'cgrpoplar1.cfr.washington.edu', however, I couldn't find a server that would recognize the address. Others seem to be having the same problem. Does anyone have any suggestions? Bob Barstead Oklahoma Medical Research Foundation barsteadr@omrf.uokhsc.edu From owner-acedb@net.bio.net Tue Jun 29 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!usc!sdd.hp.com!saimiri.primate.wisc.edu!ames!agate!headwall.Stanford.EDU!nntp.Stanford.EDU!genome.Stanford.EDU!cherry From: cherry@genome.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: solaris acedb Message-ID: <1993Jun30.053836.771@leland.Stanford.EDU> Date: 30 Jun 93 05:38:36 GMT References: <1993Jun29.110507.1@omrf.uokhsc.edu> Sender: news@leland.Stanford.EDU (Mr News) Organization: Stanford Yeast Genome Project Lines: 36 In article <1993Jun29.110507.1@omrf.uokhsc.edu> barsteadr@omrf.uokhsc.edu writes: >I recently read a note here saying the Carl Riches had a Solaris >version of acedb. The note has subsequently disappeared, so I can't >reply to it directly. I also saw Dr. Riches name in a README >file at the NCBI. When I tried to retrieve it from >'cgrpoplar1.cfr.washington.edu', however, I couldn't find a server >that would recognize the address. Others seem to be having the same >problem. Does anyone have any suggestions? The repository/acedb/README.SOLARIS file on ncbi.nlm.nih.gov says: This port was done by Carl g Riches cgrpoplar1.cfr.washington.edu it has not been tested by mieg/durbin who do not yet have access to a solaris but is ok as far as we know. jean That should be: cgr@poplar1.cfr.washington.edu It is an address (an e-mail address) not a hostname. Also the binary compressed tar file is on ncbi.nlm.nih.gov in the repository/acedb directory and is called: bin.solaris2.1_9_1.tar.Z Note the last line of Jean's README.SOLARIS above. Mike -- J. Michael Cherry Project Manager, Yeast Genome Database Stanford Genome Sequencing Center, Department of Genetics Stanford University School of Medicine, Stanford, CA 94305-5120 Voice: 415-723-7541 FAX: 415-723-7016 Internet: cherry@genome.stanford.edu