From owner-acedb@net.bio.net Tue Sep 07 23:00:00 1993 Path: biosci!rutgers!cis.ohio-state.edu!math.ohio-state.edu!uwm.edu!spool.mu.edu!agate!dog.ee.lbl.gov!slavsing.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Notes from ACEDB Workshop, part I Message-ID: Date: 8 Sep 93 16:42:17 GMT Followup-To: bionet.software.acedb Organization: Lawrence Berkeley Laboratory Lines: 688 NNTP-Posting-Host: 128.3.252.43 By popular request, here are some very rough outline notes I took at the ACEDB Workshop in Boston last month. I cannot vouch for their accuracy, but hope I have not misquoted anyone too badly. Please post corrections and clarifications to this newsgroup. The full set of notes are about 20 pages long. I have broken them into two parts to accomodate my news reader and mail software. If you have questions about particular points, you probably should send them directly to the people who made those points at the workshop. A list of workshop attendees with Email addresses was posted to this newsgroup a few weeks ago. A copy of this document is available via anonymous ftp on weeds.mgh.harvard.edu under pub/acedb-dev/doc -John McCarthy, Lawrence Berkeley Laboratory ================================================================== ACEDB Workshop Wed 28-31 July 1993 Boston, MA Highlight notes from John McCarthy (LBL) jlmccarthy@lbl.gov more or less in chronological order, with TOPICS IN CAPS see list of attendees for full names, addresses, etc. Wed 28 July ================================= COMMUNICATIONS, GOPHER Mike Cherry is providing ACEDB archive on his gopher server at Stanford -- genome.stanford.edu. Mike asks if people could please send notes to bionet.software.acedb another thing that would be nice to have is FAQ - Brad will do this weeds.mgh.harvard.edu has anonymous gopher+ login/server Also experimenting with remote anonymous AATDB login aatdb user name c-aatdb used for MacX Mike used Richard's acedump to create gopher files. WAIS paragraph format / from acedump also textace Brad notes that his gopher archive includes USDA sysad archive. Brad Sherman did research for secure anonymous ftp Mike: weeds is a separate machine, not cross mounted to anything, and not used for anything else stty script -- Otto points out that you can trap interupts with Bourne shell Brad points out that most vulnerable spot is within application. anonymous FTP setup instructions, thor.ece.uc.edu /pub/sun-faq/anon-ftp.script guidelines: . cert.org /pub/tech.tips/anonymous.ftp ========================================================= PRINTING FOR REMOTE USERS richard: set ACEDB_LPR to null -- code checks for this. maybe could do a script that turns print script into Email. Michelle: also may want to print to a file (richard: currently always goes into /PS directory). Stan: might be nice to have switch to disable all writing could do changeroot to keep people restricted to specified area. ================================= ACEDB NEW DEVELOPMENTS - Richard Durbin: ORGANIZATIONAL STATUS, what Richard and Jean are doing: RD -worm sequencing (2,5,10 Mb/yr) -sanger Centre (RD joint head of informatics) -CGC map -> Cambridge (worm cytogenetics center) Mary O'Callaghan doing this (moc@mrc-lmb.cam.ac.uk) -in house use: sequence (worm, yeast, human) worm genetic map so RD will have less time for kernal development Jean: -Human mapping - Frensal (Genethon) -IGD -ports to various unix systems - management of kernal (want to keep unified version) incorporate changes from others & redistribute also would like to make other's tools & modules available RELEASES: 1-10 now (still backwards compatible with old databases) 2-0 September? (model changes for maps, sequences) running this in Cambridge now but want to make other changes before release would like to get some feedback from this workshop first developers can get 2-0 code but should not use for databases that will be distributed, etc. Will have AWK scripts for database restructuring from 1-10 to 2-0 Extra things in specifications directories, PS fonts, Xfonts.wrm, NEW ARCHITECTURE FOR MAP DISPLAY-- RD columnar architecture/format will help would also be nice to have developers style guide Stan: would be nice to have another level of indirection, so people could map different names to std display code names -- intermediate layer to make it easier to change models and yet maintain compatibility with display modules. RD: not convinced that another layer of indirection is good idea may slow things down RD: people should not expect that all the good ideas that get suggested here will get implemented. Commitment to maintain kernal. ------------------- break----------------------- NEW DEVELOPMENTS (mostly in 1-10) SUBCLASSES -can appear on main window -can use in queries, .ace files -no code change required specification -wspec/subclasses.wrm -read after models.wrm -ace file class genome_Sequence Subclass-of Sequence //can be a subclass (can have 2 parents?) Visible //indicates whether displayed on main window Filter "Genomic_canonical" query How it works: Have 8 bits free per key in memory -uses 1 bit per filter checks on object save when filter changes -- rescans entire class with query can't change entries in class class directly, reads from subclasses.wrm May be possible in future: to have different default display type for different subclasses Used in 2.0 ?Map - Chromosome ?Locus - gene, RFLP, etc. ?Interval - rearrangement, Chrom_Band, Hybrid cell line, ... ?Df_dup_defic Inside Outside ?Probe 2-0 has a models class so won't have ?class as part of keyset you will get this type of info in other ways 2 possible ways to do sub-maps 1 scale with some linear transformation 2 interpolate between shared loci (now done in 1-10 physical map) Otto: IGD has used clone grid as general model for 2-D maps RD: map display now automatically transforms contig info in this way maybe could do some graphic to indicate where there are conflicts between different versions of maps GRAPH PACKAGE additions filled arcs filled polygons (from Suzanna) IMAGES (grey level: 256-->128) (a) in subwindow graphPixels() (b) PIXEL_SCROLL graph type (coordinates are pixels) graph Pixel Background() Possible Development -ASCII dump format for draw stack -stand alone drawing editor full color images will require more thought! now easier to attach sub-menus to boxes Otto: can pick up X colors and coordinates to use from XV Suzanna: has done some things to display TIFF images MAP PACKAGE map.h w7/mapcontrol.c A. drawing coordinates (zoom, centre, scroll, etc.) B. columns of data (user toggleable) C Cursor MAP *map Look -> map -> mapCreate(column, ... ) {float min, max Coordinate Functions Locator (small green bar) Stan: is this the way you would draw multiple (synteny) maps? RD: not yet..., in the meantime can use TableMaker multi-map Planned Enhancements 1. add a help line per column for display control 2. allow >32 columns 3. give names to sets of columns 4 ? Multiple ?MAP's per window Code: separate columns further ==>library of columns separate SEG's array per column (convert (store), destroy) put PICK control in MAP package -select / follow - neighbor on/off (key) [e.g., to light up related objects] Sequence Fetch/Align -------------------------- a. summon up SwissProt/PIR entry(s) b. show multiple alignment based on BLAST segments =BLIXEM uses unix command fetch -Bdbname (SP,PIR,EMBL,GB) -a accession number -P Pearson (FASTA) format -s just sequence ... no new line our version uses the EMBL CDROM index structu From owner-acedb@net.bio.net Tue Sep 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!pipex!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!agate!dog.ee.lbl.gov!slavsing.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Notes from ACEDB Workshop, part 2 of 2 Message-ID: Date: 8 Sep 93 16:44:30 GMT Followup-To: bionet.software.acedb Organization: Lawrence Berkeley Laboratory Lines: 326 NNTP-Posting-Host: 128.3.252.43 This is the second part of some very rough outline notes I took at the ACEDB Workshop in Boston last month. I cannot vouch for their accuracy, but hope I have not misquoted anyone too badly. Please post corrections and clarifications to this newsgroup. The full set of notes are about 20 pages long. I have broken them into two parts to accomodate my news reader and mail software. If you have questions about particular points, you probably should send them directly to the people who made those points at the workshop. A list of workshop attendees with Email addresses was posted to this newsgroup a few weeks ago. A copy of this document is available via anonymous ftp on weeds.mgh.harvard.edu under pub/acedb-dev/doc -John McCarthy, Lawrence Berkeley Laboratory ====================FRIDAY============================= AM demos & tutorial (very popular!) GENETIC MAPS an item gets put on genetic map if it has a name and coordinates can set center and extent within ?Chromosome interesting links to 2 and 3 point data, which displays distance difs nice quick visual summary of how well map fits expmtl data menu items for show/highlight selected objects (from KeySet) show = only display ones on keyset, highlight keeps others [need better names of menu items "show Keyset items", "Highlight ] middle button lets you recenter, also at bottom of page it scrolls 1/2 page at a time middle button to left of left green bar (locator), also zooms if you move it left and right with middle button, scales continuously in ?Chromosome Centre x y y=initial spread when loci are displayd Extent x y map coords of left & rt ends of black bar Error_factor x=number that multiplies times 2nd number (treat with grain of salt because things get bumped right] Bigwood: might be nice to have this not be linear Otto knows how this all works can be set different for dense maps also can put anchor loci beside black bar by setting tag Marker gene in ?Gene class [really need Richard and Jean to define tags like these!!] Private maps ... may go away (no longer in RD's 2.0) physical chromo map: contigs can have gMap coords & get displayed on map if you choose this item, it strings together contigs with gaps shows boxes to left of scale representing clones, cDNA's etc via Keyset in order to see distribution along the physical map tied via pMap tags Chrom-band class: can have dark, light, and color also can set centromere, don't have telomere's deficiencies and duplications 1,2, or thick bar -- set as tag in rearrangement class click to see name displayed above GMap Data button shows things inside or outside rearrangements displayed in dif colors - linked via ??? tags linkage data has been tailored to C. elegans, but some use elsewhere 2ptdata, 3ptdata will be changed a lot in 2-0 2pt_data is for "selfed" Wild Type A B AB mendelian ratio 9 3 3 1 slots to show calculated distance and errors they have 19 dif types of crosses represented in 2-0 data file there is a description file that goes along with it (wdoc--should be part of help/hints/metadata) 3pt_data: A-non-B recombinants B-non-A recombinants one or more unknown markers a5c12b a 0 c 8 b does not unambiguously determine order with new system, can enter multi-point data, not just 3-point could use to test RFLP's between known markers on gMap, main markers shown by large squares, others by small function lets you display relative likelihoods for selected locus red line end points constrained by mult point data, def/dup, pMap framework probably appropriate even if detailed calculations are not Frank: what happens if you have contradictions (highlight in dark) RD: can fix certain loci and recalculate others via keyset [would also be nice to have screen dump with lines to explain each component] can throw out any particular data item and recalculate local set Jean may be putting in additional info re LOD scores, etc for Genethon for dif kinds of experimental data ======================lunch============================= DATA LOADING Dave Matthews asks RD to eliminate setenv ACEDB_SU should give full main menu for everyone with write access RD: C.elegans has moved towards on-line updates & master is db DM: would like transaction report new objects created explicitly, implicitly objects changed, new fields added, fields replaced links made to existing objects deletes, renames of individual objects, data fields SL: before a load, she dumps current db, then dumps new & does dif also knows what things should not happen. Otto: could you query the lexique to see if new objs created? RD: in past has thought would be good idea to have dry run input Mike: does script to look up objects he expects to find in db Brad: in prior project, did a transaction log and tools to operate on it it took a lot of time to do, and was very little used RD: thinks it would be easier to produce big file and tools to use it maybe code in front of each input line to indicate what happens to it Otto: what about dump option including session # for each object&tag Mike: essentially an ACEDIFF where you do dump before you save can do query to get all newly created & updated objects RD: this gets back to yesterday's idea to be able to do keyset of changed objects. JM: can we do search for empty objects? RD: other thing would be to do a more efficient acedif make list of all things touched, acedump, quit RD: it would be a good idea and not hard to do query for all items that have been changed, and/or all empty items (italicized) also thinks its reasonable to do acefile annotated with what happens tool could pass over this to create summary report of what happened Problem with dry run is that it would not reflect load A, then XREF A Brad: no one has proposed automated solution to all this Wants data providers to give him a text file that explains data file that can be understood by undergraduate. Thinks .ace files are going to be the database for some time to come. Needs to establish new strategies for data collection in the lab. =================IMAGES Otto: Alex virtual file system can keep correspondence of virtual and real machines Frank: most neuroscience is 3-D image data, acquired via dif methods hard to register dif types of info with one another (same scales, etc.) proposes new standard class ?Image ?Image Text //path to where image is stored Class //type of image (postscript, gif, pict) size //bits preferred display program might give many images Box x y width height parts of image another thing you want to do is overlay, with approx registration PACS - picture archiving and communications systems most use Sybase, etc. Dave and Brad want to integrate geographic maps where stuff grows RD: Hotspot x y w h #Class #Class Locus ?Locus Clone ?Clone etc. for all classes (could be useful elsewhere) Frank: general... how to indicate hotspots-draw box (or shade) as mouse passes over it, menu choice for display hotspots, Eric: medical community just beginning to do smart things with images, so not likely to learn much from PACs, but GIS has already done a lot and may have more to offer. ============break============= METADATA: Cartinhour, McCarthy Sam: already a fair amount of metadata in acedb model itself, help files, hints can extend in several directions... e.g., to document tags and data fields e.g., Chrom_band gMap ?Chromosome int int ===================================================== DOCUMENTATION Mike: can take many forms ... Ian Dunham has chap in book on physical map databases FAQ, tutorial, on-line help, clean up doc/ directory, doc list, 4 ace docs: intro, installation guide, config guide, syntax Sam & John white papers on metadata Sam: need new docs on table-maker, query language, tools perhaps a list of canned queries to cut & paste along with explanation of what it was intended to do (perhaps via //comment on query line) RD has some too programmers guide, how to do a new module, application RD: biblio.c is a nice eg for this weeds has anonymous ftp incoming Mary Callahan has written intro thing with RD Sam & Mike contrib to book RD not too enthusiastic about making help more of a database Dave M: README would be even more helpful for installation RD: this is currently in "Notes" Mike: other newsgroups have had one person do FAQ and then put on newsgroup & get redone periodically Brad: volunteers to put together intial FAQ other volunteers: Marc, Otto, Lisa, Sam, John, Richard, Jean, David, Staffan, Brad, Edie (for review, etc. -- worked on commercial doc) Eric: what about TeX info ala Gnu project? Sam: will do intro manual re how to do create models Doug: need virgin users to critique documents, interfaces, etc. ======================================================== ACEDB PLATFORMS & PERFORMANCE (Richard) Performance Sun Sparc I (ipc) II (ipx, 470) 10 From owner-acedb@net.bio.net Sat Sep 11 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!mcsun!julienas!jouy!moulon!decoux From: decoux@moulon.inra.fr (ts) Newsgroups: bionet.software.acedb Subject: gateway WWW-ACEDB Message-ID: <1993Sep12.144428.14066@inra.fr> Date: 12 Sep 93 14:44:28 GMT Sender: decoux@moulon (ts) Organization: INRA - Moulon Lines: 37 Nntp-Posting-Host: moulon-gw Gateway WWW-ACEDB ================= If you want to consult ACeDB and MycDB, try : * "http://moulon.inra.fr/acedb/acedb.html" to consult "A Caenorhabditis elegans Data Base" (ACeDB). * "http://moulon.inra.fr/acedb/mycdb.html" to consult "Mycobacterium DataBase". "Mycobacterium DataBase" is funded by the WHO and the Fondation Raoul Follereau and is maintained by the Unite de Genetique Moleculaire Bacterienne at the Institut Pasteur. To consult these databases, you can : * If you know syntax of "tace" commands, enter your query in "SearchText". * otherwise you can make a complete Consultation of the database. For more precisions, about "tace" syntax, just enter "help". If you want to create an ACEDB gateway, see (or contact me) : "http://moulon.inra.fr/acedb_conf_eng.html" ou "http://moulon.inra.fr/acedb_conf.html" (version francaise) -- Guy Decoux From owner-acedb@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!HERMES.CHPC.UTEXAS.EDU!mwitten From: mwitten@HERMES.CHPC.UTEXAS.EDU Newsgroups: bionet.software.acedb Subject: CONGRESS: COMPUTATIONAL MEDICINE AND PUBLIC HEALTH (long) Message-ID: <9309141757.AA08577@morpheus.chpc.utexas.edu> Date: 14 Sep 93 17:57:00 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 555 ** NOTE CHANGES IN SUBMISSION AND REGISTRATION DEADLINES ** FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE, PUBLIC HEALTH AND BIOTECHNOLOGY 24-28 April 1994 Hyatt Regency Hotel Austin, Texas ----- (Feel Free To Cross Post This Announcement) ---- 1.0 CONFERENCE OVERVIEW: With increasing frequency, computational sciences are being exploited as a means with which to investigate biomedical processes at all levels of complexity; from molecular to systemic to demographic. Computational instruments are now used, not only as exploratory tools but also as diagnostic and prognostic tools. The appearance of high performance computing environments has, to a great extent, removed the problem of increasing the biological reality of the mathematical models. For the first time in the history of the field, practical biological reality is finally within the grasp of the biomedical modeler. Mathematical complexity is no longer as serious an issue as speeds of computation are now of the order necessary to allow extremely large and complex computational models to be analyzed. Large memory machines are now routinely available. Additionally, high speed, efficient, highly optimized numerical algorithms are under constant development. As these algorithms are understood and improved upon, many of them are transferred from software implementation to an implementation in the hardware itself; thereby further enhancing the available computational speed of current hardware. The purpose of this congress is to bring together a transdisciplinary group of researchers in medicine, public health, computer science, mathematics, nursing, veterinary medicine, ecology, allied health, as well as numerous other disciplines, for the purposes of examining the grand challenge problems of the next decades. This will be a definitive meeting in that it will be the first World Congress of its type and will be held as a follow-up to the very well received Workshop On High Performance Computing In The Life Sciences and Medicine held by the University of Texas System Center For High Performance Computing in 1990. Young scientists (graduate students, postdocs, etc.) are encouraged to attend and to present their work in this increasingly interesting discipline. Funding is being solicited from NSF, NIH, DOE, Darpa, EPA, and private foundations, as well as other sources to assist in travel support and in the offsetting of expenses for those unable to attend otherwise. Papers, poster presentations, tutorials, focused topic workshops, birds of a feather groups, demonstrations, and other suggestions are also solicited. 2.0 CONFERENCE SCOPE AND TOPIC AREAS: The Congress has a broad scope. If you are not sure whether or not your subject fits the Congress scope, contact the conference organizers at one of the addresses below. Subject areas include but are not limited to: *Visualization/Sonification --- medical imaging --- molecular visualization as a clinical research tool --- simulation visualization --- microscopy --- visualization as applied to problems arising in computational molecular biology and genetics or other non-traditional disciplines --- telemedicine *Computational Molecular Biology and Genetics --- computational ramifications of clinical needs in the Human Genome, Plant Genome, and Animal Genome Projects --- computational and grand challenge problems in molecular biology and genetics --- algorithms and methodologies --- issues of multiple datatype databases *Computational Pharmacology, Pharmacodynamics, Drug Design *Computational Chemistry as Applied to Clinical Issues *Computational Cell Biology, Physiology, and Metabolism --- Single cell metabolic models (red blood cell) --- Cancer models --- Transport models --- Single cell interaction with external factors models (laser, ultrasound, electrical stimulus) *Computational Physiology and Metabolism --- Renal System --- Cardiovascular dynamics --- Liver function --- Pulmonary dynamics --- Auditory function, coclear dynamics, hearing --- Reproductive modeling: ovarian dynamics, reproductive ecotoxicology, modeling the hormonal cycle --- Metabolic Databases and metabolic models *Computational Demography, Epidemiology, and Statistics/Biostatistics --- Classical demographic, epidemiologic, and biostatistical modeling --- Modeling of the role of culture, poverty, and other sociological issues as they impact healthcare --- Morphometrics *Computational Disease Modeling --- AIDS --- TB --- Influenza --- Statistical Population Genetics Of Disease Processes --- Other *Computational Biofluids --- Blood flow --- Sperm dynamics --- Modeling of arteriosclerosis and related processes *Computational Dentistry, Orthodontics, and Prosthetics *Computational Veterinary Medicine --- Computational issues in modeling non-human dynamics such as equine, feline, canine dynamics (physiological/biomechanical) *Computational Allied Health Sciences --- Physical Therapy --- Neuromusic Therapy --- Respiratory Therapy *Computational Radiology --- Dose modeling --- Treatment planning *Computational Surgery --- Simulation of surgical procedures in VR worlds --- Surgical simulation as a precursor to surgical intervention --- The Visible Human *Computational Cardiology *Computational Nursing *Computational Models In Chiropractice *Computational Neurobiology and Neurophysiology --- Brain modeling --- Single neuron models --- Neural nets and clinical applications --- Neurophysiological dynamics --- Neurotransmitter modeling --- Neurological disorder modeling (Alzheimer's Disease, for example) --- The Human Brain Project *Computational Models of Psychiatric and Psychological Processes *Computational Biomechanics --- Bone Modeling --- Joint Modeling *Computational Models of Non-traditional Medicine --- Acupuncture --- Other *Computational Issues In Medical Instrumentation Design and Simulation --- Scanner Design --- Optical Instrumentation *Ethical issues arising in the use of computational technology in medical diagnosis and simulation *The role of alternate reality methodologies and high performance environments in the medical and public health disciplines *Issues in the use of high performance computing environments in the teaching of health science curricula *The role of high performance environments for the handling of large medical datasets (high performance storage environments, high performance networking, high performance medical records manipulation and management, metadata structures and definitions) *Federal and private support for transdisciplinary research in computational medicine and public health 3.0 CONFERENCE COMMITTEE *CONFERENCE CHAIR: Matthew Witten, UT System Center For High Performance Computing, Austin, Texas m.witten@chpc.utexas.edu *CURRENT CONFERENCE DIRECTORATE: Regina Monaco, Mt. Sinai Medical Center Dan Davison, University of Houston Chris Johnson, University of Utah Lisa Fauci, Tulane University Daniel Zelterman, University of Minnesota Minneapolis James Hyman, Los Alamos National Laboratory Richard Hart, Tulane University Dennis Duke, SCRI-Florida State University Sharon Meintz, University of Nevada Los Vegas Dean Sittig, Vanderbilt University Dick Tsur, UT System CHPC Dan Deerfield, Pittsburgh Supercomputing Center Istvan Gyori, University of Veszprem (Hungary) Don Fussell, University of Texas at Austin Ken Goodman, University Of Miami School of Medicine Martin Hugh-Jones, Louisiana State University Stuart Zimmerman, MD Anderson Cancer Research Center John Wooley, DOE Sylvia Spengler, University of California Berkeley Robert Blystone, Trinity University Gregory Kramer, Santa Fe Institute Franco Celada, NYU Medical Center David Robinson, NIH, NHLBI Jane Preson, MCC Peter Petropoulos, Brooks Air Force Base Marcus Pandy, University of Texas at Austin George Bekey, University of Southern California Stephen Koslow, NIH, NIMH Fred Bookstein, University of Michigan Ann Arbor Dan Levine, University of Texas at Arlington Richard Gordon, University of Manitoba (Canada) Stan Zeitz, Drexel University Marcia McClure, University of Nevada Las Vegas Renato Sabbatini, UNICAMP/Brazil (Brazil) Hiroshi Tanaka, Tokyo Medical and Dental University (Japan) Shusaku Tsumoto, Tokyo Medical and Dental University (Japan) Additional conference directorate members are being added and will be updated on the anonymous ftp list as they agree. 4.0 CONTACTING THE CONFERENCE COMMITTEE: To contact the congress organizers for any reason use any of the following pathways: ELECTRONIC MAIL - compmed94@chpc.utexas.edu FAX (USA) - (512) 471-2445 PHONE (USA) - (512) 471-2472 GOPHER: log into the University of Texas System-CHPC select the Computational Medicine and Allied Health menu choice ANONYMOUS FTP: ftp.chpc.utexas.edu cd /pub/compmed94 POSTAL: Compmed 1994 University of Texas System CHPC Balcones Research Center 10100 Burnet Road, 1.154CMS Austin, Texas 78758-4497 5.0 SUBMISSION PROCEDURES: Authors must submit 5 From owner-acedb@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!FRODO.MGH.HARVARD.EDU!CHERRY From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: ACEDB 1-21 available via Gopher Message-ID: <930915130145.2020011c@Frodo.MGH.Harvard.EDU> Date: 15 Sep 93 17:01:45 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 73 The information from ACeDB release 1-21 is now available via Internet Gopher from weeds.mgh.harvard.edu. Once connected to the weeds.mgh.harvard.edu Gopher server select the following menu item: 5. Arabidopsis Information (thale cress)/ --> 6. Caenorhabditis Inform/ 7. Department of Molecular Biology, MGH/ Then the menus will change to: --> 1. Help Searching the "" databases. 2. ACEDB, A Caenorhabditis elegans Database (1-21) 3. C. elegans Strains and Alleles (University of Texas)/ 4. Caenorhabditis Genetics Center (CGC)/ See the Help document for more details on performing searches. The ACEDB release 1-21 physcial map is also included in a text format. For example: select menu item 2 and entering K09A10 . The search result will be shown as: --> 1. Clone_Pic : K09A10. 2. Contig : ctg1. The Clone_Pic item looks like: Clone_Pic : K09A10 Member of Contig: ctg1 Contig: ctg1 limits: -154 to 436 Limits of this partial view are: -117 to 53 ----------------------Y48E9---------------------- ---------------Y67G4--------------- -----------------------------------Y53C6----------------------------------- -------------Y48A8------------- -----Y27H10----- ------Y68B7------ ---K05C4--- --R10E1-- ---C43D5--- ----F14B11---- ====K09A10==== -------------------Y54F6!------------------- ---T10A7--- -----C13G1----- ---SG25/36--- ------K05G4------ -SG23/3- ------C03C9------ This release of ACEDB include many abstracts from the Worm Breeder's Gazette so you can search for general terms like kinase, neuro* or homeo* to find several items of interest. The Gopher .Link entry, for those that like this form, is: Type=7 Name=ACEDB, A Caenorhabditis elegans Database (1-21) Path=7/.index/Caenorhabditis_elegans_Genome Host=weeds.mgh.harvard.edu Port=70 The ACEDB software for Unix X-windows and the ACeDB database is developed and maintained by Richard Durbin (MRC-LMB, U.K.) and Jean Thierry-Mieg (CNRS, France). Durbin R and Thierry-Mieg J (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. Mike Cherry cherry@frodo.mgh.harvard.edu From owner-acedb@net.bio.net Thu Sep 16 23:00:00 1993 Path: biosci!FRODO.MGH.HARVARD.EDU!CHERRY From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: AAtDB 1-5 now available Message-ID: <930917010317.202008b5@Frodo.MGH.Harvard.EDU> Date: 17 Sep 93 05:03:17 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 242 AAtDB release 1-5 Release 1-5 of AAtDB, An Arabidopsis thaliana Database, is now available for Unix workstations as well as through the Internet using the Gopher and WAIS software clients. This release of AAtDB includes several new and updated types of information: o New and revised stock information provided by Mary Anderson of the Nottingham Arabidopsis Stock Centre. o Over one hundred new images of Arabidopsis ecotypes and mutations available from either the Ohio State or Nottingham stock centers. o Over one thousand new DNA sequences from GenBank including the sequence similarity of these sequences to entries in the protein sequence databases as defined by NCBI's BLASTX software. o Several new and updated Colleague entries. o New bibliographic information from Medline. AAtDB Class Sizes in release 1-5: Class Name Total Entries New Entries in 1-4 =============== ================= ==================== Allele 293 165 Author 4272 243 Chromosome 25 0 Clone 14606 0 Clone_Grid 2 0 Colleague 1277 15 Contig 1196 0 DNA 2485 1066 Gene_Class 243 2 Gene_Product 187 40 Image 235 113 Journal 361 8 KeySet 22 4 Keyword 5369 256 Locus 1398 143 Paper 3535 187 Phenotype 1449 54 Population 26 6 Probe 426 1 Restriction 338 0 Sequence 9006 4097 Source 58 1 Strain 5567 1081 2_point_data 3741 0 AAtDB uses the ACEDB software developed by Richard Durbin (MRC-LMB, U.K.) and Jean Thierry-Mieg (CNRS, France). The AAtDB project is funded by the U.S. Department of Agriculture Plant Genome Research Program through the National Agricultural Library. The AAtDB project is staffed by members of the Department of Molecular Biology at Massachusetts General Hospital and Harvard Medical School, Boston USA. AAtDB is available without charge via Internet FTP transfer and remote X-windows access (see below). AAtDB features a wide variety of public information that is presented using graphical, text, and tabular formats. The user interface, which was designed to invite browsing, allows users to explore information by pointing and clicking with the workstation mouse or by using a versatile query facility. ACEDB allows all parts of the database to be cross-referenced with each other. The large number of interconnections provides a dense navigable network in which information can be located from many different starting points (see sample screen in appendix). All information contained within AAtDB was obtained directly from the original authors or from publicly available collections and databases. Updates to AAtDB are periodically distributed and the database is now in its fifth data release. A partial list of the information AAtDB 1-5 contains includes: -- The Hauge/Goodman cosmid physical map including greater than 14,000 cosmid clones. The contigs of the physical map are associated with the genetic maps. -- Genetic markers, including RFLP, RAPD, and "classical" markers. -- Genetic maps, including the Integrated map from Hauge et al. (1993) The Plant Journal, a visible marker map including many embryo defective loci from David Meinke, and RAPD maps from Scolnik et al. (1992) PNAS. -- Primary F2 and RI population recombination data from the Goodman, Meyerowitz, Scolnik, and Dean laboratories. -- Primary 2-point data from M. Koorneef, D. Meinke, and others. -- Strain list, now maintained and entered for AAtDB by Mary Anderson at the Nottingham Arabidopsis Stock Centre. Includes many new entries from the Nottingham and Ohio State stock centers. -- List of Arabidopsis researchers, including postal mail address, telephone and FAX numbers, electronic mail address, publications, research interests, and research associates. Information on over 1200 colleagues is included. -- All Arabidopsis DNA sequences from GenBank and EMBL DNA sequence databases as well as the EST (expressed sequence tags, i.e., cDNA) reports from the NCBI's dbEST database on the MSU and French sequencing efforts, with over 2400 entries total. -- NCBI BLASTX (six frame translations searched against the NCBI non-redundant peptide database) defined peptide sequence homologies for all DNA sequences included in AAtDB. -- Phenotype descriptions from the Green Book by Meyerowitz and Pruitt, updated with descriptions from the Nottingham and Ohio State stock centers. -- Scanned images of RFLP autoradiograms from the Goodman lab, photographs of mutant plants from G. Redei and M. Anderson, and ethidum bromide-stained restriction enzyme digests of RFLP probes distributed by the ABRC. -- Bibliographic citations, including references for all articles from the Arabidopsis Information Service, currently numbering 3400. AAtDB 1-5 utilitzes the new ACEDB 1.10 software providing fixes and new features. Note that the ACEDB software is now available for the public Unix version called Linux that runs on Intel 386 and 486 based systems! For more information about Linux retrieve the linux.readme file via anonymous ftp or Gopher. The ACEDB software is developed by Richard Durbin (MRC-LMB, Cambridge, UK) and Jean Thierry-Mieg (CNRS, Montpellier, France). Precompiled executables of ACEDB are available for Sun SPARC (SunOS and Solaris), DEC MIPS and Alpha, NeXT, IBM-6000, and Silicon Graphics workstations under the X-windows environment plus Intel 386 and 486 computers running Linux. ACEDB can be compiled on Suns under Sunview or Sun386i under OpenWindows, Alliant, and CONVEX computers. A Macintosh version is in development. All the AAtDB information in text form is available via the Arabidopsis Research Companion, an Internet Gopher server available from the host Weeds.MGH.Harvard.EDU. For convenience the bibliographic references have been converted to Macintosh EndNote and the general bibliographic format called refer. The new images obtained from the ABRC at Ohio State University are available as GIF files. All these files are available via Gopher and anonymous ftp from the host Weeds.MGH.Harvard.EDU (IP 132.183.190.21). Using Gopher to search AAtDB and retrieve information: Internet Gopher was developed by the University of Minnesota. It requires a computer that is connected to the worldwide Internet network. Software referred to as a Gopher client is available for most types of computer, most of these are available via anonymous ftp from boombox.micro.umn.edu. If your computer manager cannot provide you with one of the free Gopher clients but you have access to telnet you can use a public access account provided by the Department of Molecular Biology at Massachusetts General Hospital. Simply telnet to the host Weeds.MGH.Harvard.EDU (IP 132.183.190.21), use the username gopher, there is no password. A Gopher client will start that automatically connects with the AAtDB Research Companion. Text information can be mailed from the public gopher account by using the "m" option. However the images cannot be viewed using the public telnet account. A Gopher client on your local computer is required to view images, or you can transfer the images via an ftp or Gopher client to an intermediate computer subsequently transferring the image to a workstation or personal computer that can display GIF and JPEG images. Remote Access to the Unix AAtDB database using X-windows Remote access to the full Unix version of AAtDB is now available to computers with a good Internet network connection and X-windows software. This means that most Unix workstations using OpenWindows, Motif, or any of a large number of other windowing environments based on MIT's X-windows can access a remote server that will display the graphic interface of AAtDB on the local computer's display. For personal computers a variety of commercial X-windows emulation software is available: Macintosh users can purchase eXodus (White Pine Software) or MacX (Apple Computer), MS Windows users can use Vista eXceed plus (Hummingbird Communications) or DESQview/X (Quarterdeck Office Systems). The basic procedure is to login on the host weeds.mgh.harvard.edu using the username 'aatdb'; no password is required. If you are on a Unix X-windows workstation you will need to issue the following command before connecting with the server: % xhost weeds.mgh.harvard.edu The above command is required to allow the AAtDB server to creat From owner-acedb@net.bio.net Tue Sep 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!pavo.csi.cam.ac.uk!nntp-serv!esr From: esr@al.mrc-lmb.cam.ac.uk (Sonnhammer E./Durbin) Newsgroups: bionet.software.acedb Subject: Re: Notes from ACEDB Workshop, part I Message-ID: Date: 22 Sep 93 16:40:05 GMT References: Sender: news@infodev.cam.ac.uk (USENET news) Followup-To: bionet.software.acedb Organization: /hgmp0/esr/.organization Lines: 35 In-Reply-To: jlmccarthy@lbl.gov's message of 8 Sep 1993 16:42:17 GMT Nntp-Posting-Host: al.mrc-lmb.cam.ac.uk Thanks John McCarthy for your excellent notes of the ACEDB workshop! I feel obliged, however, to correct your notes on 'fetch' which retrieves sequence data from external databases for either annotation pop-up or multiple alignment of blast segments in 'Blixem'. Your notes say: > Sequence Fetch/Align > -------------------------- > a. summon up SwissProt/PIR entry(s) > b. show multiple alignment based on BLAST segments = BLIXEM > uses unix command > fetch -Bdbname (SP,PIR,EMBL,GB) > -a accession number > -P Pearson (FASTA) format > -s just sequence ... no new line > our version uses the EMBL CDROM index structure The -P and -s options are incorrect. They should be -f Pearson (FASTA) format -q just sequence (on one line) The fetch program used here in Cambridge is available by anonymous FTP on cele.mrc-lmb.cam.ac.uk in /pub/acedb/fetch.tar.Z, which contains further instructions. There are actually about 15 options at the moment. If you prefer to call your own 'fetch' from ACEDB, only the -q option is necessary though. Erik Sonnhammer Sanger Centre Cambridge, UK From owner-acedb@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!fly2.berkeley.edu!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: Write locks in Acedb [Long and boresome, for code nerds only] Message-ID: Date: 23 Sep 93 21:06:12 GMT References: <1993Sep23.182732.1681@gserv1.dl.ac.uk> Distribution: bionet Organization: University of California, Berkeley Lines: 49 NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: rd@uk.ac.cam.mrc-lmb's message of Thu, 23 Sep 1993 18:20:03 GMT I did not ask the question clearly enough, so let me take another stab at it. My understanding of this program is somewhat incomplete (i.e.: I haven't managed to read through the TAGS file...), but my presumption is that the user grabs "write access" to the database and is then allowed an extended browsing period where they build up a "delta" to be applied to the database, which is then committed in a single call to sessionClose(true). The effect being that other readers of the database will see a sudden, consistent change to the database, but that only one session will be allowed into the "gather and modify" mode at a time. My suggestion was along the lines of only locking the database at the "moment" of committing a change, with the option of alerting other sessions (that were contemplating changes) that a change had been made to the database, and giving them the option to abandon their (uncommitted) changes or run a check for overlaps, or whatever. I would also like to hack the session ID "numbers" to include the machine, user and (Unixy) process ID number. This would be a step along the way to providing a "virtual server" implemented in the file system itself. The end result of my little plot would have "minor version numbers" attached to the database where at certain points readers of the database would notice that the version number had changed beneath them and flush their little caches, while browsers would be left alone to complete their "delta" and then when they choose to commit it be informed that a change had taken place in the database and be allowed to step through the records involved and combine the original, their changes and the other changes. This would, of course, update their "snapshot" of the database and if further changes occurred while they were back into this browsing mode they would face the same process over (from the new snapshot) when they again try to commit. (This also might prove helpful in merging together versions of the database from different user sites). Now (fortunately) I wasn't born a biologist. So it really isn't my place to decide upon the policy of how the multiple writers, multiple machine case should be handled. But as a "Bjarne again" hacker I'd like to implement the mechanism in the cleanest, simplest, most general manner, exactly once. I realize that the only program "guaranteed to work on all machines" is Microsoft Word for Windows, but I do not want to pile up a bunch of redundant backup systems. Given the choice, I'd put my locking code into a few functions and let the end-users replace those as needed. -- Henry J. Cobb hcobb@fly2.berkeley.edu SFB Tyrant From owner-acedb@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: rd@uk.ac.cam.mrc-lmb (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: Write locks in Acedb Message-ID: <1993Sep23.182732.1681@gserv1.dl.ac.uk> Date: 23 Sep 93 18:20:03 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 23 Precedence: first-class Original-To: acedb@uk.ac.daresbury, hcobb@fly2.berkeley.edu Original-Cc: mieg@ppsw.cam.ac.uk It is clear that semaphores are inappropriate for ACEDB, since they are machine specific, and these days people almost always run in a NFS network environment. In fact I always disable them by setting SEM = 0! There is in fact a lock file operating (database/lock.wrm), but that has problems if a program dies ungracefully without removing the lockfile. For that reason ACEDB puts up a warning explanation if the lock file is set, but allows you to override it. I understood that there is an advisory record locking mechanism that works across NFS, breaks the lock when the locking process dies, and even handles remote disk server downs well. This seems to me a good candidate to replace semaphores. Is the problem that it requires lockd, which Henry says is not always available? Even if so, we could use this, with the overidable lock file as a backup. The history of the code that manages all this (session.c) is that it is old and has had a number of solutions layered on each other. I apologise for the mess. Cleanups guaranteed to compile and work on all machines would be appreciated. Richard From owner-acedb@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!pipex!howland.reston.ans.net!agate!fly2.berkeley.edu!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Write locks in Acedb Message-ID: Date: 23 Sep 93 17:59:46 GMT References: Followup-To: bionet.software.acedb Organization: University of California, Berkeley Lines: 14 NNTP-Posting-Host: fly2.berkeley.edu The semaphore system in Acedb seems to be slightly misused, and anyway won't scale over NFS mounts. NFS guarantees only one atomic action (without the presence of lockd, which is not universal): File creation. So is there any objection to throwing out the Semaphores and other junk and replacing this with a simple: open( lockfile, O_RDWR | O_CREATE | O_EXCL) or fail in sessionClose()? -- Henry J. Cobb hcobb@fly2.berkeley.edu SFB Tyrant From owner-acedb@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: rd@uk.ac.cam.mrc-lmb (Richard Durbin) Newsgroups: bionet.software.acedb Subject: more on locks Message-ID: <1993Sep23.214236.3664@gserv1.dl.ac.uk> Date: 23 Sep 93 21:35:09 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 45 Precedence: first-class Original-To: acedb@uk.ac.daresbury Hmm. I think there are technical difficulties with Henry's suggestions. We lock the whole database so that only one user can every be accumulating changes at one time. When one user gets write access that starts a new session and you lock against any others from getting write access. As changes are made they get written to disk (depends on caches etc), but all objects touched in the new session are written to new disk blocks. Only when the user saves a session are the indices and superblock rewritten, so up to that point any other user starting up will get the old version. (Also any crash will leave the old version intact.) Other users can not detect the update being made -- they have to quit and start up again to pick it up. Perhaps we could implement something to check the superblock to check for this, but essentially they would have to flush everything, in case it had changed. The only alternative would be a scan of all dynamically held data of all sorts, which is a nightmare. The problem with locking only during saving, which allows parallel updating, is that if two users A and B take an object X, A edits it and writes it back, and then B edits it tries to write it, the state B is editing it from is not the last state of the database. One solution is to lock at the object level, not at the database level, allowing several individuals to check out different objects. However that rapidly leads to deadlock situations, where two users are waiting for each other to free something. All very nasty. Another is to do a comparison when you save, to see if the object has changed under you. But what to do if it has? Of course you are right that this is the same problem involved in merging databases. There we agreed that we need tools to highlight clashes, but final fixing is up to the curator to manage. As it is, the current sessions keep track of the user. I don't see the point in keeping the Unix pid. Maybe the machine, though this does not seem that relevant. The date and time really should be there -- currently they are not. It is easy to add more information, since the session is not just a "number", but also an ACEDB object. We can extend its model like any other (almost). The "(almost)" is because the sessions get treated slightly differently, being not under session control themselves, and can only contain tags and data (Int, Float, Text), not pointers to other objects. From owner-acedb@net.bio.net Thu Sep 23 23:00:00 1993 Path: biosci!agate!overload.lbl.gov!dog.ee.lbl.gov!slavsing.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Re: gateway WWW-ACEDB Message-ID: Date: 24 Sep 93 15:49:02 GMT References: <1993Sep12.144428.14066@inra.fr> Followup-To: bionet.software.acedb Organization: Lawrence Berkeley Laboratory Lines: 60 NNTP-Posting-Host: 128.3.252.43 In article <1993Sep12.144428.14066@inra.fr>, decoux@moulon.inra.fr (ts) wrote: > > Gateway WWW-ACEDB > ================= > > If you want to consult ACeDB and MycDB, try : > > * "http://moulon.inra.fr/acedb/acedb.html" to consult "A Caenorhabditis > elegans Data Base" (ACeDB). > > * "http://moulon.inra.fr/acedb/mycdb.html" to consult "Mycobacterium > DataBase". "Mycobacterium DataBase" is funded by the WHO and the Fondation > Raoul Follereau and is maintained by the Unite de Genetique Moleculaire > Bacterienne at the Institut Pasteur. > > > To consult these databases, you can : > > * If you know syntax of "tace" commands, enter your query in "SearchText". > * otherwise you can make a complete Consultation of the database. > > For more precisions, about "tace" syntax, just enter "help". > > > If you want to create an ACEDB gateway, see (or contact me) : > > "http://moulon.inra.fr/acedb_conf_eng.html" > ou > "http://moulon.inra.fr/acedb_conf.html" (version francaise) > -- > > Guy Decoux -- I finally had a chance to try these yesterday, and they are VERY impressive. It is the next best thing to running ACEDB itself. For Mac users, the just-released NCSA Mosaic B1 (beta) is a very nice way to access them on a color Macintosh. To get NCSA Mosaic for the Mac, you can just ftp ftp.ncsa.uiuc.edu cd Mac/Mosaic get NCSAMosaicMac.B1.sit.hqx If you use Fetch (also from NCSA), it will automatically unbinhex the result. Then you can double click the result to decompress into working files. +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Thu Sep 23 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!usc!howland.reston.ans.net!agate!fly2.berkeley.edu!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: more on locks Message-ID: Date: 24 Sep 93 19:18:39 GMT References: <1993Sep23.214236.3664@gserv1.dl.ac.uk> Distribution: bionet Organization: University of California, Berkeley Lines: 22 NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: rd@uk.ac.cam.mrc-lmb's message of Thu, 23 Sep 1993 21:35:09 GMT Thanks, OK I won't mess with the policy of global database locking. But unless there is something else I've overlooked, I'll add a section to filopen() (protected by a #ifndef NO_ATOMIC_CREATION (I hope that nothing is really that broken)). I'll check for spec == "atomic" and do an open() with O_WRONLY | O_CREAT | O_EXCL followed by an fdopen() for lockfile itself. Then I'll change the ...WriteLock functions to atomically create the lockfile, or remove it, etc. Also I'd like to set a special protocol in the client/server setup to request a break of the lock. All of the OS'es I am aware of have some procedure for atomic file creation, and I know of no other IPC which is common to all of them. If this is a problem under say VMS or MVS or Novell or Appleshare, etc., please let me know. -- Henry J. Cobb hcobb@fly2.berkeley.edu SFB Tyrant From owner-acedb@net.bio.net Fri Sep 24 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: more on locks Message-ID: <281t94$5ss@overload.lbl.gov> Date: 25 Sep 93 16:57:08 GMT References: <1993Sep23.214236.3664@gserv1.dl.ac.uk> Distribution: bionet Organization: Dendrome, A Genome Database for Forest Trees Lines: 24 NNTP-Posting-Host: s27w007.pswfs.gov In article hcobb@fly2.berkeley.edu (Henry J. Cobb) writes: > ... > I'll check for spec == "atomic" and do an open() with O_WRONLY | >O_CREAT | O_EXCL followed by an fdopen() for lockfile itself. > ... > All of the OS'es I am aware of have some procedure for atomic file >creation, and I know of no other IPC which is common to all of them. If >this is a problem under say VMS or MVS or Novell or Appleshare, etc., >please let me know. > ... There was a nasty problem with NFS and SunOS 3.x where calls such as this (open (...O_CREAT...)) appeared to succeed but which did not preempt similar calls from other workstations. This was caused by local file caching. I do not know if this feature of Sun/NFS interaction has been fixed in subsequent releases, or whether it plagues other NFS implementations. --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Sat Sep 25 23:00:00 1993 Path: biosci!agate!fly2.berkeley.edu!hcobb From: hcobb@fly2.berkeley.edu (Henry J. Cobb) Newsgroups: bionet.software.acedb Subject: Re: more on locks Message-ID: Date: 26 Sep 93 17:37:06 GMT References: <1993Sep23.214236.3664@gserv1.dl.ac.uk> <281t94$5ss@overload.lbl.gov> Distribution: bionet Organization: University of California, Berkeley Lines: 23 NNTP-Posting-Host: fly2.berkeley.edu In-reply-to: bks@s27w007.pswfs.gov's message of 25 Sep 1993 16:57:08 GMT OK gang, time for ultimate defensive driving here! First: the semaphores will not help NFS one little bit, so drop em. Now the plan: 1) Check to see if the file exists. 2) If it doesn't then open it for exclusive create with no buffering (O_SYNC). 3) Write out the usual stuff. 4) (redundantly) flush it then close it. 5) Reopen the file for reading and check to see if it has what we (hopefully) just wrote to it, and nothing more. Fail on any error, complain to the log files (with an option to mail the Admin) and clean up whatever seems to be resonable. -- Henry J. Cobb hcobb@fly2.berkeley.edu SFB Tyrant From owner-acedb@net.bio.net Sun Sep 26 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: bionet.software.acedb FAQ Summary: Frequently Asked Questions about finding and getting started with the database system ACEDB. ACEDB is used to collect information regarding the molecular biology of the genome. Message-ID: <287bt8$fg4@overload.lbl.gov> Date: 27 Sep 93 18:37:28 GMT Reply-To: acedbfaq@s27w007.pswfs.gov Followup-To: poster Organization: Lawrence Berkeley Laboratory, Berkeley CA Lines: 375 NNTP-Posting-Host: s27w007.pswfs.gov Archive-name: acedb-faq Last-modifed: 9/27/93 Version: 1.1 ---------------------------------------------------------------------- Common Questions and Answers about ACEDB. This is the zeroth posting of this document. Errors of commission or omission are unintentional. Please send comments and corrections to acedbfaq@s27w007.pswfs.gov. Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. I will submit the next version of this FAQ for Usenet archival storage. --Bradley K. Sherman ---------------------------------------------------------------------- List of questions in the ACEDB FAQ: 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? Q411:Who contributed to this document? ---------------------------------------------------------------------- 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 data about diverse species [see Q4]. ACEDB allows for automatic cross-referencing of items when loaded and allows for hypertextual navigation of the links using a mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the efforts of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the European integrated Genome Project. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage -missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Current display modes are: TREE for text type objects: papers, authors, genes etc. GMAP genetic map PMAP physical map (Sulston contig style) SEQ DNA sequence - symbolic, features, sequence and translation GRID hybridisation patterns for a probe to a clone grid BIBLIO bibliography attached to any object display modules under development: CMAP whole chromosome physical map plot GEL agarose gel simulation derived from sequence ---------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: 1-10. It was released Summer 1993. The next release will be 2.0. ---------------------------------------------------------------------- Q2: What {hardware | software} do I need to run ACEDB? A2: ACEDB currently runs on the following Unix sytems, under X11: Sun SPARCstation 1, 1+, 2, IPC, IPX: SPARCstation 10 running Solaris: DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series PC 386/486 with Linux (public domain Unix) Other Unix: There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, NeXT, Convex. You may have to contact the developer responsible for the port to make these real. Macintosh: A port to the Macintosh may become available by the end of 1993. ---------------------------------------------------------------------- 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) genome/acedb cele.mrc-lmb.cam.ac.uk (131.11.84.1) pub/acedb ncbi.nlm.nih.gov (130.14.20.1) repository/acedb ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: Database : ACeDB Species : Caenorhabditis elegans Availability : Current version: 1-10 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@cele.mrc-lmb.cam.ac.uk Contact : mieg@kaa.cnrs-mop.fr Last_update : Sept. 1993 Database : AAtDB Species : Arabadopsis thaliana Availability : Curator : John Morris Current version: 1-5 Contact : curator@frodo.mgh.harvard.edu Last_update : Sept. 1993 Database : GrainGenes Species : Wheat, barley, oats, relatives Availability : Gopher greengenes.cit.cornell.edu port 70 Availability : ACEDB version by ftp, on request from the curators Curator : David E. Matthews PI : Olin D. Anderson Contact : matthews@greengenes.cit.cornell.edu Contact : oandersn@wheat.usda.gov Last_update : Sept. 1993 Database : SolGenes Coverage: Solanaceae - tomato, potato, pepper (eventually) Availability : Beta ACEDB via login or tar file Curator : Edie Paul Contact : epaul@nightshade.cit.cornell.edu Last_update : Sept. 1993 Database : RiceGenes Species : Rice (O. sative) Availability : under development, login at own risk Curator : Edie Paul Contact : epaul@nightshade.cit.cornell.edu Last_update : Sept. 1993 Database : SoyBase Species : Soybeans Curator : Lisa Lorenzen PI : Randy Shoemaker Contact : lorenzen@mendel.agron.iastate.edu Last_update : Sept. 1993 Database : TreeGenes Species : Forest trees, Pinus taeda Availability : contact curator 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 : Sept. 1993 Database : 21Bdb Species : Homo sapiens Availability : by request, via ftp, gopher Curator : Donn F. Davy Contact : DFDavy@lbl.gov Contact : aggarwal@genome.lbl.gov Focus : STS content mapping & sequencing of Human Chromosome 21 PI : Jasper Rine PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng Last_update : Sept. 1993 Database : Flydb Species : Drosophila melanogaster Availability : by request only, via ftp Curator : Suzanna E. Lewis Contact : SELewis@lbl.gov Focus : STS content mapping project summary PI : Gerald Rubin PI : Mike Palazzolo PI : Dan Hartl PI : Alan Spradling Last_update : Sept. 1993 Database : ChlamyDB Species : Chlamydomonas PI : Elizabeth Harris Last_update : Sept. 1993 Database : AAnDB Species : Aspergillus nidulans PI : LeLand Ellis Last_update : Sept. 1993 Species : Bovine PI : LeLand Ellis Last_update : Sept. 1993 Species : Sorghum PI : LeLand Ellis Last_update : Sept. 1993 Darabase : MycDB Species : Mycobacterium PI : Staffan Bergh PI : Thierry Garnier Last_update : Sept. 1993 Database : EcoDB Species : E. coli PI : Staffan Bergh Last_update : Sept. 1993 PI : Scott Chasalow Species : Potato Contact : Scottish Crop Institute, Dundee Last_update : Sept. 1993 PI : George Murphy PI : David Flanders Species : Arabidopsis t. Contact : J. Innes Center, Norwich, England Last_update : Sept. 1993 PI : David Bentley Species : Homo sap. Contact : Sanger Centre, Cambridge, England Last_update : Sept. 1993 Database : MaizeDB Species : Maize Curator : Mary Polacco Contact : University of Missouri, Columbia, MO Last_update : Sept. 1993 [Curators: Please submit an entire paragraph in this format for inclusion or update. --bks] ---------------------------------------------------------------------- Q5: What written documentation exists for ACEDB? A5: The primary documents are included in the Software distribution in the wdoc subdirectory: acedb -- A C. elegans Database: I. Users' Guide. acedb -- A C. elegans Database: II. Installation Guide. acedb -- A C. elegans Database: III. Configurat From owner-acedb@net.bio.net Sun Sep 26 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!gatech!europa.eng.gtefsd.com!library.ucla.edu!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: bionet.software.acedb FAQ Message-ID: <287ef9$g17@overload.lbl.gov> Date: 27 Sep 93 19:21:13 GMT References: <287bt8$fg4@overload.lbl.gov> Organization: Dendrome, A Genome Database for Forest Trees Lines: 20 NNTP-Posting-Host: s27w007.pswfs.gov The first error in the FAQ is that my Organization was listed as Lawrence Berkeley Laboratory. This is an artifact of the posting software and route and will be corrected in future postings. The Institute of Forest Genetics is part of the United States Forest Service of the USDA. Funding for the Dendrome project comes in large part from the USDA ARS / National Agricultural Library Plant Genome Database project. Sorry for any misunderstanding. --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Wed Sep 29 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!pipex!uunet!haven.umd.edu!cville-srv.wam.umd.edu!usenet From: asmarina@next03epsl.wam.umd.edu (Ghermay Araya) Newsgroups: bionet.software.acedb Subject: RESAMPLING SOLUTIONS TO PROBLEMS Message-ID: <28fj81$1a8@cville-srv.wam.umd.edu> Date: 30 Sep 93 21:31:45 GMT Reply-To: THE ACM BUT HEADS Organization: University of Maryland College Park Lines: 178 NNTP-Posting-Host: next02wor.wam.umd.edu SOLUTIONS AND PROBLEMS TO PREVIOUS POSTING: Resampling, (bootstrapping, etc.), is revolutionizing the practice of statistic, and the way it is taught. For articles, and information on software + books, results of classroom trails, and descriptions of pending projects in which teachers can become involved, contact the University of Maryland's Resampling Project. We are especially interested in class testers. Contact: Resampling Project, attn. P.G. Bruce College of Business University of Maryland, College Park, MD 20742. Phone: 703-522-2713 FAX 703-522-5846 email pcbruce@wam.umd.edu (mark attn. P. C. Bruce). please provide both postal and email address. SOLUTIONS: Solution, Puzzle 1: 1. Three urns - "0,0"; "0,1"; "1,1". 2. Choose an urn at random. [Can do this on the computer with random selection of urn numbers, and then "If"] 3. Choose the first element in the chosen urn's vector. If "1", stop trial and make no further record. If "0", continue. 4. Record the second element in the chosen urn's vector on the scoreboard. 5. Repeat (2 - 5), and calculate the proportion "0s" on scoreboard. (Answer should be 2/3.) NUMBERS (1 2 3) a '"1" denotes a selection of urn 1 (u1), '"2" urn 2, "3" urn 3 NUMBERS (6 6) u1 '"u1" has two pennies (6's) NUMBERS (7 7) u2 '"u2" has two nickels (7's) NUMBERS (6 7) u3 '"u3" has one penny & one nickel REPEAT 1000 SAMPLE 1 a b 'Select an urn at random IF b =1 'If urn selector says urn 1 SHUFFLE u1 u1 'shuffle urn 1 TAKE u1 1 c11 'take one coin from urn 1, call it c11 IF c11=6 'if the coin is a penny TAKE u1 2 c12 'take the second coin IF c12=6 'if the second coin is a penny SCORE 6 z 'keep track of the second coin result END 'end IF conditions END END IF b =2 'if urn selector says urn 2 SHUFFLE u2 u2 'etc. as above TAKE u2 1 c21 IF c21=6 TAKE u2 2 c22 IF c22=6 SCORE 6 z END END END IF b =3 SHUFFLE u3 u3 TAKE u3 1 c31 IF c31=6 TAKE u3 2 c32 IF c32=6 SCORE 6 z END END END END 'End the experiment, go back and 'repeat until 1000 repetitions 'are complete COUNT z = 6 k DIVIDE k 1000 kk PRINT kk Answer: KK = 0.34 Solution: Puzzle 2 1. Put a white ball (later have the computer call it "7" to avoid confusion) or black (call it "8") in the urn with probability .5. 2. Put in a white and shuffle the two balls. 3. Take out a ball. If black, stop and make no record. 4. (If result of (3) is white): Take out the remaining ball, examine, and record its color. 5. Repeat steps 1-4 (say) until 1000 trials (with 1000 recordings) have been completed. (Alternatively, one can divide the number of repetitions by the number of records in the scoreboard). 6. Count the number and compute the proportion of whites (7s) among the trials where the result of step (3) is white. Carroll gives the answer as 2/3 (p. 32). COPY (7 8) A '7=WHITE COUNTER, 8=BLACK COUNTER. REPEAT 1000 SHUFFLE A B 'SHUFFLE THE TWO COUNTERS TAKE B 1 C 'TAKE A COUNTER FOR THE BAG CONCAT C 7 D 'JOIN A WHITE COUNTER TO THE BAG SHUFFLE D E 'SHUFFLE THE BAG TAKE E 1 F 'TAKE OUT A COUNTER IF F =7 'IF THE COUNTER YOU TAKE OUT IS WHITE TAKE E 2 G 'TAKE THE OTHER ONE SCORE G Z 'RECORD THIS SECOND ONE'S COLOR END END 'END THE REPEAT LOOP, GO BACK AND REPEAT COUNT Z =7 K 'COUNT HOW MANY TIMES SECOND ONE WAS WHITE DIVIDE K ZZ KK 'EXPRESS AS A PROPORTION OF THE NUMBER OF 'TRIALS ON WHICH THE FIRST ONE WAS WHITE. PRINT KK Answer: KK = 0.66356 FROM PREVIOUS MESSAGE: PROBLEMS: Two Puzzles: Does your reasoning lead you astray on the following puzzles? Most people's does. Here are resampling (simulation) solutions that illustrate how such an approach, though less sophisticated than a formulaic one, yields correct answers and offers fewer opportunities to go wrong. 1) "Three identical boxes each contain two coins. In one box both are pennies, in the second both are nickels, and in the third there is one penny and one nickel. A man chooses a box at random and takes out a coin. If the coin is a penny, what is the probability that the other coin in the box is also a penny?" [from Goldberg, 1960, p. 99] 2) A bag contains one counter, known to be either white or black. A white counter is put in, the bag shaken, and a counter drawn out, which proves to be white. What is now the chance of drawing a white counter? From Lewis Carroll's PILLOW PROBLEMS (1895/1958) (p. 2, via Martin Gardner) From owner-acedb@net.bio.net Thu Sep 30 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.software.acedb Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9310010900.AA04979@net.bio.net> Date: 1 Oct 93 09:00:03 GMT Sender: kristoff@net.bio.net Distribution: biosci Lines: 243 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** 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. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** 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/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). 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 and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. 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 our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. 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.welch.jhu.edu 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) or alter any of the field identifiers such as "first name: ". 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., 05-05-93 for 5 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., 05-05-93, not 5-5-93. 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 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 BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage 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 MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast 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: