From owner-gdb@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!darwin.sura.net!news.gdb.org!freya.gdb.org!patty From: patty@gdb.org (Patty Haley) Newsgroups: bionet.molbio.gdb Subject: GDB Services on Monday, Nov. 8th Message-ID: <1993Nov1.144727.13337@news.gdb.org> Date: 1 Nov 93 14:47:27 GMT Sender: news@news.gdb.org Reply-To: help@gdb.org Organization: Genome Database Lines: 17 Nntp-Posting-Host: freya.gdb.org Some GDB Services Unavailable Monday November 8 from 7-11am EST ============================================================================== Due to computer maintenance, the following GDB services will be unavailable on Monday November 8, 1993 from 7-11am EST (Eastern Standard Time) from Johns Hopkins University in Baltimore, MD. . FTP server (ftp.gdb.org) . GDB/Accessor . Public ISQL We apologize for any inconvenience this may cause. Please note that access to the GDB application via telnet to Johns Hopkins University (gdb.gdb.org) WILL BE AVAILABLE as usual during this time. From owner-gdb@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!darwin.sura.net!news.gdb.org!freya.gdb.org!patty From: patty@gdb.org (Patty Haley) Newsgroups: bionet.molbio.gdb Subject: Services on November 8th Message-ID: <1993Nov1.185803.15110@news.gdb.org> Date: 1 Nov 93 18:58:03 GMT Sender: news@news.gdb.org Reply-To: help@gdb.org Organization: Genome Database Lines: 17 Nntp-Posting-Host: freya.gdb.org Some GDB Services Unavailable Monday November 8 from 7-11am EST ============================================================================== Due to computer maintenance, the following GDB services will be unavailable on Monday November 8, 1993 from 7-11am EST (Eastern Standard Time) from Johns Hopkins University in Baltimore, MD. . FTP server (ftp.gdb.org) . GDB/Accessor . Public ISQL We apologize for any inconvenience this may cause. Please note that access to the GDB application via telnet to Johns Hopkins University (gdb.gdb.org) WILL BE AVAILABLE as usual during this time. From owner-gdb@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.molbio.gdb Subject: URGENT: DEADLINE CHANGE FOR WORLD CONGRESS Message-ID: <9311031731.AA07956@morpheus.chpc.utexas.edu> Date: 3 Nov 93 17:31:16 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 68 UPDATE ON 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) ---- Due to a confusion in the electronic distribution of the congress announcement and deadlines, as well as incorrect deadlines appearing in a number of society newsletters and journals, we are extending the abstract submission deadline for this congress to 31 December 1993. We apologize to those who were confused over the differing deadline announcements and hope that this change will allow everyone to participate. For congress details: 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 (all documents and forms are stored here) POSTAL: Compmed 1994 University of Texas System CHPC Balcones Research Center 10100 Burnet Road, 1.154CMS Austin, Texas 78758-4497 SUBMISSION PROCEDURES: Authors must submit 5 copies of a single-page 50-100 word abstract clearly discussing the topic of their presentation. In addition, authors must clearly state their choice of poster, contributed paper, tutorial, exhibit, focused workshop or birds of a feather group along with a discussion of their presentation. Abstracts will be published as part of the preliminary conference material. To notify the congress organizing committee that you would like to participate and to be put on the congress mailing list, please fill out and return the form that follows this announcement. You may use any of the contact methods above. If you wish to organize a contributed paper session, tutorial session, focused workshop, or birds of a feather group, please contact the conference director at mwitten@chpc.utexas.edu . The abstract may be submitted electronically to compmed94@chpc.utexas.edu or by mail or fax. There is no official format. If you need further details, please contact me. Matthew Witten Congress Chair mwitten@chpc.utexas.edu From owner-gdb@net.bio.net Tue Nov 09 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!news.gdb.org!org.gdb!help From: help@gdb.org Newsgroups: bionet.molbio.gdb Subject: GDB Release 5.2 Coming November 29 Features Enhanced Output Message-ID: <1993Nov10.182902.13906@news.gdb.org> Date: 10 Nov 93 18:29:02 GMT Sender: news@news.gdb.org Reply-To: bionet.molbio.gdb Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 28 Nntp-Posting-Host: velociraptor.gdb.org GDB Release 5.2 Coming November 29 Features Enhanced Output ----------------------------------------------------------- The new GDB release is scheduled to be installed on the computer at Johns Hopkins University in Baltimore on Monday November 29. Access to GDB and to the Public ISQL server at JHU will be unavailable on this day while the database is converted. This release of the software will feature revised output report generation and includes an Output Manager with the look-and-feel of the data managers as well as several new output features requested by the user community. Due to the change in how output is handled, any User Defined reports saved in GDB 5.1 will be lost when the conversion to 5.2 occurs. Users will need to define and save these reports again. We apologize for the inconvenience and will be glad to provide assistance in redefining reports for 5.2. When the new GDB software has been installed, we will post a detailed description of how to use the Output Manager as well as other enhancements included in this release. People with GDB/Accessor installed on their Macs will be able to update their software automatically. We will post a description of how to do this as soon as the new version of the GDB/Accessor software is available. For information about accessing GDB, please contact: GDB User Support help@gdb.org From owner-gdb@net.bio.net Wed Nov 10 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rice From: rice@embl-heidelberg.de (Peter Rice) Newsgroups: bionet.molbio.gdb Subject: Re: GDB Release 5.2 Coming November 29 Features Enhanced Output Message-ID: <1993Nov11.173546.127366@embl-heidelberg.de> Date: 11 Nov 93 16:35:46 GMT References: <1993Nov10.182902.13906@news.gdb.org> Organization: EMBL, European Molecular Biology Laboratory Lines: 17 In article <1993Nov10.182902.13906@news.gdb.org>, help@gdb.org writes: > GDB Release 5.2 Coming November 29 Features Enhanced Output > > People with GDB/Accessor installed on their Macs will be able to update > their software automatically. We will post a description of how to do this > as soon as the new version of the GDB/Accessor software is available. I saw a nice demo of GDB/Accessor on the Mac recently, but when will an MS-Windows or an X-Windows version appear? ----------------------------------------------------------------------------- Peter Rice, EMBL | Post: Computer Group | European Molecular Internet: Peter.Rice@EMBL-Heidelberg.DE | Biology Laboratory | Postfach 10-2209 Phone: +49-6221-387247 | 69012 Heidelberg Fax: +49-6221-387306 | Germany From owner-gdb@net.bio.net Thu Nov 11 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!sunic!trane.uninett.no!nntp.uio.no!NewsWatcher!user From: olam@radium.uio.no (Ola Myklebost) Newsgroups: bionet.molbio.gdb Subject: GDB/Accessor in Sweden Message-ID: Date: 12 Nov 93 10:04:48 GMT Followup-To: bionet.molbio.gdb Organization: Inst for Cancer Research, Oslo Lines: 19 NNTP-Posting-Host: pcdnr05.uio.no Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit I have just received a version of GDB/Accessor 1.0b which is set up to work on the Swedish GDB node. This works very well in this part of the world and can be highly recommended. I assume the program can be obtained from through help@gdb.embnet.se, although I never got any response directly from them (I got the program from our local embnet administrator after his visit there). Thanks to everyone who has helped me on the way! Ola -- Ola Myklebost Email ola.myklebost@dnr.uio.no Dept of Tumor Biology Inst for Cancer Research The Norwegian Radium Hospital N-0310 OSLO, Norway Tel +47-22-50-60-50, xtn 9830, Fax +47-22-52-24-21 From owner-gdb@net.bio.net Mon Nov 15 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!paladin.american.edu!europa.eng.gtefsd.com!uunet!EU.net!hp4at!news.univie.ac.at!swidir.switch.ch!news.unige.ch!medsun.unige.ch!mike From: mike@medsun.unige.ch (Mike Morris) Newsgroups: bionet.molbio.gdb Subject: Re: GDB Release 5.2 Coming November 29 Features Enhanced Output Message-ID: <1993Nov15.162412.22180@news.unige.ch> Date: 15 Nov 93 16:24:12 GMT References: <1993Nov10.182902.13906@news.gdb.org> <1993Nov11.173546.127366@embl-heidelberg.de> Sender: usenet@news.unige.ch Organization: University of Geneva, Switzerland Lines: 13 I too vote for an X-Windows version! Who else? ******************************************************************* Mike Morris PhD * * Division of Medical Genetics * * tel (Switzerland) (22) 702.56.94 University of Geneva * * fax (Switzerland) (22) 702.57.06 Geneva * * email mike@medsun.unige.ch Switzerland * * ******************************************************************* From owner-gdb@net.bio.net Fri Nov 19 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!darwin.sura.net!news.gdb.org!org.gdb@help From: help@gdb.org (GDB User Support) Newsgroups: bionet.molbio.gdb Subject: New Genethon Data Entered Into GDB Message-ID: <1993Nov18.210551.16240@news.gdb.org> Date: 18 Nov 93 21:05:51 GMT Sender: news@news.gdb.org Reply-To: bionet.molbio.gdb Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 24 Nntp-Posting-Host: velociraptor.gdb.org New Genethon Data Entered Into GDB ================================== The PCR and microsatellite data from the latest set of highly- informative markers from Genethon have been loaded into GDB. This set consists of over 1200 new clone, PCR, polymorphism and locus records, complete with PCR conditions and allele frequency information. The easiest way to access this data in GDB is to first retrieve the GDB ID # G00-230-332, then call the Locus, Probe or Polymorphism Managers to retrieve the Genethon data. ====================================================================== David Kitaguchi, Sr. User System Specialist WHOIS - DGK2 GDB/OMIM User Support Phone: (410) 955-9664 Johns Hopkins University School of Medicine FAX: (410) 614-0434 2024 E. Monument Street Baltimore, MD 21205-2100 help@gdb.org davidk@gdb.org ====================================================================== From owner-gdb@net.bio.net Fri Nov 19 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!library.ucla.edu!europa.eng.gtefsd.com!darwin.sura.net!news.gdb.org!oscar.gdb.org!ken From: ken@oscar.gdb.org (Ken Fasman) Newsgroups: bionet.molbio.gdb Subject: Re: GDB Release 5.2 Coming November 29 Features Enhanced Output Summary: we're working on it Keywords: GDB Macintosh Windows Message-ID: <1993Nov20.221508.16358@news.gdb.org> Date: 20 Nov 93 22:15:08 GMT References: <1993Nov10.182902.13906@news.gdb.org> <1993Nov11.173546.127366@embl-heidelberg.de> Sender: Ken Fasman Followup-To: bionet.molbio.gdb Organization: Genome Data Base, Johns Hopkins University Lines: 39 Nntp-Posting-Host: oscar.gdb.org In article <1993Nov11.173546.127366@embl-heidelberg.de> rice@embl-heidelberg.de (Peter Rice) writes: > >I saw a nice demo of GDB/Accessor on the Mac recently, but when will an >MS-Windows or an X-Windows version appear? GDB/Accessor was written at Cold Spring Harbor by Corp Reed and Tom Marr, using MPW C, a development system native to the Macintosh. Because of this, it cannot be easily ported to other systems. We will shortly release an experimental SmallTalk-based GUI browser for GDB which will run on Macs, MS Windows, and Unix systems using ParcPlace's SmallTalk 80 run time system. Watch this newsgroup or the Human Genome News newsletter for more details about this software, including how to get the necessary run-time license for SmallTalk. We are also working with another group on implementing a program comparable to GDB/Accessor under MS-Windows, possibly using MS Access as the development system. We are shooting for delivery by the end of 1994 (possibly sooner) for this program. For further information, please contact GDB User Support at: help@gdb.org (410) 955-7058 (voice) (410) 614-0434 (fax) 2024 E. Monument St. Baltimore MD 21205 Ken Fasman Informatics Director Genome Data Base Johns Hopkins University School of Medicine 2024 E. Monument St. Baltimore MD 21205 ken@gdb.org From owner-gdb@net.bio.net Tue Nov 23 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!news.moneng.mei.com!howland.reston.ans.net!darwin.sura.net!news.gdb.org!org.gdb!help From: help@gdb.org Newsgroups: bionet.molbio.gdb Subject: Internet access to GDB unavailable for short time on Friday Nov. 26 Message-ID: <1993Nov23.220137.29685@news.gdb.org> Date: 23 Nov 93 22:01:37 GMT Sender: news@news.gdb.org Reply-To: help@gdb.org Followup-To: bionet.molbioo.gdb Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 7 Nntp-Posting-Host: velociraptor.gdb.org Internet access to GDB unavailable for short time on Friday Nov. 26 =================================================================== On Friday November 26, 1993 the SURAnet router which provides Internet access to GDB will be down for maintenance between 4am-5am Eastern Time. Total downtime once maintenance is started should not exceed 15 minutes. From owner-gdb@net.bio.net Tue Nov 23 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!paladin.american.edu!darwin.sura.net!news.gdb.org!org.gdb!help From: help@gdb.org Newsgroups: bionet.molbio.gdb Subject: GDB Release 5.2 Coming November 29 Features Enhanced Output Message-ID: <1993Nov23.220900.29830@news.gdb.org> Date: 23 Nov 93 22:09:00 GMT Sender: news@news.gdb.org Reply-To: help@gdb.org Followup-To: bionet.molbio.gdb Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 29 Nntp-Posting-Host: velociraptor.gdb.org GDB Release 5.2 Coming November 29 Features Enhanced Output ----------------------------------------------------------- The new GDB release is scheduled to be installed on the computer at Johns Hopkins University in Baltimore on Monday November 29. Access to GDB and to the Public ISQL server at JHU will be unavailable on this day while the database is converted. This release of the software will feature revised output report generation and includes an Output Manager with the look-and-feel of the data managers as well as several new output features requested by the user community. Due to the change in how output is handled, any User Defined reports saved in GDB 5.1 will be lost when the conversion to 5.2 occurs. Users will need to define and save these reports again. We apologize for the inconvenience and will be glad to provide assistance in redefining reports for 5.2. When the new GDB software has been installed, we will post a detailed description of how to use the Output Manager as well as other enhancements included in this release. People with GDB/Accessor installed on their Macs will be able to update their software automatically. We will post a description of how to do this as soon as the new version of the GDB/Accessor software is available. For information about accessing GDB, please contact: GDB User Support help@gdb.org From owner-gdb@net.bio.net Mon Nov 29 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!howland.reston.ans.net!darwin.sura.net!news.gdb.org!org.gdb!hgelp From: help@gdb.org Newsgroups: bionet.molbio.gdb Subject: New GDB 5.2 Temporarily 0ff-line Message-ID: <1993Nov30.184110.25375@news.gdb.org> Date: 30 Nov 93 18:41:10 GMT Sender: news@news.gdb.org Reply-To: help@gdb.org Followup-To: bionet.molbio.gdb Organization: The Johns Hopkins University - Genome Data Base (GDB) Lines: 24 Nntp-Posting-Host: velociraptor.gdb.org ******************************************************************************* * * * New GDB 5.2 Temporarily 0ff-line * * * ******************************************************************************* GDB Version 5.2 was due to be installed and loaded by 8:00am this morning. As we are in the process of completing the load of GDB data into the new software, the database has been taken off-line until late this afternoon (30 November 93). We will post an additional message once the database is fully loaded and on-line for use. Any questions or comments, please contact us at help@gdb.org From owner-gdb@net.bio.net Mon Nov 29 22:00:00 1993 Path: biosci!mrc-crc.ac.uk From: smercer@mrc-crc.ac.uk (Mr. S.J. Mercer) Newsgroups: bionet.announce,bionet.genome.chromosomes,bionet.molbio.gdb Subject: Chromosome Database available on Gopher Keywords: Chromosome Database Gopher Message-ID: <1993Nov30.145230.28881@crc.ac.uk> Date: 30 Nov 93 14:52:30 GMT Sender: kristoff@net.bio.net Followup-To: poster Organization: MRC Human Genome Resource Centre Lines: 31 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.announce:814 bionet.genome.chromosomes:115 bionet.molbio.gdb:135 ANNOUNCEMENT The Chromosome Abnormality Database is now available by Gopher from the UK Human Genome Mapping Project Resource Centre (HGMP-RC). This database was established early in 1991,to collect records of chromsosome abnormalities (of all types) from the fifty or so laboratories in the United Kingdom which perform routine diagnostic karyotyping. Ordinarily, the records of abnormal samples were held separately by each laboratory, but the Chromosome Abnormality Database (CAD) acts as a centralised repository for this information and enabling researchers to locate samples of interest without having to contact all of the laboratories individually. The CAD now stores over forty thousand records of chromosome abnormality and for each record holds the sex, date of birth, tissue type and karyotype, as well as details of the lab from which the record was collected. It also holds information on the availability of stored samples and cell lines where these are available. Point your gopher at menu.hgmp.mrc.ac.uk port 70 or make a link: Name: Chromosome Abnormality Database Type: 1 Port: 70 Path: 1/HGMP_DBs/Cad_DB Host: menu.hgmp.mrc.ac.uk If you have any further questions, please email me at simon@bioch.ox.ac.uk. Applications for an account at the UK HGMP-RC should be made to cbates@hgmp.mrc.ac.uk Tel: +44 81 869 3446 Fax: +44 81 869 3807 From owner-gdb@net.bio.net Mon Nov 29 22:00:00 1993 Path: biosci!GAS.UUG.ARIZONA.EDU!covingtt From: covingtt@GAS.UUG.ARIZONA.EDU (Tatiana A Covington) Newsgroups: bionet.molbio.gdb Subject: enzymes in glucose pathway to ascorbic acid Message-ID: <9311301121.AA18560@GAS.uug.Arizona.EDU> Date: 30 Nov 93 11:21:41 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 I already know the genetic sequence for gulonolactone oxidase, which is the lAst in the set of 4 which take glucose to ascorbic acid. But the first 3 are, in order, UDP-glucose dehydrogenase (EC 3.1.1.8), glucoronate reductase (EC 1.1.1.19), and aldonolactonase (EC 1.1.1.22). Does anyone have any more info on these--where the genes are, their sequences, enzymology, etc.? Tatiana Covington covingtt@gas.uug.arizona.edu From owner-gdb@net.bio.net Mon Nov 29 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!news.gdb.org!freya.gdb.org!patty From: help@gdb.org Newsgroups: bionet.molbio.gdb Subject: new GDB 5.2 online Message-ID: <1993Nov30.214310.28221@news.gdb.org> Date: 30 Nov 93 21:43:10 GMT Sender: news@news.gdb.org Reply-To: help@gdb.org Organization: Genome Database Lines: 2 Nntp-Posting-Host: freya.gdb.org Effective 4:30 pm EST, the new GDB 5.2 has been installed and the data loaded. It is online for use. From owner-gdb@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!cs.utexas.edu!howland.reston.ans.net!darwin.sura.net!news.gdb.org!org.gdb!help From: help@gdb.org Newsgroups: bionet.molbio.gdb Subject: Bionet posting - Internet down Dec 2 Message-ID: <1993Dec1.160038.10032@news.gdb.org> Date: 1 Dec 93 16:00:38 GMT Sender: news@news.gdb.org Reply-To: help@gdb.org Followup-To: bionet.molbio.gdb Organization: The Johns Hopkins University - Genome Data Base (GDB) Lines: 6 Nntp-Posting-Host: velociraptor.gdb.org Internet access to GDB unavailable for short time on Thursday Dec. 2 ==================================================================== On Thursday December 2, 1993 the SURAnet router which provides Internet access to GDB will be down for maintenance between 6:00am - 6:30am Eastern Time. From owner-gdb@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!daresbury!keele!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!news.gdb.org!sif.gdb.org!ksg From: GDB User Support Newsgroups: bionet.molbio.gdb Subject: GDB 5.2 Release Notes Message-ID: <1993Dec1.191640.12931@news.gdb.org> Date: 1 Dec 93 19:16:40 GMT Sender: news@news.gdb.org Reply-To: help@gdb.org Organization: The Johns Hopkins University - Genome Data Base (GDB) Lines: 642 Nntp-Posting-Host: sif.gdb.org GDB Release 5.2 Featuring New Output Manager Installed November 29 ------------------------------------------------------------------ The new GDB release was installed on the computer in Baltimore November 29. This release of the software features the new Output Manager for user defined and standard reports. A description of how to use Output Manager as well as a summary of other enhancements are included in the Release Notes below. For information about accessing GDB, please contact: GDB User Support help@gdb.org ***** GDB Version 5.2 29 November 1993 ***** ENHANCEMENTS for ALL USERS Output * Output report generation with "look-and feel" of data managers. Manager The new Output Manager is similar to the data managers with a retrieve and a Table/Detail view screen. It has two additional screens for defining and scheduling reports. The notes below about Output Manager provide details about using each screen. Output Manager provides all the functions of output in GDB 5.1 and includes new features. In the following descriptions, major new features are marked with =======> . * Two types of reports for output Output Manager lets you output two types of reports: User Reports are defined by the user and can include: Retrieved data from any data manager and user management =======> Field Values =======> Online Help topics Standard Reports are generated by GDB staff and include: GDB statistics GDB and OMIM documentation and release notes News about meetings, exhibits, training Note: Chromosome reports in HGM11 report format will be available soon * Overview of Output Manager The following descriptions briefly summarize the Output screens. See further below for detailed instructions on using each one. ADD/MODIFY REPORT DEFINITION - define the sub-options and format of User Reports based on your search criteria. You cannot modify the content of Standard Reports. SCHEDULE REPORT - define where and when User Reports or Standard Reports will be sent. You can modify your own schedule for Standard Reports. OUTPUT RETRIEVE - use to retrieve User or Standard reports to view on Output Manager screen. You can modify the definition and/or schedule of a report by selecting an Edit option from Output Manager screen. OUTPUT MANAGER - Table/Detail display of the definition and output schedule of retrieved User or Standard reports. Note that to get a report you must 1. define the report (except Standard reports) AND 2. schedule the report The Output Manager is available from the MAIN MENU and from all data managers by selecting TOOL->OUTPUT. If you select Output Manager from the MAIN MENU, you will go to the OUTPUT RETRIEVE screen. If you select it from any screen within a data manager where a retrieve has been defined, you will go to the ADD/MODIFY REPORT DEFINITION screen. You can define and schedule a report without actually retrieving data. In any manager, fill in the retrieve screen with your search criteria. Instead of retrieving the data, select TOOL->OUTPUT from the retrieve screen. Select a sort option and you will go to the ADD/MODIFY REPORT DEFINITION screen. The same search results will be available for output as if you had retrieved the data and then called Output. * Field Values fields in Output Manager accept single letters. To enter a value in any Field Values field on an Output Manager screen, you can just type the unique letter(s) for the value you want. The complete value will be filled in when you either out of the field or select a menu option. To change a value, first erase the current value and then type the unique letter(s). Note that the Output Manager is the *only* manager in GDB that will accept field values entered this way. Example from OUTPUT RETRIEVE screen To retrieve your User Reports, type 'u' in the Report Category field - Report Category: (u ) When you select Retrieve & Sort from the menu, the complete value is displayed - Report Category: (User Reports ) You may also select a value through HELP->FIELD VALUES. * ADD/MODIFY REPORT DEFINITION screen for defining user reports Use this screen to define new user reports and modify previously saved user reports. The Category field will be automatically filled in with "User Reports". The information you fill in on this screen will be displayed in OUTPUT MANAGER Table/Detail view. The following fields let you specify the content and format of the report: Report Name: free text field - type in a unique name =======> Include: SQL? include the Sybase SQL query used to generate the report - default is No =======> Include: Page Brks ? include page breaks and page headers in the report - default is Yes Content: Field Values field for defining the data includes the following: Retrieve Set: all objects retrieved by the query Selected Objects: all objects selected from the current retrieve set Current Object: only the object where the cursor was located when entering Output Manager =======> Updates: only those objects modified or added to the retrieve set since the last time the report was generated. The first time the report is generated, it will include the entire retrieve set. The following objects currently do not support updates: Locus Breakpoint Set, PCR Condition, Population, Consensus Map, Field Values, and Online Help. If you do not select any objects, the default content is Retrieve Set. If you do select one or more objects, the default content is Selected Objects. Brief Description: free text field - up to 72 characters Detailed Description: free text field - up to 255 characters Sub-Options: The types of related data available for inclusion in a report depend on the data manager where you did your retrieve. Some data managers have unique data, such as Abstracts and MeSH Headings for Citation data. Some types of data, such as Locus, are available through several managers. The following is part of the sub-options list for defining reports generated in the Locus Manager. Order Locus Sub-Options 1 [>>] Locus (Table Format ) [ ] Polym (Table Format ) [ ] Disorders (Fixed Format ) [ ] Citation (Table Format ) =======> The Locus sub-option is already selected with the number "1" in the Order column. To select additional types of data, to the data you want and press . The sub-options will be numbered in the order you select them, and will appear in your report in this order. If you deselect a sub-option by moving the cursor to it and pressing , the remaining selected ones will be automatically renumbered. Some sub-options are available in either Table or Detail format; Table is the default. To change Table to Detail, to the format column, erase the current value, and type the letter "d". Fixed format cannot be changed. When you have finished defining the report, select SAVE! Once the report is saved, you can select SCHEDULE! to specify when and where to send the output. =======> Note that you can define or modify a report independent of scheduling it. You define a report one day and while still logged in schedule it to run whenever you want. You can also define it one day, log out, and log back in another time to schedule it. Remember that you *must* schedule the report in order to receive it. * SCHEDULE REPORT screen for specifying when/where to send output When you enter this screen, the schedule status of your report is shown in the upper left corner. The possible statuses are: INACTIVE report is not currently scheduled WORKING output program is working on the report WAITING report is waiting for the next run date + FAILED report is unable to advance to next run date + GEN-FAILED report generation has failed + ACC-FAILED report distribution has failed + If you see a report status indicating your report has FAILED, contact GDB User Support. The Report Name and Brief Description fields filled in on the ADD/MODIFY REPORT DEFINITION screen are displayed on this screen but cannot be changed here. The information you fill in on this screen will be displayed in OUTPUT MANAGER Table/Detail view. The Run field is a rotating choice field. Press to cycle through the choices: Once: runs the report once and saves it (default) Repeating: runs the report according to your specified repeat intervals Once and Delete: runs the report once and then deletes it If you select Repeating, you must also specify how often you want the report generated. to the Repeat Every field. The number "1" appears as the default in the first half of this field; Month appears as the default in the second half. Repeat Every: 1 [Month] To specify a different number, erase the "1" and type a new number between 1 and 99. To change to a week-based cycle, to the second half of the field and press to change [Month] to [Week]. The following three Field Values fields all have default values and cannot be blank. Format: the format of the data or text in the report ASCII text: all user defined reports some standard reports PostScript: some documentation standard reports Tab Delimited: some standard reports When you are scheduling a report, the appropriate format appears as the default in this field. Access Method: type of output to be generated The available access methods depend on your GDB site and are listed in Field Values. Users accessing GDB at JHU in Baltimore can send output by EMAIL or FTP. Other sites may also provide the PRINT or COPY option. Destination: the specific destination where report will go A default destination is automatically filled in for the Access Method you choose. If you choose EMAIL and you have an email address saved in GDB, it appears in this field. To send the report to a different email address, erase the current address and type in the complete new address. You can email a report to multiple addresses by separating them with a space or comma. If you choose FTP, the name of the FTP server and the appropriate directory will appear in this field. Example for JHU: ftp.gdb.org/outgoing/ You must add a filename after the final "/". Use a filename you will easily recognize when you FTP to that directory. Example: ftp.gdb.org/outgoing/locus-c8.yourname Output reports should normally appear at their destination within one day. Small reports will arrive more quickly. * OUTPUT RETRIEVE screen for retrieving User and Standard reports. You can define a search for user or standard reports based on a variety of data associated with report definitions or schedules. Report Category is a Field Values field for retrieving all the reports in a specified category. "User Reports" will retrieve all your personal reports. The other categories are different types of Standard Reports and will retrieve all the available reports for that category. You can also retrieve user or standard reports based on the fields on the Detail View screen related to: Report names and descriptions Output schedule and status Output format, method, and specific destination Dates reports were run or modified The Retrieve & Sort menu lets you sort the retrieved reports by Name, Status, Next Run Date, and Category. * OUTPUT MANAGER screen for displaying retrieved reports Table and Detail views of the definition, output schedule, and current status of retrieved User or Standard reports. This screen displays the information filled in on the ADD/MODIFY REPORT DEFINTITION screen and the SCHEDULE REPORT screen. To change the definition or the schedule, you must use the the appropriate EDIT->MODIFY menu option described below. This screen includes the following menu options not found on the data manager screens. =======> VIEW->SQL QUERY displays the Sybase SQL query used to generate the report. This information can also be included in the output report. EDIT->MODIFY->DEFINITION displays the ADD/MODIFY REPORT DEFINITION screen so you can change the descriptions, sub-options, or format of the report. EDIT->MODIFY->SCHEDULE displays the SCHEDULE REPORT screen so you can change where and/or when the report will be sent. EDIT->DELETE use to delete the current report where your cursor is located. This deletes the report definition and it cannot be restored. =======> EDIT->UNSCHEDULE use to cancel either the next or all scheduled output for the current report, without deleting the report itself. * Summary of how to output different types of reports To output a NEW user defined report: 1. define your search in one of the data managers 2. select TOOL->OUTPUT from retrieve or Table/Detail screen 3. fill in the ADD/MODIFY REPORT DEFINITION screen and save 4. fill in the SCHEDULE REPORT screen and save To change the content, format, or output schedule of a previously defined and saved user report: 1. select TOOL->OUTPUT from the MAIN MENU or select RETRIEVE from the OUTPUT MANAGER Table/Detail screen. 2. from the OUTPUT RETRIEVE screen, retrieve Category: (User Reports ) 3. from the OUTPUT MANAGER screen, select EDIT->MODIFY->DEFINITION - change content and/or format ->SCHEDULE - change output schedule 4. edit the appropriate fields and save To output a standard report: 1. from the OUTPUT RETRIEVE screen, enter the unique letter(s) or select HELP->FIELD VALUES from the Category field to enter the appropriate category of standard reports 2. from the OUTPUT MANAGER screen, select EDIT->MODIFY->SCHEDULE 3. edit the appropriate fields and save To output Field Values or Online Help topics 1. from the FIELD VALUES screen or the GDB HELP screen, select TOOL->OUTPUT 2. follow the same procedure described above for new user defined reports 3. your report will contain the Field Values or the Help topic displayed when you called output =======> * Save and use session defaults (optional) When you change the default values for content, format, or output destination, you can save them for the duration of your GDB session and use them for other reports. Both the REPORT DEFINITION and SCHEDULE REPORT screens have a CUSTOMIZE menu. CUSTOMIZE->SAVE SESSION DEFAULTS - save current settings ->USE SAVED DEFAULTS - use saved settings for a another report On the REPORT DEFINITION screen, defaults can be saved for: Content field Sub-options: Selection, Order, and Format On the SCHEDULE REPORT screen, defaults can be saved for: Run, Repeat Every, Next Run Date, Format, Access Method, Destination --------------------------------------------------------------------- Locus * Expressed Sequence Tag (EST) numbers now available for loci Manager The EST Number field has been added to the LOCUS RETRIEVE and LOCUS MANAGER (Detail View) screens. The format of these numbers is ESTnnnnn, where 'n' is a number. * Retrieve reference marker loci To retrieve reference markers, set the Reference Marker field on the LOCUS RETRIEVE screen to [Yes]. * Unassigned loci can be excluded from a query To retrieve only loci with an assigned location on *any* chromosome, enter 'assigned' or 'asgn' in the Cyto Location field. * Mitochondrial loci can be retrieved To retrieve all the mitochondrial loci, enter 'mt' in the Location field. Cyto Location: mt If you sort by location, heavy chain loci sort before light chain loci. The format of the location field is: MT[L,H]seqstart-seqend All mitochondrial locations begin with "MT" The third letter is L for Light Chain H for Heavy Chain The start and end nucleotide numbers are given as follows: Heavy chains are numbered "clockwise" ex. MTH545-567 MTH"low-high" Light chains are numbered "counterclockwise" ex. MTL260-233 MTL"high-low" * Call OMIM with 200 selected loci You can select up to 200 loci to send to OMIM. --------------------------------------------------------------------- Probe * Expressed Sequence Tag (EST) numbers now available for probes Manager The EST Number field has been added to the PROBE MANAGER (Detail View) screen. The format of these numbers is ESTnnnnn, where 'n' is a number. --------------------------------------------------------------------- Citation * Citation rank displayed in Table and Detail views Manager When you call Citation Manager from another manager and only send one object, the rank of each citation relative to that object is now displayed. Table View has a new column, 'R', to display the Rank left of the 'Year' column. The Important citation(s) for the object are indicated by an 'I'. Note that a locus can have two important citations, while all other objects can only have one. In Detail View, the Rank field is under the Language field and indicates Important, Supportive, or Background. If you call Citation Manager with more than one object, the Rank field does not appear because all citations linked to *any* of the objects are displayed together. * Meeting Abstracts available Meeting Abstract has been added as a new type of citation. To retrieve abstracts, select 'Abstracts' in the Type field on the CITATION RETRIEVE screen. The Detail View screen for Meeting Abstracts includes the name and dates of the meeting; and the country and city where the meeting occurred. If the meeting name is too long to fit on the screen, to the Meeting field and you will see '>' at the end of the text. Press to see the more text. Table View of CITATION MANAGER displays an abbreviation for the meeting name; for example, SCWX for Single Chromosome Workshop, Chromosome X. --------------------------------------------------------------------- GDB Id * Count number of GDB IDs before retrieving data Manager The menu option Count! has been added to the GDB Id RETRIEVE screen and works the same way as other managers. Fill in the retrieve screen and select Count! The total number of objects that would be retrieved by your search is displayed. --------------------------------------------------------------------- Contact * Pre-city post code displayed Manager The PreCity PostCode field has been added to the Detail View screen of CONTACT MANAGER. --------------------------------------------------------------------- User Management * Output available from User Management You can now define and send output reports from User Management. The reports can be for user account records actually retrieved or those merely defined on the retrieve screen. The reports have the same format as Contact Manager reports. * Pre-city post code displayed The PreCity PostCode field has been added to the Detail View screen of USER MANAGEMENT. ===================================================================== ENHANCEMENTS for GDB EDITORS All * Edit citation rank from the Edit menu Manager In all managers that can link to citations, there is a new edit option on the main manager screen, the edit screen, and the Link Manager. When you select EDIT->CITATION RANK, you will see a table view of all the citations linked to the current object. The ranks are listed in a rotating choice field on the left: I (Important), S (Supportive), or B (Background). The important citation(s) are listed first. To change the rank of a citation, move the cursor to the field and press to cycle through the options. You can change the rank of multiple citations before saving. When you are done, select SAVE! --------------------------------------------------------------------- Locus * Add GenBank and EST numbers to loci Manager You can now add/modify GenBank numbers and EST numbers for genes and DNA segments. * Consensus Map feature available The description of the how to define a consensus order of markers for a chromosome will be distributed to the editors by December 1. --------------------------------------------------------------------- Probe * Add GenBank and EST numbers to probes Manager You can now add/modify GenBank numbers and EST numbers for PCR and Cloned probes. You can also add/modify GenBank numbers for ASO probes. --------------------------------------------------------------------- Map * All committees update maps and add/modify map distances Manager All committees (including NC, MDNA, DNA, and MIM) that can add maps can now also update them and add/modify map distances. * Zero map distance automatically set to 0 When the map string indicates that the distance between two loci is zero (denoted by a "/" separating the loci), the entry for that pair of loci in the EDIT MAP DISTANCES table is automatically set to '0'. --------------------------------------------------------------------- Citation * Note: Meeting Abstracts cannot be added or modified by the Manager editors. They are entered by GDB staff. --------------------------------------------------------------------- Contact * Contacts can be deleted Manager You can delete any contact that has not added, modified, or been linked to GDB data. ===================================================================== PROBLEMS FIXED All Users: * In the Locus Manager, you can retrieve loci assigned to a linkage group by entering 'ulg' (unassigned linkage group) and the number (1-5) of the linkage group in the Location field. * When calling the Citation Manager or the GDB Id Manager from Polymorphism Manager, all selected Polymorphisms are sent to the new manager. * The Max Het field in Polymorphism and Probe Managers displays the highest heterozygosity value associated with that particular polymorphism or probe. * In the Cell Line Manager, the Coriell number is correctly displayed in the Coriell field. * In Map Manager, angle brackets < > are not displayed around the Map Symbol for maps that are not fully approved. Use of angle brackets is now consistent in Locus and Map Managers; only genes and breakpoint sets which are not fully approved have angle brackets. * A VIEW STATE screen has been added to the Map Manager. ===================================================================== PROBLEMS FIXED Editors: Locus * The date in the Last Modified field is updated only when a Manager field on the MODIFY LOCUS screen is modified. It is not updated when objects linked to the locus are modified. Note that if you do a Save from the MODIFY LOCUS screen without changing any fields, the Last Modified date will still be updated. * One History record is now generated correctly when a field on the MODIFY LOCUS screen is modified. NOTE: the two items above also apply to the other data managers that have a Last Modified field or maintain History records. * The database can only process one data save command at a time. If you are trying to save a new or modified locus or any other object at the same time another editor is trying to save a different object, you will now get a "Please Note:" message describing the situation, rather than Error Code 1205. * Breakpoint sets that span multiple chromosomes can now be added. * Loci can be modified regardless of whether they are in an active or deleted map string. * The Link button on the ADD/MODIFY DNA SEGMENT screen is now greyed/ungreyed correctly. --------------------------------------------------------------------- Citation * A citation can be deleted by any committee, regardless of Manager which committee added it; provided that the citation is not the only citation linked to a GDB data object (e.g. locus, probe, map) or is included in the most recent HGM/CCM report. --------------------------------------------------------------------- Cell Line Manager Library Manager * All chromosome committees can link and unlink cell lines and libraries. - END -