From owner-gdb@net.bio.net Wed Mar 02 22:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!darwin.sura.net!news.gdb.org!news From: help@gdb.org (GDB User Support) Subject: Public server updated Tuesdays until April 12 Message-ID: <1994Feb28.214923.27193@news.gdb.org> Sender: news@news.gdb.org Nntp-Posting-Host: sif.gdb.org Reply-To: bionet.molbio.gdb Organization: The Johns Hopkins University - Genome Data Base (GDB) Date: Mon, 28 Feb 1994 21:49:23 GMT Lines: 26 ============================================================================== GDB Public Server to be updated on Tuesdays until April 12 ============================================================================== The GDB public server in Baltimore is normally updated every Monday morning between 7-11 am Eastern Time. For the next 7 weeks (starting March 1 and ending April 12) the public server will be updated at the same time on Tuesdays instead of on Mondays. This change in update schedule will effect users of the ISQL server and GDB/Accessor in Baltimore, and these services may not be available while the server is being updated. We apologize for any inconvenience this may cause. - GDB User Support - Genome Data Base From owner-gdb@net.bio.net Sat Mar 05 22:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!bloom-beacon.mit.edu!news.kei.com!sol.ctr.columbia.edu!howland.reston.ans.net!darwin.sura.net!news.gdb.org!news From: help@gdb.org (GDB User Support) Subject: NEW Phone Number for GDB User Support Message-ID: <1994Mar1.215439.6742@news.gdb.org> Sender: news@news.gdb.org Nntp-Posting-Host: sif.gdb.org Reply-To: bionet.molbio.gdb Organization: The Johns Hopkins University - Genome Data Base (GDB) Date: Tue, 1 Mar 1994 21:54:39 GMT Lines: 18 ============================================================================ GDB User Support has a new phone number ============================================================================ The phone number for the GDB User Support helpline at Johns Hopkins University in Baltimore, MD has been changed. The new number is: Phone (410) 955-9705 The fax number has not changed and is still (410) 614-0434 We apologize for any inconvenience this may cause. - GDB User Support - Genome Data Base Johns Hopkins University From owner-gdb@net.bio.net Mon Mar 07 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!news-feed-1.peachnet.edu!umn.edu!msus1.msus.edu!vax1.mankato.msus.edu!vengeance Newsgroups: bionet.molbio.gdb Subject: Omaha Project Message-ID: <1994Mar8.084516.2361@vax1.mankato.msus.edu> From: vengeance@vax1.mankato.msus.edu Date: 8 Mar 94 08:45:16 -0500 Organization: Mankato State University Lines: 9 I am trying to build a list of names and E-Mail addresses of people in the Omaha Nebraska area for a school related project. If you live in Omaha or go to school there or know someone that does and will be around for three months or more, please reply via E-Mail to Vengeance@vax1.mankato.msus.edu. Thank you very much! Ryan Krueger From owner-gdb@net.bio.net Thu Mar 10 22:00:00 1994 Path: biosci!infomed.sld.cu!monoclon From: monoclon@infomed.sld.cu (Ctro Inmunologia Molecular) Newsgroups: bionet.molbio.gdb Subject: (none) Date: 11 Mar 1994 05:15:11 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9403102200.AA13440@infomed.sld.cu> NNTP-Posting-Host: net.bio.net Hi: We would really appreciate some general information about the genoma research project, something like who are working on it, what are its purposes, advantages, , possible applications and other interesting information. Thank you very much!!! From owner-gdb@net.bio.net Sat Mar 12 22:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!news.doit.wisc.edu!psl.wisc.edu!news From: Rapu Lak Subject: constructing a subset of all sequences Message-ID: <1994Mar13.210507.9680@pslu1.psl.wisc.edu> X-Xxdate: Sun, 13 Mar 94 23:10:07 GMT Sender: news@pslu1.psl.wisc.edu (USENET News System) Organization: UW-Madison X-Useragent: Nuntius v1.1.1d17 Date: Sun, 13 Mar 94 21:05:07 GMT Lines: 47 This is the problem: We are interested in various questions about RNA. Many of these interests are about eukaryotic mRNA and specifically, the 3' ends, 3' UTRs, 3'-most exons and the 3'-most introns. I would like to construct a database that contains these data. But I know that I don't know how to do this. I imagine it is possible to search the entire DNA sequence database for all eukaryotic DNA sequences, and then search for ones that identify a translation STOP codon (from some annotation??), and then limit the search to those that also identify the site of the 3' most intron-exon boundary. Finally, from among these files identify those that also have a comment (annotation?) about the site of cleavage and polyadenylation. Then we would like to extract only the DNA sequence that corresponds to the last exon as well as the exon containing the translation stop codon (if they are different) and the sequence of the 3'UTR up to and including the site of cleavage and polyadenylation. So we want to identify the DNA sequence files that have this information and then create a new file that contains only the DNA sequence corresponding to the specific part of the mRNA we are interested in. I then imagine that we would have a large group of new files, each containing annotations to the site of the translation stop codon, maybe the translation reading frame, the site of cleavage and polyadenylation, .... (what else?). These files would define the database that we are interested in analyzing. Am I dreaming the impossible dream? I suppose I can ask at least one relevant question. Are there tools or some established programs for doing this kind of database search and database creation? I'd like to hear from people who have used such programs, from people who have written such programs, and from people who might be interested in trying such a program to actually create such a database for us. I would like to make contact with those of the "net" who are comfortable doing these kinds of manipulations and could possibly guide me to success. Also, what and where are the relevant FAQs to this subject/problem? Have I posted this question to the appropriate newgroup? Please reply to me directly by email and I will post a SUMMARY of what comes my way. Rock Pulak UW-Biochemistry rapulak@macc.wisc.edu From owner-gdb@net.bio.net Sun Mar 13 22:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!news.gdb.org!news From: help@gdb.org (GDB User Support) Subject: Attention WAIS users of GDB databases Message-ID: <1994Mar9.171520.4056@news.gdb.org> Sender: news@news.gdb.org Nntp-Posting-Host: sif.gdb.org Reply-To: bionet.molbio.gdb Organization: The Johns Hopkins University - Genome Data Base (GDB) Date: Wed, 9 Mar 1994 17:15:20 GMT Lines: 26 *** Attention WAIS users of GDB databases *** Effective April 1, 1994, the source "gdb.src" will no longer be available. This will have *no effect* on the data contained in its component databases: gdb-citation.src gdb-contact.src gdb-locus.src gdb-map.src gdb-mutation.src gdb-polym.src gdb-probe.src If you previously used "gdb.src" as a shortcut to search through the 7 databases above, simply select all 7 before issuing your query. We regret the loss of convenience this might cause, but hope it will provide more dependable and consistent service to our WAIS users. If you have any questions, please contact help@gdb.org. From owner-gdb@net.bio.net Tue Mar 15 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!netnews.jhuapl.edu!stc-hld-mac.aplnis From: dantzhl1@jhuapl.edo (lee dantzler) Newsgroups: bionet.molbio.gdb Subject: cloning ethics Date: Wed, 16 Mar 1994 13:16:44 +0000 Organization: Johns Hopkins University Applied Physics Lab Lines: 9 Message-ID: <9403161316.AA44812@stc-hld-mac.aplnis> Reply-To: dantzhl1@jhuapl.edo (lee dantzler) NNTP-Posting-Host: stc-hld-mep.jhuapl.edu X-Newsreader: InterCon TCP/Connect II 1.2 Can anyone provide a lead on sources for information on the ethics of bio- engineering, specifically cloning? From owner-gdb@net.bio.net Fri Mar 18 22:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!news.gdb.org!news From: help@gdb.org (GDB User Support) Subject: GDB Release 5.3 Installed March 14 at Johns Hopkins University Message-ID: <1994Mar16.221450.4964@news.gdb.org> Sender: news@news.gdb.org Nntp-Posting-Host: sif.gdb.org Reply-To: bionet.molbio.gdb Organization: The Johns Hopkins University - Genome Data Base (GDB) Date: Wed, 16 Mar 1994 22:14:50 GMT Lines: 174 ----------------------------------------------------------------------------- GDB Release 5.3 Installed March 14 ----------------------------------------------------------------------------- The new GDB release was installed on the computer at JHU in Baltimore March 14 and features replication of the GDB data to the remote nodes. A summary of this feature and other enhancements are incldued in the Release Notes below. For information about accessing GDB, please contact: GDB User Support help@gdb.org ***** GDB Version 5.3 14 March 1994 ***** The major enhancement in GDB Version 5.3 is the ability to replicate the GDB data from Johns Hopkins University in Baltimore to the GDB nodes around the world. Previously the remote nodes received weekly deliveries of tapes containing the most recent GDB data. The new replication feature will enable the nodes to automatically update their database daily, without the time and resources required to prepare, distribute, and load the data updates via tapes. Replication of GDB is based on a scheme originally developed at the Los Alamos National Laboratory for the relational version of GenBank. The replication function does not alter how GDB looks to the user. In addition to the automated updating feature for the nodes, GDB 5.3 also includes the following enhancements and fixed problems for general users and editors. ENHANCEMENTS for ALL USERS Locus * Loci with same location are sorted by locus symbol Manager When you retrieve loci and sort them by location, groups of loci which occur at the same cytogenetic location are sorted by locus symbol. * Retrieve heavy chain or light chain mitochondrial loci You can retrieve all mitochondrial loci or only the light or heavy chain loci by entering the following text in the Location field: mt all mitochondrial loci mth heavy chain loci mtl light chain loci --------------------------------------------------------------------- Output * Menu option and status renamed on SCHEDULE REPORT screen. Manager When you enter the SCHEDULE REPORT screen, the schedule status of your report is shown in the upper left corner. If your report is not scheduled, the status displayed will be ** Not Scheduled **. When you have filled in the scheduling information, to schedule the report to run, select the menu option SEND! (This was previously "Save"). When the report is waiting for the next run date, the status will be ** SCHEDULED **. (This was previously "WAITING"). * Output can include locus proposals The Locus Sub-Options on the Add/Modify Report Definition screen for Locus Manager now includes Locus Proposals. ===================================================================== ENHANCEMENTS for GDB EDITORS All * Edit citation rank includes GDB Id of the citation Managers When you select EDIT->CITATION RANK, you will see a table view of all the citations linked to the current object. The GDB Id of each citation is now displayed in addition to primary author, citation, and year. --------------------------------------------------------------------- Locus * Citation required to approve a locus Manager When a committee adds a new locus, it must be linked to a citation to save and approve. Previously a linked citation was only required when the locus was ready to be fully approved. * Loci in the qter pseudoautosomal region on X and Y can be added D-segments in the qter pseudoautosomal region can now be added with a symbol of the format DXYS123. * Nomenclature Committee notified when gene is deleted Whenever a gene is deleted, the Nomenclature Committee will receive a GDB message. * Reference marker status for D-segments maintained during edit Editing a D-segment behaves the same as editing a gene; if the D-segment is a reference marker, the Ref Marker field on the edit screen is set to "Yes". * Comparative Mapping Committee can edit mouse homology data To edit mouse homology data for genes and D-segments, enter the Locus Manager as "comap" committee. Retrieve the locus and select Edit->Modify. On the MODIFY LOCUS screen, select Edit->Mouse Homology. --------------------------------------------------------------------- Probe * View and edit the chimeric key value for cloned probes Manager The chimeric key value for cloned probes can now be viewed in detail view and edited on the Add/Modify Clone screen. --------------------------------------------------------------------- Polymorphism * Detection Methods approved without gel percent and Mutation Managers You can now approve a Detection Method without entering gel percent data. --------------------------------------------------------------------- Map * History commment available for maps Manager When a map string is modified, you will now be prompted for a history comment. --------------------------------------------------------------------- Citation * Add book chapters from book Add/Modify screen Manager You can now add a book chapter directly from the ADD/MODIFY screen for books. --------------------------------------------------------------------- Contact * Call User Management from Add/Modify Contact screen Manager The Tool menu option on the Add/Modify Contact screen now includes User Mgmt, just like on the Main Menu. --------------------------------------------------------------------- Messages * Database object field included in Message output When outputting messages that are associated with a specific database object, the data from the Database Object field is now included in Detail View output. ===================================================================== PROBLEMS FIXED All Users: * In the Locus Manager, proposed Locus Symbols with 12 characters surrounded by angle brackets < > are now completely displayed in Detail View. * In the Probe Manager, probes which are linked to each other are correctly retrieved when starting from either probe. * In the Probe Manager, entering text in the Locus Name field on the PROBE RETRIEVE screen will retrieve the correct data. Previously retrieving probes based on Locus Name produced an error message. ===================================================================== PROBLEMS FIXED Editors: * If you enter any manager retrieve screen from the Main Menu, your first retrieve will correctly bring back the data. Previously if prior to entering the manager you had been in GDB Messages, the first retrieve would just return you to the Main Menu. * In the Locus Manager, you can now set the EC Number field to NULL. * In the Probe Manager, you can now successfully add and save ASO probes. * In the Map Manager, DNA committee can add and modify a map, but only the committee for the chromosome on which the map resides can fully approve it. * In GDB Messages, any committee can save a message to notes for locus even regardless of whether the locus is included in a map. - END - From owner-gdb@net.bio.net Tue Mar 22 22:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!news.gdb.org!news From: help@gdb.org (GDB User Support) Subject: GDB and OMIM Available via WWW (World Wide Web) Message-ID: <1994Mar21.195534.8517@news.gdb.org> Sender: news@news.gdb.org Nntp-Posting-Host: sif.gdb.org Reply-To: bionet.molbio.gdb Organization: The Johns Hopkins University - Genome Data Base (GDB) Date: Mon, 21 Mar 1994 19:55:34 GMT Lines: 188 *** GDB and OMIM Available via World Wide Web (WWW) *** The installation of GDB Version 5.3 in Baltimore on Monday March 14, 1994 includes access to GDB and OMIM data via World Wide Web (WWW), a "universe of network-accessible information" presented as hypertext. Documents include embedded links to text within the same document and to other network resources, so users can move easily within a document as well as move to different data sources. The GDB and OMIM data displayed contain links to other data; for example, an OMIM entry may have links to citations, other OMIM entries, and related GDB data. XMOSAIC and X-WINDOWS USERS --------------------------- Users who are running X-windows to access the JHU computer in Baltimore can use the XMosiac client at JHU to make full use of the WWW point-and-click interface for all GDB and OMIM applications. The WWW-OMIM interface replaces IRX for searching OMIM. NOTE: Users with a Mosaic 1.X client for the Macintosh and MS-Windows can access most options on the GDB WWW server. However, "GDB Browser" and "OMIM via HTML+" (the forms-based interfaces) are not available to these users. To access WWW through your GDB/OMIM login, 1) At the Main Menu, select 5. Local Databases 2) At the Local Databases menu, select 4. Internet WWW Access NOTE: Users accessing JHU through front-end software installed at their site do NOT have access to Local Databases from their Main Menu. The remote nodes have the option to offer their own set of local databases. Users who are familiar with WWW and have access to a WWW client are encouraged to access the GDB Home Page directly. The URL is: http://gdbwww.gdb.org/ TERMINAL USERS -------------- Users with character-based terminals (or terminal emulation software) can still access the GDB/OMIM server using Lynx, a text-based WWW client program. We recommend the use of Lynx instead of IRX for terminal-based users of OMIM. NOTE: Lynx may not work properly with some types of terminals or terminal emulation software. For example, we have reports of problems with Wyse-50 terminals which we are attempting to solve. If you get into Lynx and the screen display is garbled, type "Q" (capital letter Q) to exit from Lynx. ADVANTAGES OF SEARCHING OMIM VIA WWW (Xmosiac and Lynx) ------------------------------------------------------- There are several advantages to using the WWW server to access OMIM: 1. OMIM documents are displayed as hypertext, with embedded links to citations, cross-references to other OMIM entries, and cross-references to GDB. 2. Since the WWW operates in a client/server mode, editorial changes to OMIM entries are immediately available to users accessing the WWW server. CHOOSING OMIM SEARCH VIA WWW ---------------------------- The default for searching OMIM from either the Main Menu or from within GDB is via IRX. To search OMIM via WWW, do the following: 1) At the Main Menu, select 4. Change Working Environment 2) At the Change Working Environment menu, select 5. Access OMIM via WWW 3) At the prompt on the Change $OMIMWWW Value screen, type "y" [yes] and press . 4) You will return to the Change Working Environment menu. Select 0. Return to Main Menu If you are running X-windows, when you select OMIM, a Mosaic window will appear. If you are accessing GDB/OMIM from a terminal environment, when you select OMIM, a Lynx window will appear. In either case, a Query form or the appropriate OMIM document will be automatically displayed. DIFFERENCES BETWEEN LYNX and IRX INTERFACES FOR SEARCHING OMIM -------------------------------------------------------------- The differences between the Lynx (WWW) and IRX interfaces for accessing OMIM are listed below. OMIM via IRX OMIM via Lynx ------------ ------------- LIST OF COMMANDS Some commands are on the Question Commands are at the bottom of Input screen; some are on the every screen. Command screen. ENTERING A QUERY Enter questions on numbered Use the same query screen for each Question Input screens. query by clearing the fields. NARROWING SEARCHES Use field restrictors to limit Use the 'x' key to mark checkboxes query terms to specific document to limit query terms to specific sections. e.g. eye[ti] document sections. Use Boolean operators (AND,OR,NOT) Use AND, OR, NOT to specify to specify relationships among relationships among query terms. query terms. e.g muscular AND dystrophy You can still write queries as in IRX; the checkboxes are provided as a alternative. Complex queries using field restrictors as well as AND, OR, NOT should be written out. e.g. heart[ti] and smith[rf] USING WILDCARDS Typing in milk* gives you a Typing in milk* searches for all Wild-card Matching screen, where matching terms automatically; there you may select terms for your is no Wild-Card Matching screen. search. DOCUMENT RANKING Lynx uses an improved program to rank returned documents, so the order may differ from the order returned by IRX. The number of documents is identical. QUERY SEARCH TERMS MARKED All occurrences of the search The search terms used on the Query terms used on the Question Input screen are NOT identified in a screen are highlighted within document. a document. LINKS TO RELATED DATA All references are in bold text. The cursor is positioned on the first reference or link to another MIM document on each page (screen) of text. MOVE WITHIN DOCUMENT Use letter keys for navigating Use the arrow keys for navigating within IRX. Do NOT use the within Lynx. The key is arrow keys! optional for selecting a document from the list; using the space bar to move between pages is also optional. SEARCH FOR TERMS WITHIN A DOCUMENT Use the "=" key to search for terms Use the "/" key to search for terms within the document currently within the document currently displayed. displayed. TERMS SEARCHED WITHIN DOCUMENT MARKED If a term, such as "milk", is If a term, such as "milk", is searched within a document, then searched within a document, then all occurrences of the word are all occurrences of the word are highlighted in that document only. underlined in that document, in all other documents returned by the original query, and in all subsequent queries until you specify a new search-within-document term. MOVE BETWEEN DOCUMENT SECTIONS Use 'j' key to jump to the next Use "/" to search for a specific section in the document. section heading. e.g /references OUTPUT Print options in IRX: Print options in Lynx: Email to user Mail file to yourself Screen dump Print to the screen Welcomm Print QUESTION HISTORY Move to the Command screen and press Use the key from any screen "H" to see the question history. to see the question history, or use the left arrow key to move backward as many screens as is necessary. GENE MAP / DEFECTS LIST Gene map and defects list are Gene map and defects list are not available. available. SENDING COMMENTS ABOUT OMIM On the Command screen, use the While you are displaying a document, 'c' key to display the Comment use the 'c' key and follow the Input screen where you enter prompts to send a message to the your message to the OMIM editors. OMIM editors. - END - From owner-gdb@net.bio.net Tue Mar 22 22:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!library.ucla.edu!europa.eng.gtefsd.com!darwin.sura.net!news.gdb.org!news From: davidk@gdb.org (David G. Kitaguchi) Subject: Internet Outage Message-ID: <1994Mar21.225545.13045@news.gdb.org> Sender: news@news.gdb.org Nntp-Posting-Host: dev.gdb.org Reply-To: davidk@gdb.org Organization: The Johns Hopkins University - Genome Data Base (GDB) Date: Mon, 21 Mar 1994 22:55:45 GMT Lines: 25 Tomorrow morning (Tuesday March 22) our T-1 connection will be disabled for SURAnet operations. Between 6:00am and 8:00am (note time has been extended) internet connections will be unavailable. The actual total complete abscence of the T-1 will most likely only be 15 minutes. However, during this two hour period, it is possible that gdb.org could be isolated until 8:00am. ====================================================================== David Kitaguchi, Sr. User System Specialist WHOIS - DGK2 GDB/OMIM User Support Phone: (410) 955-9705 Johns Hopkins University School of Medicine FAX: (410) 614-0434 2024 E. Monument Street Baltimore, MD 21205-2100 help@gdb.org davidk@gdb.org Try our E-mail Query Service ask for "help" at mailserv@gdb.org WWW Users! Try "http://gdbwww.gdb.org/" ====================================================================== From owner-gdb@net.bio.net Sat Mar 26 22:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!agate!howland.reston.ans.net!wupost!darwin.sura.net!news.gdb.org!news From: help@gdb.org (GDB User Support) Subject: New GDB Node in Israel Message-ID: <1994Mar25.193357.24614@news.gdb.org> Sender: news@news.gdb.org Nntp-Posting-Host: sif.gdb.org Reply-To: bionet.molbio.gdb Organization: The Johns Hopkins University - Genome Data Base (GDB) Date: Fri, 25 Mar 1994 19:33:57 GMT Lines: 38 *** New GDB Node in Israel *** The GDB Israel Node is located at the Bioinformatics Unit, Weizmann Institute of Science, Israel. The main objective of this site is to serve the scientific community needs in the area of Molecular Biology, with emphasis in the Human Genome project. To register to access data through the GDB and OMIM applications, contact: Dr. Jaime Prilusky Bioinformatics Unit Weizmann Institute of Science 76100 Rehovot, Israel Phone 972-8-343456 Fax 972-8-344113 Email lsprilus@weizmann.weizmann.ac.il GDB and OMIM data can also be accessed from client software communicating with the following servers: 1. GDB/Accessor: Description: GDB at Weizmann Institute [Israel] Server: inherit1.weizmann.ac.il 2. World Wide Web server: URL= "http://bioinformatics.weizmann.ac.il:70" 3. Gopher server: Name=BioInformatics (Weizmann Institute, Israel) Host=bioinformatics.weizmann.ac.il Port=70 4. Anonymous FTP server: Name: bioinformatics.weizmann.ac.il Address: 132.76.55.12 --------------------------------------------