From owner-gdb@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!news.clark.net!rahul.net!a2i!bug.rahul.net!a2i!infoseek.com!uunet!in1.uu.net!pipeline!psinntp!psinntp!psinntp!interramp.com!usenet From: Honk@interramp.com (Honker) Newsgroups: bionet.molbio.gdb Subject: Test Date: 5 Oct 1995 05:08:49 GMT Organization: Your Organization Lines: 4 Message-ID: <44vp91$5qs@usenet1.interramp.com> NNTP-Posting-Host: ip93.herndon4.va.interramp.com Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 Test. davidk From owner-gdb@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!paladin.american.edu!news.jhu.edu!oscar.gdb.org!ken From: ken@gdb.org (Ken Fasman) Newsgroups: bionet.molbio.gdb Subject: comments on the proposed GDB 6.0 schema Followup-To: bionet.molbio.gdb Date: 5 Oct 1995 17:53:24 GMT Organization: Genome Data Base, Johns Hopkins University School of Medicine Lines: 60 Distribution: world Message-ID: <45162k$1sl@news.jhu.edu> NNTP-Posting-Host: 192.239.76.36 Keywords: GDB 6.0 schema enhancements [The following message was sent to the e-mail address schema@gdb.org, in reply to GDB's request for comments on our new schema proposal. Please see our Web server (http://gdbwww.gdb.org/) for a copy of the draft schema document.] Thank you very much for your comments. This sort of feedback from the community is essential if we are to keep the schema accurate and relevant. We look forward to further input from you in the future. The decision to leave out genotype data for now was a conscious one, arrived at based on the input of the GDB advisory committee. It was felt that projects like CEPH and CHLC were handling a lot of this sort of data for now, and that other issues were more pressing (e.g. physical mapping data). However, we are planning to revisit the issue with our advisors at this month's meeting, and so may implement this in the near-term (6.1 or 6.2 release perhaps?), depending on their position. Your suggestion will be raised during this discussion. As for clone grids, again there is some opinion that others are handling this, at least for particular data sets (e.g. IMAGE consortium, Lehrach's RefDB). We will consider this one as well, relative to our other short term priorities, and put it on the list of requested enhancements. We may wish to get further input from you regarding the format and utility of such data to you and your colleagues. Again, thank you for your input. We really need it in order to stay useful. Thank you very much, Ken Fasman Informatics Director On Monday, 2 Oct 1995, Richard Bruskiewich wrote: > In a preliminary review of the proposed schema, I thought of the following: > > 1. Where do gridded (i.e. high density) clone (hybridization) blots > fit into the schema? They are in common use in many genome mapping > projects and are probably best considered as "MappingReagents"; however, > of what type? They are not necessarily complete libraries nor cell-lines, > nor singular clones. I suppose that they could be considered specialized > "MappingPanels". They often reflect the indexing schemes of 96 well > (or similar) storage plates for libraries, but are unique subsets of the > libraries. In some cases, the grid points represent pooled clones. > > I would suggest that "CloneGrid" represents a unique type of > "MappingReagent" and should be represented separately in the schema. > > > 2. It appears to me that no direct provisions are made in the current GDB > database for "raw" genotyping data (e.g. marker typings in the CEPH > families or phenotype families). Should (or could) such data be > incorporated into GDB 6? Such data could be in a federated database, > initially based upon the official CEPH release database? > > I suspect that the GDB 6 Schema could incorporate such data under an > Object class derived from "Population" (or "VariationObject"). From owner-gdb@net.bio.net Thu Oct 05 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!howland.reston.ans.net!paladin.american.edu!news.jhu.edu!gromit.gdb.org!user From: jamie@mitre.org (A. Jamie Cuticchia Ph.D.) Newsgroups: bionet.molbio.gdb Subject: New Contact Information Date: Fri, 06 Oct 1995 13:57:11 -0500 Organization: Genome Data Base - The Johns Hopkins University Lines: 37 Message-ID: NNTP-Posting-Host: 192.239.76.156 Subject: New Contact Information Author: A_J_Cuticchia at w50s1 Date: 10/6/95 12:13 PM I just wanted to inform you that effective 2 October I have left my post as Director of Data Acquisition and Curation for the Genome Data Base to pursue a new challenge in the MITRE Corporation. For those of you who do not know, MITRE is a FFRDC (federally funded research and development center) which has a strong reputation in information technology. I have joined MITRE for a quest to develop bioinformatics. I will very much miss my interactions with each of you in my previous capacity, but hope to continue contact as MITRE begins development in this area. My new contact information is as follows: A. Jamie Cuticchia, Ph.D. Principal Scientist ERAS (Center for Environment, Resources, and Space) The MITRE Corporation 7525 Colshire Drive MS W766 McLean, VA 22102-3481 Phone: 703-883-7152 Fax: 703-883-6332 E-mail: jamie@mitre.org Additionally, I will remain on faculty at Johns Hopkins in my post as Assistant Professor of Biomedical Information Science, with the appointment being moved from full-time to adjunct. From owner-gdb@net.bio.net Fri Oct 13 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.gdb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 14 Oct 1995 02:01:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 97 Sender: daemon@net.bio.net Distribution: world Message-ID: <199510140900.CAA14082@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. 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The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. From owner-gdb@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!ns1.faseb.org!lamarck.sura.net!ra.nrl.navy.mil!news.math.psu.edu!CTCnet!newsfeed.pitt.edu!uunet!in2.uu.net!news.sprintlink.net!newsfeed.internetmci.com!howland.reston.ans.net!paladin.american.edu!news.jhu.edu!oscar.gdb.org!ken From: ken@gdb.org (Ken Fasman) Newsgroups: bionet.molbio.gdb Subject: GDB and SIGMA Followup-To: bionet.molbio.gdb Date: 24 Oct 1995 13:13:22 GMT Organization: Genome Data Base, Johns Hopkins University Lines: 30 Distribution: world Message-ID: <46iopi$ead@news.jhu.edu> NNTP-Posting-Host: 192.239.76.36 Keywords: GDB SIGMA mapping Peter White, of the Division of Oncology at Children's Hospital of Philadelphia writes: > Our laboratory uses the Sigma program extensively to map human 1p36. I have > been referred to you both by Chris Fields and Chris Porter as being the > best current contact for Sigma. As GDB plans support for Sigma maps in > version 6.1, we are considering using Sigma as a template for an integrated > chromosome 1 map for the chromosome 1 community. In this regard, I am > wondering what the future of Sigma is. Apparently, the NCGR is no longer > supporting the program. Do you know if anyone is still developing Sigma? > Any information you might provide would be greatly welcomed. Dr. White, Thank you for your inquiry regarding Sigma and GDB version 6.0. There are currently no plans to enhance Sigma beyond its current version. Sigma is no longer under development at NCGR or Los Alamos. There is no more funding for this project, and none of the programmers who worked on the software are currently available. However, GDB is actively working to allow Sigma maps to be deposited in the database, definitely with release 6.1 (late spring/early summer release) and probably in 6.0 (January release). We hope that in the coming months, the release of the GDB map viewer and map editor software will help to complement, if not actually replace, Sigma. Sincerely, Ken Fasman Informatics Director, GDB From owner-gdb@net.bio.net Sat Oct 28 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news.umkc.edu!news From: Larry Prince Newsgroups: bionet.molbio.gdb Subject: Trisomy-9 Date: Sun, 29 Oct 1995 16:24:02 -0600 Organization: University of Missouri - Kansas City Lines: 12 Message-ID: <3093FF02.2F22@umslvma.umsl.edu> NNTP-Posting-Host: umslts1_20.umsl.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b1 (Macintosh; I; 68K) I am looking for any information on the genetic disease trisomy-9. I am not aware of any other name for this genetic defect or mutation. My sister is a an LD/BD special education teacher and recently got a girl in class who has this genetic defect. The girl's mother and doctor's no almost nothing about this defect. From what I've been told, this is an extremely rare defect and I have not been able to find anything on the Internet (including WWW, gopher, newsgroups, telnet, etc.) Any information or sources of information on this topic would be greatly appreciated. Thank you very much. Larry Prince From owner-gdb@net.bio.net Mon Oct 30 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!newsfeed.internetmci.com!in2.uu.net!news.compuserve.com!news.production.compuserve.com!news From: Brian B. Jiang <73344.437@CompuServe.COM> Newsgroups: bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genbank Subject: Anti-Immigration Law Status/Seminar Date: 31 Oct 1995 08:32:15 GMT Organization: The Law Office of Brian B. Jiang Lines: 105 Message-ID: <474muf$9r9$5@mhafm.production.compuserve.com> Xref: biosci bionet.molbio.bio-matrix:663 bionet.molbio.embldatabank:565 bionet.molbio.evolution:3749 bionet.molbio.gdb:381 bionet.molbio.genbank:2148 RE: New Development On the Anti-Immigration Bill(HR 2202) and Upcoming Seminar Hi folks: As of today, the House Judiciary Committee has completed its markup on the Lamar Bill after 9 days of debate over several weeks. Despite all the bad news, such as reduction of legal immigration and elimination of some family categories, there are a few signs of relief. Both outstanding researchers/professors and national interest waivers were restored to the Bill. So professionals( scientists, post-docs, engineers etc.) can still apply for permanent residence without labor certification and sponsorship of their employers. On the other hand, for those who have to apply through labor cert, they are, as usual, still at the mercy of the Labor Dept. Any positive change is yet to be seen. Although waiver of labor certification and employer sponsorship is still obtainable for those who qualify, difficulties have been on the rise and more are expected. Nearly all four Service Centers have implemented some newly proposed requirements that make it very difficult to obtain an approval. According to administrative rules no law should be carried out until it is final. Despite the rules, INS is already treating the proposals like enforceable law. In the real world, things are not always the way they are supposed to be. This is even more so in immigration practice with today's anti-immigration fervor. I am an immigration attorney specializing in employment based immigration(1st and 2nd preference). I will hold seminars on how to apply for a green card without labor certification and sponsorship of the employer. The intended audiences of my seminar are professionals with advanced degrees or a bachelor degree plus five years of work experience. I will also cover the impact of HR 2202 on future immigration. The locations of the seminar will include: 1. University of Florida at Gainesville University Center Hotel (President's Ballroom) 1535 SW Archer Road Gainesville, FL Tel: (904)371-3333 Time: 11/12/95 Sunday 2:00-4:00pm 2. Columbia University at New York City Columbia University 517 Hamilton Hall (close to W. 116th St. & Broadway) Time: 11/13/95 Monday 7:30-9:30pm 3. Princeton University Location to be decided Time 11/14/95 Tuesday 4. Baltimore near University of Maryland Holiday Inn Baltimore Inner Harbor (Chesateake Ballroom #1) 301 W. Lombard Street Baltimore, MD Tel: (410)685-3500 Time: 11/15/95 Wed. 7:30-9:30pm 5. Pittsburgh near Univ. of Pittsburgh Pittsburgh Green Tree Marriott (Near University of Pittsburgh) 101 Marriott Drive Pittsburgh, PA Tel: (412)922-8400 Time: 11/16/95 Thursday 7:30-9:30pm 6. Boston at Cambridge Hyatt Regency Cambridge 575 Memorial Drive Cambridge, MA Tel: (617)492-1234 Time 11/17/95 Friday 7:30-9:30pm 7. University of Connecticut Location to be decided Time 11/18/95 Saturday 2:30-4:30pm 8. Palo Alto near Stanford University Holiday Inn Palo Alto (Near Stanford University) 625 El Camino Real Palo Alto, CA Tel: (415)328-2800 Time 11/19/95 Sunday 7:30-9:30pm I will conduct these seminars during these time. All questions, comment, and suggestions are welcome. You can also reach me at tel. (619)278-5480 or (619)278-5492. Brian B. Jiang Esq. Email: 73344.437@compuserve.com