From owner-gene-linkage@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!unixg.ubc.ca!leblanc From: leblanc@unixg.ubc.ca (Heidi N LeBlanc) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Followup-To: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Date: 2 Feb 1995 17:45:59 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 9 Message-ID: <3gr5on$amt@nnrp.ucs.ubc.ca> References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> NNTP-Posting-Host: interchg.ubc.ca X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.ageing:1224 bionet.molbio.bio-matrix:537 bionet.molbio.embldatabank:439 bionet.molbio.evolution:2394 bionet.molbio.gdb:285 bionet.molbio.genome-program:1148 bionet.molbio.hiv:865 bionet.molbio.rapd:954 bionet.molbio.yeast:2287 bionet.molbio.gene-linkage:519 One of the problems isn't so much what we *do* with biotechnology, as how what we do is generally perceived. We as scientists think "Oh, what a clever idea, putting an arctic fish gene into strawberries". Non-scientists, with whatever level of education, often seem to think this is just monstrous. The issue might not really be whether what we are doing is ethical, or whether the ethics are unique to biotech, but rather that the level of tinkering we can achieve is vaguely felt to be just plain unnatural. The ethical problems might really be PR problems, and no less real for that. From owner-gene-linkage@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!daresbury!hgmp.mrc.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!emu.pmms.cam.ac.uk!rgep From: rgep@emu.pmms.cam.ac.uk (Richard Pinch) Newsgroups: bionet.molbio.gene-linkage Subject: DNA profiling statistics Followup-To: sci.math Date: 2 Feb 1995 18:12:16 GMT Organization: DPMMS University of Cambridge Lines: 9 Message-ID: <3gr7a0$9f2@lyra.csx.cam.ac.uk> NNTP-Posting-Host: emu.pmms.cam.ac.uk Summary: Reference wanted to mathematical techniques used Keywords: DNA profiling; statistical techniques Can anyone provide me with a reference to the statistical techniques used in DNA profiling (`fingerprinting')? I would prefer an explanation which assumes little or no knowledge of molecular biology but addresses the mathematical problems in a reasonably sophisticated way. Thanks, Richard Pinch; Queens' College, Cambridge From owner-gene-linkage@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.gene-linkage Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!cs.utexas.edu!uunet!world!chi From: chi@world.std.com (Cambridge Healthtech Institute) Subject: Genetic Screening Meeting Message-ID: Organization: Cambridge Healthtech Institute X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 3 Feb 1995 20:02:39 GMT Lines: 43 Xref: biosci bionet.molbio.methds-reagnts:23957 bionet.molbio.gene-linkage:527 Cambridge Healthtech Institute is sponsoring a conference: "Advances in Genetic Screening and Diagnosis of Human Diseases," to be held March 9-10, 1995 in San Francisco, California. Breakthroughs in understanding the genetic basis for inherited diseases and genes that determine predisposition to a number of other more common disorders are occurring almost weekly. This is the result of technical advances spinning off of the Human Genome Project, and a recognition of the tremendous medical and commercial value of such capabilities. A number of the disorders for which gene identification is being pursued will be highlighted. Part of the growth in genetic testing will occur as the number of genes for which tests become available explodes in the next few years. Another key factor will be the potential for drastic reductions in costs, which will shift the emphasis from single application testing of high risk individuals to preventive screeniing of much broader populations. New technology, including chip-based devices, will make it possible to simultaneously test for many genes and mutations. These developments will force enormous changes in healthcare, insurance and society. A number of speakers will address the anticipated impact of these changes, as well as commercial implications of these new tests. A panel of executives from four of the leading diagnostic companies will conclude the meeting with discussion of their vision of the key issues and challenges for this field. For more information contact Cambridge Healthtech Institute: chi@world.std.com *********************************************************************** *>>>>>>>>>>>> Cambridge Healthtech Institute <<<<<<<<<<<<<* *>>>>> 1000 Winter Street, Suite 3700 <<<<<* *~~~~~~~~~~~~~~~~~ Waltham, MA 02154 ~~~~~~~~~~~~~~~~~* *tel: 617.487.7989 fax: 617.487.7937* *e-mail: chi@world.std.com ++++++++ ftp: ftp.std.com: /pub/chi* *>>>>>>>>>>>>World Wide Web: http://id.wing.net/~chi/homepg.html<<<<<<* *********************************************************************** From owner-gene-linkage@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!news.unige.ch!usenet From: mike@medsun.unige.ch (Mike Morris) Subject: LOD score too high - answers Message-ID: <1995Feb3.154305.27274@news.unige.ch> Sender: usenet@news.unige.ch Reply-To: mike@medsun.unige.ch Organization: University of Geneva -Medical Center-, Switzerland Date: Fri, 3 Feb 1995 15:43:05 GMT Lines: 26 You may remember I posted this query a few days ago (if you don't remember, you are probably not interested!). Thanks for all your answers - the group is read by a lot more people than you might suspect! To remind you, when testing a disease against two closely-linked (to each other) markers, using MLINK, I got: 1 (disease), 2 lod = 4.7 1, 3 lod = 2.7 1, 2, 3 lod = 16! The consensus was (which makes perfect sense - I was simply ignorant) that the third value is "Ott's generalized lod score", which is based on the probability of ALL THREE LOCI BEING LINKED versus ALL 3 BEING UNLINKED. And I know that 2 of them are linked. So there you are! Thanks, folks Mike Morris ******************************************************************* Division of Medical Genetics tel (Switzerland) (22) 702.56.94 CMU, University of Geneva fax (Switzerland) (22) 702.57.06 Geneva, Switzerland email mike@medsun.unige.ch From owner-gene-linkage@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!waikato!auckland.ac.nz!NewsWatcher!user From: JEB.Harrison@auckland.ac.nz (Jane E B Harrison) Newsgroups: bionet.molbio.gene-linkage,bionet.molbio.gene-org,bionet.molbio.genome-program Subject: Databases Date: Fri, 03 Feb 1995 15:15:03 +1200 Organization: University of Auckland Lines: 17 Message-ID: NNTP-Posting-Host: 130.216.55.60 Xref: biosci bionet.molbio.gene-linkage:521 bionet.molbio.genome-program:1151 Hullo all, A Collegue of mine is after a database for human chromosomal translocations. Does such a beast exist? How would a person get to the database? Please email responses. Thanks x 10E6 JAne -- Jane E B Harrison "Science is like being God- Medical School only I have time and budget constraints" University of Auckland 'All opinons are MINE and MINE alone' From owner-gene-linkage@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!spool.mu.edu!uwm.edu!caen!newsxfer.itd.umich.edu!gatech!swrinde!howland.reston.ans.net!pipex!uknet!festival!leeds.ac.uk!news From: gen6ads@sun.leeds.ac.uk (A D Stewart) Subject: Re: My LOD score is too high! Message-ID: <1995Feb3.125632.23783@leeds.ac.uk> Reply-To: gen6ads@sun.leeds.ac.uk Organization: University of Leeds, U.K. Date: Fri, 3 Feb 1995 12:56:31 +0000 (GMT) References: <1995Feb1.073351.16180@news.unige.ch> Lines: 46 In article 16180@news.unige.ch, mike@medsun.unige.ch (Mike Morris) writes: > Not a common complaint, I guess. But I cannot understand (or believe) >a result we recently had from LINKAGE 5.1. > > We have a consanguineous family, with a monogenic AR disease (locus >1). We have two perfectly linked markers (2 and 3), which complement >each other in terms of informativity. The markers are at most 1% apart >(no rec. in this family). > > I ran MLINK, "Lod score table", with the following results: > Locus order Rec fractions Rec varied lod max (always theta=0) > 1 2 .0 1 3.1 > 1 3 .0 1 1.3 > >>> 1 2 3 .0 .01 1 16.1 <<< > > As I understand this, either I have screwed up somewhere, or the >program interprets the third line as "1 vs. superlocus 2+3", and I >get a genuine result. But 16 seems much too high! > > Can anyone clarify this for me? > > Mike Morris > >******************************************************************* >Division of Medical Genetics tel (Switzerland) (22) 702.56.94 >CMU, University of Geneva fax (Switzerland) (22) 702.57.06 >Geneva, Switzerland email mike@medsun.unige.ch > > Its not possible to say what your lod score should be without knowing your pedigree structure, of course. Why don't you simulate the maximum lod score that you could get by inputting a single hypothetical 'magic marker' which is fully informative (from what you say, this would be equivalent to numbering each of the haplotypes of your existing data as a single locus, reasonable if there is no recombination with such close markers). The marker allele frequencies could be very important - try a wide range for the disease-linked allele. This is not a tidy theoretical answer, but should give you the information you need. From owner-gene-linkage@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage,bionet.software Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!cs.utexas.edu!uunet!pipex!uknet!bcc.ac.uk!dac159!dcurtis From: dcurtis@hgmp.mrc.ac.uk (David Curtis) Subject: Re: Linkage software complex trait analysis Sender: news@ucl.ac.uk (Usenet News System) Message-ID: Date: Fri, 3 Feb 1995 13:59:19 GMT References: <3g3g1k$7lc@hawk.le.ac.uk> <3gbisp$n63@nic-nac.CSU.net> Organization: Institute of Psychiatry X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 15 Xref: biosci bionet.molbio.gene-linkage:525 bionet.software:10928 >> I'm looking at genetic susceptiblity in the mouse. >>I've done an F2 cross between resistant and susceptible strains >>and now I'm trying to identify any regions of the genome that >>may have susceptiblity genes, using linkage. >Well, I've heard of a program called "LINKAGE". Maybe you can ftp somewhere >and get it. I dunno if it's public domain. Yes it's public domain.No it's no good for experimental crosses, it's for generalised pedigrees in humans. I doubt you'd find it with archie. It's available (as the FASTLINK package) at gc.bcm.tmc.edu. From owner-gene-linkage@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!newshost.lanl.gov!news.ttu.edu!aurora.LaTech.edu!darwin.sura.net!spool.mu.edu!agate!howland.reston.ans.net!cs.utexas.edu!uunet!pipex!sunsite.doc.ic.ac.uk!uknet!bcc.ac.uk!dac159!dcurtis From: dcurtis@hgmp.mrc.ac.uk (David Curtis) Subject: Re: Commenting pedfiles? Sender: news@ucl.ac.uk (Usenet News System) Message-ID: Date: Fri, 3 Feb 1995 13:52:49 GMT References: <1995Jan30.133338.15924@news.unige.ch> Organization: Institute of Psychiatry X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 5 > Is it possible to include comments in pedfiles ? They seem so >sensitive to odd spaces or returns that it seems unlikely, but... You can append comments to the ends of lines in most circumstances (not when e.g. using ERPA) From owner-gene-linkage@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!gatech!swiss.ans.net!emi.com!pauling.wadsworth.org!rebecca!labonnes From: labonnes@csc.albany.edu (S. LaBonne) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Date: 2 Feb 1995 21:41:47 GMT Organization: University at Albany, SUNY Lines: 21 Message-ID: <3grjir$n5d@rebecca.albany.edu> References: <3gm7u9$t5e@nntp1.u.washington.edu> <3gr5on$amt@nnrp.ucs.ubc.ca> NNTP-Posting-Host: bathsheba.albany.edu Xref: biosci bionet.molbio.ageing:1227 bionet.molbio.bio-matrix:539 bionet.molbio.embldatabank:442 bionet.molbio.evolution:2397 bionet.molbio.gdb:287 bionet.molbio.genome-program:1154 bionet.molbio.hiv:867 bionet.molbio.rapd:956 bionet.molbio.yeast:2301 bionet.molbio.gene-linkage:523 In article <3gr5on$amt@nnrp.ucs.ubc.ca>, Heidi N LeBlanc wrote: >One of the problems isn't so much what we *do* with biotechnology, as how >what we do is generally perceived. We as scientists think "Oh, what a >clever idea, putting an arctic fish gene into strawberries". >Non-scientists, with whatever level of education, often seem to think >this is just monstrous. The issue might not really be whether what we >are doing is ethical, or whether the ethics are unique to biotech, but >rather that the level of tinkering we can achieve is vaguely felt to be >just plain unnatural. The ethical problems might really be PR problems, >and no less real for that. I quite agree, and my fear is that we needlessly _exacerbate_ these PR problems if we single out biotechnology for the kind of special treatment exemplified by the proposed course that started this discussion. Then naturally laypeople conclude, "Gee, even the scientists think this stuff is especially problematical, so we _certainly_ should be worried". -- Steve LaBonne *********************** (labonnes@csc.albany.edu) "It can never be satisfied, the mind, never." - Wallace Stevens From owner-gene-linkage@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!swiss.ans.net!emi.com!pauling.wadsworth.org!rebecca!labonnes From: labonnes@csc.albany.edu (S. LaBonne) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Date: 2 Feb 1995 16:43:49 GMT Organization: University at Albany, SUNY Lines: 34 Message-ID: <3gr245$i9p@rebecca.albany.edu> References: <3gm7u9$t5e@nntp1.u.washington.edu> <3gml85$fb5@rebecca.albany.edu> NNTP-Posting-Host: freia.albany.edu Xref: biosci bionet.molbio.ageing:1226 bionet.molbio.bio-matrix:538 bionet.molbio.embldatabank:440 bionet.molbio.evolution:2395 bionet.molbio.gdb:286 bionet.molbio.genome-program:1152 bionet.molbio.hiv:866 bionet.molbio.rapd:955 bionet.molbio.yeast:2298 bionet.molbio.gene-linkage:522 In article , Howard M. Bomze wrote: > Steve Bonne has been saying that there are no new ethical >considerations for agricultural biotechnologies. However, he has been >missing one very important one, that is the possibility of an engineered >gene to be transfered to a different species. The transgenic plant not >only has the sequences of the desired gene, it also contains the >sequences which are necesary to insert the gene into the genome. So a >question which must be looked at is this: If a gene for herbicide >resistance has been put into a corn plant so that that herbicide can be >used to kill all of the crab grass in the corn field, what happens if >the gene is transfered to the crab grass? Is there an _ethical_ problem here? I guess I can parse this as meaning, "if we failed to be concerned about this possibility and released the engineered corn without satisfying ourselves that it won't happen, we would be behaving unethically". Certainly I agree. Since comparable transfers of desired traits have been performed by selective breeding since the Neolithic (not to mention that horizontal gene transfers occur all the time in nature), I still don't see the _qualitatively_ new ethical considerations that you seem to think exist here. (Introducing rabbits into Australia is a good pre-biotechnology example of failing to anticipate massive undesired consequences of an environmental manipulation.) Don't get me wrong- we clearly need to start thinking a lot more seriously about the potential undesired impacts of _all_ new technologies. I just think that to single out biotechnology as some kind of special case borders on superstition. -- Steve LaBonne *********************** (labonnes@csc.albany.edu) "It can never be satisfied, the mind, never." - Wallace Stevens From owner-gene-linkage@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!hubcap.clemson.edu!biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!swiss.ans.net!emi.com!pauling.wadsworth.org!rebecca!labonnes From: labonnes@csc.albany.edu (S. LaBonne) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: 31 Jan 1995 01:21:34 GMT Organization: University at Albany, SUNY Lines: 39 Message-ID: <3gk3au$pdp@rebecca.albany.edu> References: NNTP-Posting-Host: freia.albany.edu Xref: biosci bionet.molbio.ageing:1230 bionet.molbio.bio-matrix:541 bionet.molbio.embldatabank:444 bionet.molbio.evolution:2403 bionet.molbio.gdb:288 bionet.molbio.gene-linkage:529 bionet.molbio.genome-program:1158 bionet.molbio.hiv:869 bionet.molbio.rapd:957 bionet.molbio.yeast:2304 In article , Phandaal wrote: >I've been asked to give a lecture to upper-division college students on >the controversies and ethical considerations in producing transgenic >organisms, especially transgenic plants. It's been a while since I gave >this lecture, and so I was wondering if anybody had any good examples of >controversies or ethical considerations that I could incorporate into the >talk. > >Two I can think of off-hand are: > >1) introducing insecticidal proteins (such as the Bacillus thuringiensis >protein) into plants may create resistant insect populations (under the >force of heavy selection pressure), which could then overrun the resistant >plants and make worthless the efforts by conventional growers who *use* Bt >protein as a topical pesticidal spray. > >2) altering fatty acid metabolism in oil-crops (like canola) so that they >produce oils found chiefly in palm and coconut could severely damage the >palm oil and coconut oil industries in Third World countries... thus >severely depressing the economies of these already struggling countries. My problem with these examples is that I see nothing about them that is unique to transgenic technology. Similar sorts of problems are raised all the time by "conventional" technologies, including very ancient ones like selective breeding. An analogue to 1 is simply overuse of pesticides (or antibiotics for that matter), which can render them worthless in the way you describe. And 2 in no way raises ethical issues different from, say, starting a palm oil industry in Key West, possibly after selective breeding of oil palms to produce strains that give high yields there. Indeed, I doubt that there _are_ any ethical issues which depend _specifically_ on agricultural use of biotechnology as opposed to agricultural technologies in general. -- Steve LaBonne *********************** (labonnes@csc.albany.edu) "It can never be satisfied, the mind, never." - Wallace Stevens From owner-gene-linkage@net.bio.net Sat Feb 04 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!news.uh.edu!uuneo.neosoft.com!Starbase.NeoSoft.COM!mckee From: mckee@starbase.neosoft.com (George McKee) Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Followup-To: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Date: 5 Feb 1995 15:25:32 GMT Organization: NeoSoft Internet Services +1 713 968 5800 Lines: 24 Message-ID: <3h2qlc$d6o@uuneo.neosoft.com> References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> NNTP-Posting-Host: starbase.neosoft.com X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.ageing:1236 bionet.molbio.bio-matrix:543 bionet.molbio.embldatabank:445 bionet.molbio.evolution:2412 bionet.molbio.gdb:290 bionet.molbio.genome-program:1164 bionet.molbio.hiv:871 bionet.molbio.rapd:960 bionet.molbio.yeast:2314 bionet.molbio.gene-linkage:530 Howard M. Bomze (hb10+@andrew.cmu.edu) wrote: : Steve Bonne has been saying that there are no new ethical : considerations for agricultural biotechnologies. However, he has been : missing one very important one, that is the possibility of an engineered : gene to be transfered to a different species. The transgenic plant not : only has the sequences of the desired gene, it also contains the : sequences which are necesary to insert the gene into the genome. This is one of those "ethical" problems that are really biological problems in disguise. Injecting new genes into the genomes of other organisms is precisely what retroviruses such as HIV have been doing for eons longer than biologists. To consider genetic engineering per se to be unethical is the same as considering crossbreeding unethical. The ethical considerations come into play when the new variety, however it was created, is being considered for introduction into the ecosystem. Introducing the gypsy moth into North America as a silk producer was far more disastrous than any frost-free tomato is likely to be. - George McKee -- Internet: mckee@neosoft.com Voice: +1 713 890 8122 From owner-gene-linkage@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msunews!netnews.upenn.edu!sanger.bcm.tju.edu!tromp From: tromp@sanger.bcm.tju.edu (Gerard Tromp) Newsgroups: bionet.molbio.gene-linkage,bionet.software Subject: Re: Linkage software complex trait analysis Date: 6 Feb 1995 17:20:01 GMT Organization: Biochemistry Lines: 29 Distribution: world Message-ID: <3h5lo1$co6@netnews.upenn.edu> References: <3g3g1k$7lc@hawk.le.ac.uk> <3gbisp$n63@nic-nac.CSU.net> NNTP-Posting-Host: sanger.bcm.tju.edu Keywords: S.A.G.E., Mapmaker Xref: biosci bionet.molbio.gene-linkage:533 bionet.software:10961 There are packages for mapping with experimental animal crosses. One that comes to mind is S.A.G.E. , a package available from Dr. Elston at Louisiana State Medical Center in New Orleans. Another is MAPMAKER by Eric Lander et al., available by anonymous ftp from genome.wi.mit.edu. Notes about availability of LINKAGE and FASTLINK. 1. LINKAGE is available by anonymous ftp at york.cpmc.columbia.edu, the site is that of Dr. Jurg Ott, one of the co-authors of the package. The operating system is VMS - VAX - and may be somewhat unfamiliar to those who are used to unix. 2. FASTLINK is available by anonymous ftp at softlib.rice.edu, the site is that of Dr. Alejandro Schaffer. Dr. Schaffer maintains and improves FASTLINK, so it would be to your advantage to retrieve it from there rather than from other sites. -- Gerard Tromp, Ph.D. Research Assistant Professor Vox: 215-955-4487 Department of Biochemistry 215-955-4488 and Molecular Biology Fax: 215-955-5393 Thomas Jefferson University 233 South Tenth Street, Room 328 E-mail: tromp@sanger.bcm.tju.edu Philadelphia, PA 19107 U.S.A. From owner-gene-linkage@net.bio.net Sun Feb 05 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!agate!howland.reston.ans.net!pipex!news.oleane.net!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!news.unige.ch!NewsWatcher!user From: bottani@cmu.unige.ch (A. Bottani) Subject: Bartter syndrome Message-ID: Sender: usenet@news.unige.ch Organization: Division of Medical Genetics, University of Geneva Date: Mon, 6 Feb 1995 15:33:25 GMT Lines: 13 Does someone know if the Bartter syndrome gene has recently been mapped? I have the vague feeling that I saw it in one of the genetic journals, but cannot remember where... Would be glad to get the exact reference (in case I am not dreaming...) -- Armand Bottani, MD Division of Medical Genetics 9, Av. de Champel CH - 1211 Geneva 4, Switzerland Tel. (+41) - 22 - 702 5709 Fax. (+41) - 22 - 702 5706 Email bottani@cmu.unige.ch From owner-gene-linkage@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ratatosk.yggdrasil.com!news.duke.edu!godot.cc.duq.edu!hudson.lm.com!news.pop.psu.edu!news.cac.psu.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msunews!netnews.upenn.edu!sanger.bcm.tju.edu!tromp From: tromp@sanger.bcm.tju.edu (Gerard Tromp) Newsgroups: bionet.molbio.gene-linkage,bionet.software Subject: Re: Linkage software complex trait analysis Date: 6 Feb 1995 17:20:01 GMT Organization: Biochemistry Lines: 29 Distribution: world Message-ID: <3h5lo1$co6@netnews.upenn.edu> References: <3g3g1k$7lc@hawk.le.ac.uk> <3gbisp$n63@nic-nac.CSU.net> NNTP-Posting-Host: sanger.bcm.tju.edu Keywords: S.A.G.E., Mapmaker Xref: biosci bionet.molbio.gene-linkage:534 bionet.software:10975 There are packages for mapping with experimental animal crosses. One that comes to mind is S.A.G.E. , a package available from Dr. Elston at Louisiana State Medical Center in New Orleans. Another is MAPMAKER by Eric Lander et al., available by anonymous ftp from genome.wi.mit.edu. Notes about availability of LINKAGE and FASTLINK. 1. LINKAGE is available by anonymous ftp at york.cpmc.columbia.edu, the site is that of Dr. Jurg Ott, one of the co-authors of the package. The operating system is VMS - VAX - and may be somewhat unfamiliar to those who are used to unix. 2. FASTLINK is available by anonymous ftp at softlib.rice.edu, the site is that of Dr. Alejandro Schaffer. Dr. Schaffer maintains and improves FASTLINK, so it would be to your advantage to retrieve it from there rather than from other sites. -- Gerard Tromp, Ph.D. Research Assistant Professor Vox: 215-955-4487 Department of Biochemistry 215-955-4488 and Molecular Biology Fax: 215-955-5393 Thomas Jefferson University 233 South Tenth Street, Room 328 E-mail: tromp@sanger.bcm.tju.edu Philadelphia, PA 19107 U.S.A. From owner-gene-linkage@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!HELIX.MGH.HARVARD.EDU!HAINES From: HAINES@HELIX.MGH.HARVARD.EDU ("Jonathan L. Haines") Newsgroups: bionet.molbio.gene-linkage Subject: call for abstracts Date: 7 Feb 1995 08:06:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 113 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HMRKRGHHQA8XNFWF@HELIX.MGH.HARVARD.EDU> NNTP-Posting-Host: net.bio.net CALL FOR ABSTRACTS THE 1995 INTERNATIONAL CHROMOSOME 9 WORKSHOP The 1995 International Chromosome 9 Workshop will be held from April 23 to April 25, 1995 in Williamsburg, Virginia, USA. ABSTRACTS MUST BE RECEIVED NO LATER THAN MARCH 1ST, 1995. Electronic transmission in addition to hard copy submission is strongly encouraged. Abstracts should be emailed to the following address: chrom9@genemap.mc.duke.edu. If electronic submission is not possible, please send both the hard copy of your abstract and an electronic version on diskette in either WordPerfect 6.0 or ASCII format. Abstracts should be sent to the following address: Dr. M.A. Pericak-Vance Bryan Research Building Research Drive Duke University Medical Center Box 2900 Durham, NC 27705 USA Phone: (919)684-6274 FAX: (919)684-6514 The format for the abstract should include title, author's names, and affilitiations separated by two lines from the body of the abstract. The body of the abstract should be no longer than 250 words. Abstracts will be judged competitively based on their strength of contribution to the overall genetic and phyical map of chromosome 9. Abstracts dealing solely with the mapping of specific disease loci, without additional mapping information are discouraged. Notification of abstract acceptance will be by March 10, 1995. Abstract submission is not sufficient to guarantee either attendance or reimbursement. Participants with accepted abstracts must confirm attendance by March 20, 1995. Individuals who register after that time are not guaranteed a place at the workshop. In submitting your abstract please be aware of the following rules that will apply to this year's workshop. These stipulations are in accordance with the new HUGO guidelines for workshop participation and reinbursement. 1. Abstract submission is required for attendance. Reimbursement funds are available for 35 participants [17 US, 18 Other]. Reimbursement consideration will be competitive and based on abstract content and its contribution to the genetic and physical map of chromosome 9. A limited number of individuals will be able to attend if they provide their own funding. ONLY ONE INDIVIDUAL PER LABORATORY [OR RESEARCH GROUP] WILL BE REIMBURSED. THERE WILL BE NO EXCEPTIONS. 2. Abstract acceptance does not automatically guarantee reimbursement. Reimbursement for both hotel and meals [all participants] and travel [US participants only] will occur after the workshop completion and ONLY AFTER SUBMISSION OF THE INDIVIDUAL'S ABSTRACT DATA TO DRS. POVEY AND HAINES FOR GDB SUBMISSION. GDB submission forms will be included with your abstract acceptance. Completed GDB forms are required for reimbursement and MUST be submitted BEFORE the workshop, as this will hasten the reimbursement process. Individuals attending the workshop and presenting data who fail to meet the GDB submission requirements WILL NOT BE REIMBURSED for any or part of the meeting. THERE WILL BE NO EXCEPTIONS. 3. Reimbursement procedures and policies are as follows: a. All participants: 3 nights lodging [Saturday, Sunday, and Monday] and board [dinner (Saturday) until lunch (Tuesday)] at the George Washington Inn and Conference Center in Colonial Williamsburg. Additional lodging requirements are the responsibility of the participants. Prearranged ground transportation by Van from the airport to hotel and back will also be provided. b. US participants: Travel for US participants will be limited to reimbursements of no more than $600.00 in airfare. Saturday night stayover has been arranged to allow for reduced rates. Airfares OR or other travel expenditures exceeding $600.00 are the responsibility of the individual investigator. Local participants will be reimbursed for travel by car at the standard rate of 0.30 per mile. TRAVEL FOR NON-US PARTICIPANTS IS THE RESPONSIBILITY OF THE INDIVIDUAL PARTICIPANTS (BUT MAY BE COVERED BY THEIR HOME COUNTRY (SEE BELOW). HOWEVER, NON-US PARTICIPANTS WILL BE SUBJECT TO THE SAME STRICT CRITERIA FOR ABSTRACT ACCEPTANCE AND ROOM AND BOARD REIMBURSEMENT. c. Non-US participants: Europeans who hope to attend the meeting should let Dr. Sue Povey know as soon as possible. If your abstract is accepted it is hoped that you will be eligible for travel funding but the arrangements for applying for this varies from country to country. Dr. Bronwen Loder of HUGO will send individual instructions as soon as your abstracts are accepted. She will also be able to give advice to non-European/non-US applicants. United Kingdom applications go directly to the MRC but only after you are on the official list of invitees. 4. All participants will be expected to prepare a poster presentation of their submitted abstract. Additional details for poster submission will be provided after acceptance as will meeting details including local travel arrangements, maps, etc.. From owner-gene-linkage@net.bio.net Mon Feb 06 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!caen!msunews!harbinger.cc.monash.edu.au!bunyip.cc.uq.oz.au!iccu6!ppp2.ipswichcity.qld.gov.au!hanscom From: hanscom@iccu6.ipswichcity.qld.gov.au (Hany Hanna) Subject: Genetics Sender: news@ipswichcity.qld.gov.au Message-ID: Date: Wed, 8 Feb 1995 05:18:17 GMT Lines: 10 X-Nntp-Posting-Host: ppp2.ipswichcity.qld.gov.au Organization: Global Infolinks Internet Server, Ipswich Qld Australia X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hello all, I have a few questions that I need to ask a professional in the field of genetics and hereditary problems. However, because the metter must remain confidential, I must ask for a personal address and use E-mail. So if you happen to know someone who can help, send me thier E-Mail address or give them mine. This matter is very important to me, I appreciate your help. CU, HANY From owner-gene-linkage@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!panix!news.columbia.edu!namaste.cc.columbia.edu!wl101 From: wl101@namaste.cc.columbia.edu (Wentian Li) Newsgroups: bionet.molbio.gene-linkage Subject: Linkage Newsletter 9(1), Feb 1995 Date: 7 Feb 1995 16:33:13 GMT Organization: Columbia University Lines: 232 Message-ID: <3h87c9$s48@apakabar.cc.columbia.edu> NNTP-Posting-Host: namaste.cc.columbia.edu .----------------------------. | | | Linkage Newsletter | | | `----------------------------' Vol. 9 No. 1 February 1995 Published by Jurg Ott, Columbia University, New York Editorial Assistant: Katherine Montague Fax: 212-568-2750 Tel. 212-960-2507 E-mail: jurg.ott@columbia.edu Postal address: Columbia University, Unit 58 722 West 168th Street, New York, NY 10032 LINKAGE COURSES In 1995, the following linkage courses will be held: February 27 - March 3: Introductory course at the Universi- ty of Zurich (Switzerland), Irchel Campus Computer Center. This course is full. June 12-16: Introductory course at Columbia University, New York (maximum of 30 participants). We often receive many more applications than we can accept and will carry this course twice in case of high demand (date not yet set). October 2-6: Advanced course at the University of Zurich (Switzerland), Irchel Campus Computer Center. The next Advanced course at Columbia University will be held early in January 1996. To obtain information on these courses, please write to Katherine Montague, course coordinator, by e-mail or fax. The textbook to be used for theoretical background and course exer- cises is Terwilliger JD & Ott J: Handbook of Human Genetic Linkage, Johns Hopkins University Press, 1994 (additional materi- al for advanced courses will be handed out at the course). Course participants are expected to bring this book with them to the course; in case of problems please contact Katherine Monta- gue. UPGRADING OUR ftp SITE Our anonymous ftp site (york.cpmc.columbia.edu) runs on an old Vaxstation 3100 with ftp software that is not well adapted to the system. Unfortunately, the Vaxstation occasionally freezes up and must be rebooted -- there is evidently little that can be done about this. So, if you experience problems accessing the ftp site, please try again later. Also, accessing it at night or in the morning tends to be more successful than at peak hours. A new member of our team, Dr. Wentian Li, started installing a new anonymous ftp site on our Sparcstation IPC. It is expected to be much more stable then the current one. Furthermore, it runs under Unix rather than under VMS as on the Vaxstation. As soon as a larger hard disk is installed, we will transfer all files from the Vaxstation to the Sparcstation. When ready, the anonymous ftp site can be reached as linkage.cpmc.columbia.edu and the old site (york.cpmc.columbia.edu) will be taken out of service. The new ftp site is expected to be up by mid-March. SOFTWARE NEWS ESPA program We regularly receive requests for the ESPA program, which carries out affected sib pair analysis with estimation of unobserved parental marker genotypes. This pro-gram is not available from us -- please address any requests to the developer of ESPA, Dr. Lodewijk Sandkuyil (sandkuyl@rullf2.LeidenUniv.nl), Voorstraat 27 a, 2611 JK Delft, The Netherlands. Tel: 011,31-15-123 638, Fax: 011,31-15-143-925. Bug in LINKAGE regarding loops Dr. Alejandro Schaffer submitted the following report: The purpose of this message is to report a dangerous bug in LINKAGE. The bug is that if maxloop is set to a number strictly lower than the actual number of loops, then LINKAGE gives no warning. In some cases it will give plausible but incorrect results. In contrast, in FASTLINK if maxloop is set to a number strictly lower than the actual number of loops, the program gives a warning and exits with instructions on how to fix the problem, without computing anything. Editor's note: Readers of the Newsletter (January 1992) have been made aware of this problem. However, thus far no test had been implemented in LINKAGE to catch the situation that maxloop is smaller than the actual number of loops. This test has now been implemented in the DOS version of LINKAGE (available on our ftp site) and will be implemented shortly in other LINKAGE versions. Newer versions of FASTLINK The following announcement was submitted by Dr. Alejandro Schaf- fer: Since May 1993, we have been distributing faster versions of the genetic linkage analysis programs in LINKAGE 5.1. Several users have dubbed the new code "FASTLINK". Version 2.2 of FASTLINK is now ready and available. The changes from version 2.1 (distributed in March 1994) include 1. Bug fixes to bugs introduced in FASTLINK and bugs inherited from LINKAGE 2. More dynamic memory allocation 3. More diagnostics to detect user errors politely 4. Crash-recovery is now possible for LINKMAP and MLINK, in addition to LODSCORE and ILINK 5. Lots of information about portability of FASTLINK to different operating systems is included 6. A document entitled "The Mystery of the Unknown" explaining how the preprocessor program UNKNOWN works among other goodies. See the file README.updates, which comes with the distribution, for details. Like FASTLINK 2.1, this version is being distributed from a computer at Rice University. Here are the instructions for retrieving the code: ftp softlib.cs.rice.edu Login as anonymous and leave your full e-mail address as password. cd pub/fastlink In that directory you will find various files. You can get everything at once by retrieving the file: fastlink.tar.Z and then (outside of ftp) doing the commands: uncompress fastlink.tar.Z tar xvf fastlink.tar If you prefer to get your files piecemeal, instead of getting fastlink.tar.Z, start by getting README* The file README (with no extension) will give you a roadmap to all the documentation. I am maintaining a mailing list of FASTLINK users. If you have retrieved the code and would like to be on the mailing list, send me e-mail at the address below. Special thanks to many FASTLINK users including: Lucien Bachner, Alan Cox, David Featherstone, Sandep Gupta, Victoria Haghighi, Carol Haynes, Jerry Halpern, Kimmo Kallio, Luc Krols, Shriram Krishnamurthi, Tara Cox Matise, Ken Morgan, Jurg Ott, Steve Roberts, Joe Terwilliger, Gerard Tromp, Ellen Wijsman, Xiaoli Xie, who provided bug reports, suggestions for improvements, guidance on documentation, and assistance with portability. I could not have prepared FASTLINK 2.2 without your help! We are also distributing executable versions of FASTLINK for DOS. The ftp instructions are similar. Instead of doing cd pub/fastlink do cd pub/fastlink/dos binary In that directory you will find 13 files. One is an executable for UNKNOWN (called unknown.exe). We have 3 versions each of LODSCORE, ILINK, LINKMAP, and MLINK with the constant maxhap set to 48, 96, 250 respectively. For example, the file li96.exe is LINKMAP with maxhap set to 96 and the file il250.exe is ILINK with maxhap set to 250. maxhap is the maximum product allowed for the number of alleles at each locus. For example, if you want to a 3-locus analysis with 2x4x8=64 alleles, you should not use the versions with maxhap set to 48, but you can use either the 96 or 250 versions. Alejandro Schaffer, PhD Department of Computer Science Rice University Houston, TX 77251 schaffer@cs.rice.edu Phone: (713) 527-8101 x3813 FAX: (713) 285-5930 Compiling with the 'colig.bat' batch program Dr. Joseph Terwilliger made me aware of a problem with the 'colig' batch program that we distribute to facilitate recompil- ing the LINKAGE programs for DOS (Turbo/Borland Pascal): I have a question for you about the turbo pascal colig.bat file. Why does it have the line del *.tp* at the end? This seems to delete turbo.tpl, which is needed to compile the programs here on the PC's in Finland. Is it okay to change that line to DEL *.TPU instead of TP*, to preserve the *.TPL files? Response: When the LINKAGE programs are compiled with Tur- bo/Borland Pascal, intermediate files are created and are left on the hard disk. These files are named *.tpx, where x=U for regular Turbo Pascal, x=P when compiled for protected mode, and x=W when compiled to run under Windows. The statement 'del *.tp*' deletes any of these files that might have been created. This procedure was chosen under the assumption that the compiler would reside in a different directory. If it resides in the same directory as the programs to be compiled, one of the compiler files, 'turbo.tpl', will also be deleted. Thus, the 'colig.bat' and 'colit.bat' batch programs have now been restructured so that 'turbo.tpl' will no longer be deleted. Meeting Announcement The following announcement has been submitted to the Newletter by the meeting organizers: Fourth Annual meeting of the INTERNATIONAL GENETIC EPIDEMIOLOGY SOCIETY, June 20-22, 1995 - Snowbird, Utah. The meeting will be held in the Cliff Lodge (just 29 miles from Salt Lake City International Airport) in conjunction with the Society of Epidemiological Research. Abstracts for consideration of oral presentations and posters are due February 10, 1995. For abstract forms, contact Michele Brown, University of Utah, (801) 581-558099 or fax (801) 581-3165. For program information contact Melissa Austin, University of Washington, Seattle, (206) 685-9384, fax (206) 685-3407. Support through grant HG00008 from the National Center for Human Genome Research is gratefully acknowledged. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Wentian Li, Ph.D tel: 212-960-2200 ext 490 Associate Research Scientist 212-960-2507 (main office) Department of Psychiatry FAX: 212-568-2750 From owner-gene-linkage@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!JEEVES.UCSD.EDU!hoschek From: hoschek@JEEVES.UCSD.EDU (gisela hoschek) Newsgroups: bionet.molbio.gene-linkage Subject: English Language Help Date: 8 Feb 1995 10:08:51 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502081806.AB07710@jeeves.UCSD.EDU> NNTP-Posting-Host: net.bio.net Editors and reviewers let me know that there is a need for help to authors of research papers to be submitted for publication in English or for grant applications to English speaking sources. I would like to help (translating and/or proof-reading) where my expertise qualifies me: molecular biology, biochemistry, molecular genetics. I am not looking for employment, but would like to work with individual authors. Since I recently retired from the lab bench for health reasons, I want to stay connected and active, and put to use the skills and knowledge I acquired over the last 20 years. I have worked mainly in the field of plant molecular genetics (UCLA and UCSD), with excursions into entomology (bacculoviruses) and cancer research (in tissue culture). I speak German fluently, and French enough to understand. For more INFO please contact me: e-mail: hoschek@jeeves.ucsd.edu tel.: (619) 944-4233 From owner-gene-linkage@net.bio.net Wed Feb 08 22:00:00 1995 Path: biosci!vt.edu!fishgen From: fishgen@vt.edu (Bruce J. Turner) Newsgroups: bionet.molbio.gene-linkage Subject: pedigree analysis software Date: 8 Feb 1995 23:20:33 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502090720.XAA12774@net.bio.net> NNTP-Posting-Host: net.bio.net A graduate student in Jeff Walter's lab here is in need of a source of pedigree analysis software for her studies of birds. She has roughly 6000 individuals and wants to put them all in a pedigree. Any suggestions for public domain or commercial software that could do this would be appreciated. From owner-gene-linkage@net.bio.net Wed Feb 08 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!agate!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!gatech!swrinde!howland.reston.ans.net!pipex!uknet!bcc.ac.uk!dac159!dcurtis From: dcurtis@hgmp.mrc.ac.uk (David Curtis) Subject: Re: LOD score too high - answers Sender: news@ucl.ac.uk (Usenet News System) Message-ID: Date: Thu, 9 Feb 1995 10:31:33 GMT References: <1995Feb3.154305.27274@news.unige.ch> Organization: Institute of Psychiatry X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 22 > To remind you, when testing a disease against two closely-linked >(to each other) markers, using MLINK, I got: > 1 (disease), 2 lod = 4.7 > 1, 3 lod = 2.7 > 1, 2, 3 lod = 16! > The consensus was (which makes perfect sense - I was simply ignorant) >that the third value is "Ott's generalized lod score", which is based >on the probability of ALL THREE LOCI BEING LINKED versus ALL 3 BEING >UNLINKED. And I know that 2 of them are linked. Sorry, I don't quite understand this. With MLINK, you generally only vary one recombination fraction. To test the hypothesis of all linked against none linked you'd have 1 - 0.0 - 2 - 0.0 - 3 against 1 - 0.5 - 2 - 0.5 - 3, which would mean changing two intervals simultaneously. What you wanted to test was 1 - 0.0 - 2 - 0.0 - 3 against 1 - 0.5 - 2 - 0.0 - 3, i.e. the disease being linked or unlinked against the two markers tightly linked to each other. The mistake which might be relatively easy to make would be to test 1 - 0.0 - 2 - 0.0 - 3 against 1 - 0.0 - 2 - 0.5 - 3. This assumes the disease and first marker are linked, and tests whether the second marker is linked to them. That's not what you did is it? Otherwise, I don't quite see how you managed to do what you say you did. From owner-gene-linkage@net.bio.net Wed Feb 08 22:00:00 1995 Path: biosci!WATSON.HGEN.PITT.EDU!dweeks From: dweeks@WATSON.HGEN.PITT.EDU ("Daniel E. Weeks") Newsgroups: bionet.molbio.gene-linkage Subject: Re: LOD score too high - answers Date: 9 Feb 1995 11:59:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Thu, 9 Feb 1995, David Curtis wrote: > To test the hypothesis of all linked against none > linked you'd have 1 - 0.0 - 2 - 0.0 - 3 against 1 - 0.5 - 2 - 0.5 - 3, which > would mean changing two intervals simultaneously. Unfortunately, this is exactly what LINKMAP does when it computes Ott's generalized lod score (which is described in his book). I think this may be identified only as a lod score in the LRP output, but in the final.out text output, it is identified as Ott's generalized lod score (without further explanation). LINKMAP should compute multipoint lod scores, but it cannot since it only does one order at a time. For example, if 1 is the trait locus, and our given marker map is 2---0.05---3, then the multipoint lod score for the order 2---0.0---1---0.05---3 requires computation of two likelihoods: A) The likelihood under order 2---0.0---1---0.05---3 and B) The likelihood under order 1---0.5---2---0.05---3 (i.e., with the trait off the map). Thus, post-processing of LINKMAP output is required to compute valid multipoint lod scores. I believe Jurg Ott distributes a utility program to do this. I have one as well, which is now available in the file 'map.tar.Z' by anonymous ftp from watson.hgen.pitt.edu. Please note that my conversion program requires that you start each group of LINKMAP runs with the trait locus off the marker map on the left. I hope this helps clarify matters. -- Dan Weeks -- ________________________________ Daniel E. Weeks, Ph.D. The Wellcome Trust Centre Department of Human Genetics for Human Genetics University of Pittsburgh University of Oxford Crabtree Hall, Room A310 Windmill Road 130 DeSoto Street Oxford OX3 7BN Pittsburgh, PA 15261 (+44) 865 742 441 (1-412) 624-3066 FAX: (+44) 865 742 196 FAX: (1-412) 624-3020 daniel.weeks@well.ox.ac.uk dweeks@watson.hgen.pitt.edu From owner-gene-linkage@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!news.cc.utah.edu!corona!patrick From: Patrick O'Neil Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: Thu, 9 Feb 1995 23:28:35 -0700 Organization: University Of Utah Computer Center Lines: 52 Message-ID: References: NNTP-Posting-Host: corona.med.utah.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: Xref: biosci bionet.molbio.ageing:1267 bionet.molbio.bio-matrix:553 bionet.molbio.embldatabank:450 bionet.molbio.evolution:2429 bionet.molbio.gdb:295 bionet.molbio.gene-linkage:543 bionet.molbio.genome-program:1178 bionet.molbio.hiv:887 bionet.molbio.rapd:972 bionet.molbio.yeast:2369 On Mon, 30 Jan 1995, Phandaal wrote: > I've been asked to give a lecture to upper-division college students on > the controversies and ethical considerations in producing transgenic > organisms, especially transgenic plants. It's been a while since I gave > this lecture, and so I was wondering if anybody had any good examples of > controversies or ethical considerations that I could incorporate into the > talk. I spent a year working in a plant molec bio lab that was being partially funded by a private company to produce a more fungal resistent sugarbeet. Technically, it would be a transgenic in that a gene, VERY closely related to an already present gene, from Arabidopsis was/is to be introduced into the sugarbeet and overexpressed, thus bolstering the sugarbeet's fungal resistence. I enjoyed the work very much and saw absolutely nothing wrong with it. It was making use of an already existent defensive gene that resides in many plants and simply increasing its output by using an easy to maniplate gene from a common lab plant. This sugarbeet will allow, hopefully, less use of chemical fungicides. You could argue that it will simply apply selective pressure for fungi to evolve resistence...but then, so does the use of fungicides or natural defenses. A more resistent fungi will, conversely, select for more fungal-resistent plants. This can be applied to your first point below too. > > Two I can think of off-hand are: > > 1) introducing insecticidal proteins (such as the Bacillus thuringiensis > protein) into plants may create resistant insect populations (under the > force of heavy selection pressure), which could then overrun the resistant > plants and make worthless the efforts by conventional growers who *use* Bt > protein as a topical pesticidal spray. The use of the spray itself puts selective pressure on insects to develop resistence. The point is moot. > > 2) altering fatty acid metabolism in oil-crops (like canola) so that they > produce oils found chiefly in palm and coconut could severely damage the > palm oil and coconut oil industries in Third World countries... thus > severely depressing the economies of these already struggling countries. If business was nice, then companies would never be put out of business. It may be tough but I could not support artificially supporting a weakly-based economy by ignoring a possible economic boon here. Any economy that ties itself to one commodity is *automatically* doomed to bite it pretty hard. Look at Louisiana and the effects of it having placed all its economic eggs in the oil business basket -- the state is only now beginning to recover from over a decade of depressed economy and hard times. Patrick From owner-gene-linkage@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!news.cc.utah.edu!corona!patrick From: Patrick O'Neil Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Subject: Re: controversies & ethics Date: Thu, 9 Feb 1995 23:44:24 -0700 Organization: University Of Utah Computer Center Lines: 25 Message-ID: References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> NNTP-Posting-Host: corona.med.utah.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <3gm7u9$t5e@nntp1.u.washington.edu> Xref: biosci bionet.molbio.ageing:1269 bionet.molbio.bio-matrix:554 bionet.molbio.embldatabank:451 bionet.molbio.evolution:2430 bionet.molbio.gdb:296 bionet.molbio.gene-linkage:544 bionet.molbio.genome-program:1179 bionet.molbio.hiv:888 bionet.molbio.rapd:973 bionet.molbio.yeast:2370 On 31 Jan 1995, Jared Roach wrote: > 2) The human race as a whole (or national governments, or > individuals) is slow to reach consensus on ethical issues (i.e. > religion, abortion, the creation of new species, etc.) Science > should slow its pace of discovery to allow Ethics to catch up. I could never go along with this point. What, tell us all that we should quit looking at this? Stop research concerning that? Take up a new trade, like house painting? I do and will continue to study and learn just as quickly as I am physically capable. I could never say, "well, that result sure does point to a VERY exciting, very interesting, line of research that would increase my understanding of x. Well, maybe I'll just cool my jets and let it go for a decade or so. Sure don't want to upset those who can't handle the fast pace of scientific understanding." In any case, it is a pointless thought since if this or that or those countries stopped research on x, then some other country or group would take it up because there would be a possible economic boon tied to it. If not us, then someone else. Humans have never and will never all agree to the same extent on ANYTHING. I would go to any location that would support what I am interested in researching, be it transgenics or gene therapy, etc. From owner-gene-linkage@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!news.cc.utah.edu!corona!patrick From: Patrick O'Neil Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast,bionet.molbio.gene-linkage Subject: Re: controversies & ethics Date: Thu, 9 Feb 1995 23:52:53 -0700 Organization: University Of Utah Computer Center Lines: 20 Message-ID: References: <3gk3au$pdp@rebecca.albany.edu> <3gm7u9$t5e@nntp1.u.washington.edu> <3gml85$fb5@rebecca.albany.edu> NNTP-Posting-Host: corona.med.utah.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: Xref: biosci bionet.molbio.ageing:1270 bionet.molbio.bio-matrix:555 bionet.molbio.embldatabank:452 bionet.molbio.evolution:2431 bionet.molbio.gdb:297 bionet.molbio.genome-program:1180 bionet.molbio.hiv:889 bionet.molbio.rapd:974 bionet.molbio.yeast:2371 bionet.molbio.gene-linkage:545 On Wed, 1 Feb 1995, Howard M. Bomze wrote: > Steve Bonne has been saying that there are no new ethical > considerations for agricultural biotechnologies. However, he has been > missing one very important one, that is the possibility of an engineered > gene to be transfered to a different species. This already happens in nature by various means, one of which is viral. There is no absolute genetic sanctity in nature. As for transgenics, especially in plants, one tool for introducing foreign genes is agrobacteria. This microbe is fully capable of vectoring interspecific DNA without lab manipulation. The DNA so introduced in the lab does not carry any special DNA destabilizer, rather, it depends on the rather scattershot and low-yield natural method of homologous recombination or illegitimate recombination. Another method has absolutely no danger of transfering a new DNA transfer method to nature: the gene gun. DNA of interest bound to microscopic gold beads and shot into cells offers absolutely no threat of tranfering into an uncontrollable means of interspecific gene transfer in the wild. From owner-gene-linkage@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: bir1@cornell.edu (Bruce Reisch) Newsgroups: bionet.molbio.gene-linkage,bionet.software Subject: Re: Linkage software complex trait analysis Date: Fri, 10 Feb 1995 14:39:52 -0500 Organization: Cornell University Lines: 15 Sender: bir1@cornell.edu (Verified) Distribution: world Message-ID: References: <3g3g1k$7lc@hawk.le.ac.uk> <3gbisp$n63@nic-nac.CSU.net> <3h5lo1$co6@netnews.upenn.edu> NNTP-Posting-Host: 132.236.10.52 Xref: biosci bionet.molbio.gene-linkage:547 bionet.software:11027 In article <3h5lo1$co6@netnews.upenn.edu>, tromp@sanger.bcm.tju.edu (Gerard Tromp) wrote: > There are packages for mapping with experimental animal crosses. One that comes > to mind is S.A.G.E. , a package available from Dr. Elston at Louisiana State > Medical Center in New Orleans. Another is MAPMAKER by Eric Lander et al., > available by anonymous ftp from genome.wi.mit.edu. > Also, there is a program called Map Manager 2.6.2 for the Macintosh. Developed by Roswell Park Cancer Institute, Buffalo, NY, Kenneth Manly, voice 716-845-3372, internet mapmgr@mcbio.med.buffalo,edu See their WWW page at http://mcbio.med.buffalo.edu/mapmgr.html This program handles backcrosses, intercrosses, and recombinant inbred strains. From owner-gene-linkage@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!WATSON.HGEN.PITT.EDU!dweeks From: dweeks@WATSON.HGEN.PITT.EDU ("Daniel E. Weeks") Newsgroups: bionet.molbio.gene-linkage Subject: Re: LOD score too high - answers Date: 10 Feb 1995 06:59:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: References: On 9 Feb 1995, Daniel E. Weeks wrote: > > To test the hypothesis of all linked against none > > linked you'd have 1 - 0.0 - 2 - 0.0 - 3 against 1 - 0.5 - 2 - 0.5 - 3, which > > would mean changing two intervals simultaneously. > > Unfortunately, this is exactly what LINKMAP does when it computes > Ott's generalized lod score (which is described in his book). Opps, it is ILINK which computes Ott's generalized lod score, not MLINK or LINKMAP. David Curtis' discussion of MLINK was correct - MLINK does only change one theta at a time, and, as pointed out, this may result in a 'lod score' that is not a proper multipoint lod score because it was standardized by the wrong likelihood. -- Dan Weeks -- From owner-gene-linkage@net.bio.net Sat Feb 11 22:00:00 1995 Path: biosci!newshost.lanl.gov!news.ttu.edu!aurora.LaTech.edu!darwin.sura.net!maze.dpo.uab.edu!usenet From: Mpsy0l3@uabdpo.dpo.uab.edu (Flammable) Newsgroups: bionet.molbio.gene-linkage Subject: What is the Genome-Project? Date: 11 Feb 1995 23:37:33 GMT Organization: Friedman Graphix Lines: 4 Message-ID: <3hjhnt$eae@maze.dpo.uab.edu> NNTP-Posting-Host: tty17.maze.ppp.uab.edu X-Newsreader: WinVN 0.92.6+ Please send me some E-Mail to Mpsy013@uabdpo.dpo.uab.edu and in it please tell me what the Genome project is about, what it entails, who's involved, or any other information you have availible. ANYTHING you can give me would be incredibly apperciated. Thank you. From owner-gene-linkage@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.sprintlink.net!pipex!uknet!bcc.ac.uk!dac159!dcurtis From: dcurtis@hgmp.mrc.ac.uk (David Curtis) Subject: Re: LOD score too high - answers Sender: news@ucl.ac.uk (Usenet News System) Message-ID: Date: Mon, 13 Feb 1995 11:23:03 GMT References: <1995Feb3.154305.27274@news.unige.ch> Organization: Institute of Psychiatry X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 26 >> To remind you, when testing a disease against two closely-linked >>(to each other) markers, using MLINK, I got: >> 1 (disease), 2 lod = 4.7 >> 1, 3 lod = 2.7 >> 1, 2, 3 lod = 16! >> The consensus was (which makes perfect sense - I was simply ignorant) >>that the third value is "Ott's generalized lod score", which is based >>on the probability of ALL THREE LOCI BEING LINKED versus ALL 3 BEING >>UNLINKED. And I know that 2 of them are linked. The consensus here seems to have been quite wrong then, and you weren't ignorant, it's MLINK that's misleading. The short and simple answer is that when doing multipoints MLINK doesn't output a lod score (log base 10). Instead it outputs twice the natural log of the likelihood ratio, which is an anachronistic statistic called a location score. It differs from the lod score by 2ln(10), about 4.6. All talk of testing the wrong intervals, standardising on the wrong likelihood or getting "Ott's generalised lod score" is really a side issue. The real problem is that MLINK doesn't output what it says it outputs as a "log like difference", it outputs a 2ln(like) difference. My advice is to look at the raw log likelihoods you get and ignore the totals and what MLINK claims are the differences. From owner-gene-linkage@net.bio.net Sun Feb 12 22:00:00 1995 Path: biosci!TENET.EDU!dashley From: dashley@TENET.EDU (Don Ashley) Newsgroups: bionet.molbio.gene-linkage Subject: Re: What is the Genome-Project? Date: 12 Feb 1995 21:24:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3hjhnt$eae@maze.dpo.uab.edu> NNTP-Posting-Host: net.bio.net Please include me in the same request. Don dashley@tenet.edu On 11 Feb 1995, Flammable wrote: > Please send me some E-Mail to Mpsy013@uabdpo.dpo.uab.edu and in it please > tell me what the Genome project is about, what it entails, who's involved, > or any other information you have availible. ANYTHING you can give me > would be incredibly apperciated. Thank you. > > From owner-gene-linkage@net.bio.net Mon Feb 13 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Subject: THE BELL CURVE From: mike.mehta@canrem.com (Mike Mehta) Path: biosci!rutgers!gatech!swrinde!howland.reston.ans.net!news.sprintlink.net!uunet!pipex!bnr.co.uk!bmdhh222.bnr.ca!bcarh8ac.bnr.ca!bcarh189.bnr.ca!nott!torn!uunet.ca!uunet.ca!portnoy!canrem.com!mike.mehta Distribution: world Message-ID: <60.354.3898.0N1CFD8E@canrem.com> Date: Mon, 13 Feb 95 21:03:00 -0500 Organization: CRS Online (Toronto, Ontario) Lines: 34 Hello, I am reading a book called "The Bell Curve" by Richard Hernstein and Charles Murray. It is a book about intelligence and class structure in American life. Since I have started reading this book, I have become extremely interested in intelligence and genetics. I was hoping to receive as much information: opinions, facts, recent updates, regarding these topics. There are hundreds of questions I am dying to ask, so to start: - What is intelligence defined as? Does it have multiple definitions? - What methods exist of measuring intelligence? How accurate are they? Can I obtain copies of these tests or test questions? - Is Intelligence generally considered to be due to genetics or environment? What evidence is there supporting either? - What do you people see as the consequences of the revelation that intelligence may differ ON AVERAGE by racial group? - Have scientists found an 'intelligence gene'? - How does the brain function to form thought? Is it just a reaction to various chemicals being shifted around? If that is true, can we accurately predict every thought of the mind? As well, information on cases regarding tests done on identical twins, or children and parents, etc. would be appreciated. I am open to any and all comments and opinions. Please respond, Mike From owner-gene-linkage@net.bio.net Mon Feb 13 22:00:00 1995 Path: biosci!DRUID.HSC.COLORADO.EDU!mariod From: mariod@DRUID.HSC.COLORADO.EDU (Mario de la Pena) Newsgroups: bionet.molbio.gene-linkage Subject: Re: THE BELL CURVE Date: 14 Feb 1995 09:48:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <60.354.3898.0N1CFD8E@canrem.com> NNTP-Posting-Host: net.bio.net Mike, About "The Bell Curve" book, I think you shoud read the comments about the book published in Scientific American (either December 94 or February 95 - I don't remember exactly) The author made a recollection of the shaky basis on which the book stands especially when confronted with the veracity of some of the key statistics in the book and its sources. I am pretty sure you'll find those comments very interesting for the interpretation of your reading. Mario de la Pena, Ph.D. Eleanor Roosevelt Institute for Cancer Research Denver, CO From owner-gene-linkage@net.bio.net Mon Feb 13 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!news.unb.ca!coranto.ucs.mun.ca!leif!roger From: roger@kean.ucs.mun.ca (ROGER GREEN,MEDICINE,ST.JOHN'S,NF,CAN) Newsgroups: bionet.molbio.gene-linkage Subject: Re: THE BELL CURVE Date: 14 Feb 95 18:20:30 -0230 Organization: Memorial University. St.John's Nfld, Canada Lines: 62 Distribution: world Message-ID: <1995Feb14.182030.1@leif> References: <60.354.3898.0N1CFD8E@canrem.com> NNTP-Posting-Host: leif.ucs.mun.ca In article <60.354.3898.0N1CFD8E@canrem.com>, mike.mehta@canrem.com (Mike Mehta) writes: > Hello, > I am reading a book called "The Bell Curve" by Richard Hernstein and > Charles Murray. It is a book about intelligence and class structure > in American life. Since I have started reading this book, I have > become extremely interested in intelligence and genetics. I was > hoping to receive as much information: opinions, facts, recent > updates, regarding these topics. There are hundreds of questions I am > dying to ask, so to start: > > - What is intelligence defined as? Does it have multiple > definitions? Multiple definitions. Any discussion of "intelligence" should begin with the definition being used. > - What methods exist of measuring intelligence? How accurate are > they? Can I obtain copies of these tests or test questions? Any number of "IQ" tests may be used as a measure of intelligence: not because they are particularly meaningful, but because "IQ", as defined in these tests, is easy to measure and fairly reproducible. > - Is Intelligence generally considered to be due to genetics or > environment? What evidence is there supporting either? You pays your money and takes your choice. I believe that if you are talking about performance on an "IQ" test, then genetic factors outweigh environmental ones, perhaps by a wide margin. Be prepared for other opinions on this. > - What do you people see as the consequences of the revelation that > intelligence may differ ON AVERAGE by racial group? About the same consequence as the revelation that skin colour or height differs, ON AVERAGE, between "racial groups". (Not sure how you define "racial groups"). In other words, it's hardly surprising. > - Have scientists found an 'intelligence gene'? To my knowledge, not yet. However intelligence is defined, there will be several genes involved (as there are in the determination of height.) Geneticists have not had much luck in finding genes for ANY complex trait. > - How does the brain function to form thought? I have almost no idea. >- Is it just a reaction to various chemicals being shifted around? Almost certainly. >- If that is true, can we accurately predict every thought of the mind? Not yet. (I assume you're joking.) > As well, information on cases regarding tests done on identical twins, > or children and parents, etc. would be appreciated. I am open to any > and all comments and opinions. Please respond, > > Mike __________________________ This is probably not the right group for this kind of discussion. I suggest any follow-ups go to one of the other groups where discussions of "The Bell Curve" have been going on for some time. Roger C. Green, Faculty of Medicine Phone: (709)737-6884 Memorial University , St. John's, Newfoundland FAX : (709)737-7010 From owner-gene-linkage@net.bio.net Mon Feb 13 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!nntp.cac.washington.edu!max.u.washington.edu!wijsman From: wijsman@max.u.washington.edu Newsgroups: bionet.molbio.gene-linkage Subject: RE: pedigree analysis software Date: 14 Feb 95 09:25:23 PST Organization: ÿÿÿÿ Lines: 15 Distribution: world Message-ID: <1995Feb14.092523.1@max.u.washington.edu> NNTP-Posting-Host: max.u.washington.edu The only package I know of which will handle such a large dataset is PEDPAK, written largely by & distributed by Alan Thomas, who is in Bath, England. I don't have any more details on his contact address, although could find someone who does. The package is not public domain, & costs some significant $$, I believe. Nothing that is being used routinely in human genetics comes close to handling that large a number of individuals. PEDPAK uses a marriage-node representation of pedigrees. Ellen Wijsman > A graduate student in Jeff Walter's lab here is in need of a source of > pedigree analysis software for her studies of birds. She has roughly 6000 > individuals and wants to put them all in a pedigree. Any suggestions for > public domain or commercial software that could do this would be > appreciated. From owner-gene-linkage@net.bio.net Mon Feb 13 22:00:00 1995 Path: biosci!TENET.EDU!dashley From: dashley@TENET.EDU (Don Ashley) Newsgroups: bionet.molbio.gene-linkage Subject: Re: THE BELL CURVE and 'IMMORTALITY' Date: 14 Feb 1995 04:51:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <60.354.3898.0N1CFD8E@canrem.com> NNTP-Posting-Host: net.bio.net Mike, When the geneticists break through with telomerase manipulations and the aging process is arrested, the bell curve of intelligence will be harder to plot. Don On Mon, 13 Feb 1995, Mike Mehta wrote: > > Hello, > > I am reading a book called "The Bell Curve" by Richard Hernstein and > Charles Murray. It is a book about intelligence and class structure > in American life. Since I have started reading this book, I have > become extremely interested in intelligence and genetics. I was > hoping to receive as much information: opinions, facts, recent > updates, regarding these topics. There are hundreds of questions I am > dying to ask, so to start: > > - What is intelligence defined as? Does it have multiple > definitions? > > - What methods exist of measuring intelligence? How accurate are > they? Can I obtain copies of these tests or test questions? > > - Is Intelligence generally considered to be due to genetics or > environment? What evidence is there supporting either? > > - What do you people see as the consequences of the revelation that > intelligence may differ ON AVERAGE by racial group? > > - Have scientists found an 'intelligence gene'? > > - How does the brain function to form thought? Is it just a reaction > to various chemicals being shifted around? If that is true, can we > accurately predict every thought of the mind? > > As well, information on cases regarding tests done on identical twins, > or children and parents, etc. would be appreciated. I am open to any > and all comments and opinions. Please respond, > > Mike > > From owner-gene-linkage@net.bio.net Tue Feb 14 22:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!maze.dpo.uab.edu!usenet From: Mpsy0l3@uabdpo.dpo.uab.edu (Flammable) Newsgroups: bionet.molbio.gene-linkage Subject: Genome Project Updates? Date: 15 Feb 1995 02:26:34 GMT Organization: Friedman Graphix Lines: 4 Message-ID: <3hrooq$19v3@maze.dpo.uab.edu> NNTP-Posting-Host: tty5.maze.ppp.uab.edu X-Newsreader: WinVN 0.92.6+ Does anyone know of any major advances in the Genome project in the last few years? If so would you please E-Mail them to me? Thank You. From owner-gene-linkage@net.bio.net Tue Feb 14 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!world!decwrl!pa.dec.com!dibit.hsr.it!casarig From: casarig@dibit.hsr.it (Giorgio Casari) Message-ID: Subject: mac linkage software Date: Mon, 13 Feb 1995 19:07:39 +0100 X-Received: by usenet.pa.dec.com; id AA15946; Mon, 13 Feb 95 10:15:29 -0800 X-Received: by pobox1.pa.dec.com; id AA11187; Mon, 13 Feb 95 10:15:23 -0800 X-Received: from dibit.hsr.it by inet-gw-2.pa.dec.com (5.65/10Aug94) id AA28620; Mon, 13 Feb 95 10:09:36 -0800 X-Received: from [192.167.193.52] by dibit.hsr.it (AIX 3.2/UCB 5.64/4.03) id AA11068; Mon, 13 Feb 1995 19:07:39 +0100 X-Mime-Version: 1.0 X-Content-Type: text/plain; charset="us-ascii" X-To: bionet.molbio.gene-linkage.usenet@decwrl.dec.com Lines: 13 If anyone knows where to find Mac software for linkage analysis, please write me.Thanks. Giorgio ****************************************************************************** Dr Giorgio Casari Tigem - Telethon Institute of Genetics and Medicine Via Olgettina 58 20132 Milan - Italy tel 39-2-21560201 fax 39-2-21560220 temporary e-mail: casarig@dibit.hsr.it From owner-gene-linkage@net.bio.net Tue Feb 14 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!harper From: harper@ebi.ac.uk (Rob Harper) Subject: RE: pedigree analysis software Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Wed, 15 Feb 1995 11:15:17 GMT Lines: 78 Reply-To: harper@ebi.ac.uk References: <1995Feb14.092523.1@max.u.washington.edu> Organization: European Bioinformatics Institute (EMBL) - UK X-Newsreader: mxrn 6.18-16 Some information about packages that might be of interest. Info obtained from the Biocatalogue at URL http://www.ebi.ac.uk/ PAP AC BC00165 NAME PAP DOMAIN Pedigree Analysis Package DESCRIPTION The Pedigree Analysis Package (PAP) is a set of FORTRAN 77 DESCRIPTION programs for computing likelihoods of genetic models on DESCRIPTION pedigrees. AUTHOR - RT - ADDRESS - CONTACT - SITE ftp anonymous corona.med.utah.edu SITE Directory /pub/pap/unix SITE-CONTACT Peter Cartwright pc@molson.med.utah.edu OS UNIX LANGUAGE FORTRAN 77 VOLUME - FASTLINK AC BC00109 NAME FASTLINK DOMAIN Genetic Linkage software DESCRIPTION Faster Sequential Genetic Linkage Computations DESCRIPTION modified versions of the general pedigree programs of LINKAGE 5.1 AUTHOR Bob Cottingham RA Cottingham R.W., Idury R.M., Schaffer A.A.; RT "Faster Sequential Genetic Linkage Computations."; RL Am. J. Hum. Genet. 53: 252-63(1993). RX Medline; 93304419. ADDRESS Department of Cell Biology, Baylor College of Medicine, ADDRESS Houston, TX 77030, USA. CONTACT bwc@bcm.tmc.edu SITE ftp anonymous gc.bcm.tmc.edu SITE Directory /pub/linkage SITE-CONTACT bwc@bcm.tmc.edu OS Unix LANGUAGE C VOLUME - SAGE AC BC00104 NAME SAGE DOMAIN Epidemiology DESCRIPTION Statistical Analysis Package for Genetic Epidemiology DESCRIPTION is composed of 18 programs DESCRIPTION AGEON : Estimating the Distribution of Age-of-Onset DESCRIPTION ASSOC : marker-trait Associations in Pedigree Data DESCRIPTION BCROSS : Genetic Hypothesus for Quantitative Data on Inbred DESCRIPTION strains, their F1 and Backcross(es) DESCRIPTION CLUSTR : Power Transformation to Obtain Normality and DESCRIPTION Homoscedasticity from Clustered Data DESCRIPTION FCOR : Family Correlations DESCRIPTION FSP : Family Structure Program DESCRIPTION LODLINK : Lod Score Linkage Analysis DESCRIPTION MAPLOC : Mapping a Disease-Related Trait Relative to a DESCRIPTION Set of Linked markers DESCRIPTION MAXFUN : Function maximization Subroutine DESCRIPTION REGC,REGD,REGTL,REGTN : Segregation Analysis Programs DESCRIPTION RELATE : Relationship to Proband DESCRIPTION SIBPAL : Sib-Pair Linkage Analysis DESCRIPTION DBSORT, RENUM, SPLIT : Toolkit Programs AUTHOR Dr. R.C. Elston RT - ADDRESS Department of Biometry and Genetics, ADDRESS Louisiana State University Medical Center ADDRESS 1901 Perdido Street, New Orleans, Louisiana 70112, USA CONTACT sage@haldne.biogen.lsumc.edu SITE - SITE-CONTACT - OS SunOS 4.1.x, Apple Macintosh II, PC 386,486 (MSDOS) From owner-gene-linkage@net.bio.net Tue Feb 14 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!uknet!comlab.ox.ac.uk!oxuniv!ayoung From: ayoung@vax.oxford.ac.uk (Geordie +1865 740 011) Newsgroups: bionet.molbio.gene-linkage Subject: Course in analysis of multifactorial diseases Message-ID: <1995Feb15.142252.28969@oxvaxd> Date: 15 Feb 95 14:22:52 GMT Organization: Oxford University VAX 6620 Lines: 105 WELLCOME SUMMER SCHOOLS FOURTEENTH ADVANCED COURSE 16th - 21st July 1995 The Wellcome Trust Centre for Human Genetics, University of Oxford Windmill Road, Headington, Oxford, OX3 7BN All email inquiries to: wss@umds.ac.uk. HUMAN GENOME ANALYSIS: GENETIC ANALYSIS OF MULTIFACTORIAL DISEASES An intensive computer-based course aimed at scientists actively involved in genetic analysis of multifactorial traits. The following topics will be covered: Programme 1. Gel analysis Operation of GENESCAN software for defining tracks and checking size standards on the ABI fluorescent 373A DNA sequencer. Including sample sheet set up, installation of matrix files, analysis and pre-process parameters. 2. Genotyping Scoring of microsatellite results using GENOTYPER and GAS software, including setting up of macros files, export of data, allele binning and format conversions. 3. Linkage Introduction to basic concepts of linkage analysis, in particular, those related to non-Mendelian diseases. 4. Sibpair Analysis Comparison of identity-by-descent, identity-by-state and maximum likelihood methods of affected sib-pair analysis. Analysis of quantitative traits. 5. Lodscore analysis Use of LINKAGE program to calculate likelihoods for general pedigrees, including construction of locus linkage maps, error checking and analysis of marker locus linked to disease. 6. Affected Relative Methods General non-parametric tests aimed at detecting linkage by examining correlation between the affected members of a pedigree. 7. Associated Tests Use of tests for linkage disequilibrium between markers and disease, construction and analysis of haplotypes. Teaching will take the form of lectures by invited speakers, informal tutorials, hands-on computer sessions and analysis of disease family data sets. There will also be an opportunity to analyse and discuss participants' own data sets. Course Instructors SUMIT BHATTICHARYYA, HEATHER CORDELL, JUNE DAVIES, SIW DANIELS, TONY MERRIMAN, LYNN PRITCHARD, PETER REED, JOHN TODD, JOE TERWILLIGER, MARGARET TOWN, DAN WEEKS, ALAN YOUNG. Confirmed speakers include: MIKE BOEHNKE (Ann Arbor), ARAVINDA CHAKRAVARTI (Case Western), DOUG EASTON (Sutton), MARTIN FARRALL (Oxford), MARK LATHROP (Oxford), MARGARET PERICAK-VANCE (Duke). Participants Applicants should be scientists at an advanced level of research (post-doctoral or equivalent). Documentation verifying that the applicant is actively engaged in a linkage or family-based association study (animal/human) must be provided with the application, as well as evidence of access to a fluorescence-based automated genotyping system. The course is subsidised by the Wellcome Trust for scientists based in academic institutions anywhere in the world. This is a residential course, without exception, and there is a charge of 350 pounds Sterling towards board and lodging. Applications There are no formal application forms, but applicants should send a hard copy of their full CV together with a 300 word outline of their research plans and supporting documentation, to Dr Pelin Faik, Course Co-ordinator, Division of Biochemistry & Molecular Biology, UMDS, Guy's Campus, London Bridge SE1 9RT. Tel: 0171 403 6998 Fax: 0171 407 5281 Email: wss@umds.ac.uk. Closing date for applications is 14th April 1995 -- ------------------------------------------------------------------------------- ___ / \ / | / Alan Young @ uk.ac.ox.vax /____/ / ___ __ |___/ / / / / | / | / "The bigger they are, / \_/\__\__/|_/ /_________/ the harder they fall on you." From owner-gene-linkage@net.bio.net Tue Feb 14 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!panix!zip.eecs.umich.edu!umn.edu!lenti.med.umn.edu!dean From: dean@lenti.med.umn.edu (Dean Flanders) Subject: GAS and CEPH Database Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: lenti.med.umn.edu Organization: University of Minnesota, Twin Cities X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 15 Feb 1995 20:52:07 GMT Lines: 23 Where can I get GAS, which is an affected pedigree member program I believe. In addition does anyone know where I can get the Unix version of the CEPH database, I can only find the PC version. I believe the Unix version is Sybase orientated. Thanks! Dean ========================================================================= Division of Genetics and Metabolism I University of Minnesota I Box 485 UMHC I "If all you have is a hammer, Harvard Street at East River Road I you tend to look at every Minneapolis, MN 55455 I problem as a nail." I Voice (612) 625-5628 I -Maslow Fax (612) 624-6645 I Email dean@gene.med.umn.edu I ========================================================================== From owner-gene-linkage@net.bio.net Wed Feb 15 22:00:00 1995 Newsgroups: bionet.molbio.ageing,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.rapd,bionet.molbio.yeast Path: biosci!daresbury!trane.uninett.no!ugle.unit.no!news.uit.no!pclab12.hibo.no!FG1 From: FG1@stud.hibo.no Subject: Re: controversies & ethics Sender: news@news.uit.no (News admin.) Message-ID: Date: Thu, 16 Feb 1995 10:34:11 GMT Lines: 58 References: Organization: Bodoe College X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Xref: biosci bionet.molbio.ageing:1331 bionet.molbio.bio-matrix:557 bionet.molbio.embldatabank:457 bionet.molbio.evolution:2449 bionet.molbio.gdb:301 bionet.molbio.gene-linkage:562 bionet.molbio.genome-program:1199 bionet.molbio.hiv:914 bionet.molbio.rapd:987 bionet.molbio.yeast:2405 In article Patrick O'Neil writes: >From: Patrick O'Neil >Subject: Re: controversies & ethics >Date: Thu, 9 Feb 1995 23:28:35 -0700 >On Mon, 30 Jan 1995, Phandaal wrote: >> I've been asked to give a lecture to upper-division college students on >> the controversies and ethical considerations in producing transgenic >> organisms, especially transgenic plants. It's been a while since I gave >> this lecture, and so I was wondering if anybody had any good examples of >> controversies or ethical considerations that I could incorporate into the >> talk. > I spent a year working in a plant molec bio lab that was being partially >funded by a private company to produce a more fungal resistent >sugarbeet. Technically, it would be a transgenic in that a gene, VERY >closely related to an already present gene, from Arabidopsis was/is to be >introduced into the sugarbeet and overexpressed, thus bolstering the >sugarbeet's fungal resistence. I enjoyed the work very much and saw >absolutely nothing wrong with it. It was making use of an already >existent defensive gene that resides in many plants and simply increasing >its output by using an easy to maniplate gene from a common lab plant. >This sugarbeet will allow, hopefully, less use of chemical fungicides. > You could argue that it will simply apply selective pressure for fungi >to evolve resistence...but then, so does the use of fungicides or natural >defenses. A more resistent fungi will, conversely, select for more >fungal-resistent plants. This can be applied to your first point below too. >> >> Two I can think of off-hand are: >> >> 1) introducing insecticidal proteins (such as the Bacillus thuringiensis >> protein) into plants may create resistant insect populations (under the >> force of heavy selection pressure), which could then overrun the resistant >> plants and make worthless the efforts by conventional growers who *use* Bt >> protein as a topical pesticidal spray. >The use of the spray itself puts selective pressure on insects to develop >resistence. The point is moot. >> >> 2) altering fatty acid metabolism in oil-crops (like canola) so that they >> produce oils found chiefly in palm and coconut could severely damage the >> palm oil and coconut oil industries in Third World countries... thus >> severely depressing the economies of these already struggling countries. >If business was nice, then companies would never be put out of business. >It may be tough but I could not support artificially supporting a >weakly-based economy by ignoring a possible economic boon here. Any >economy that ties itself to one commodity is *automatically* doomed to bite >it pretty hard. Look at Louisiana and the effects of it having placed >all its economic eggs in the oil business basket -- the state is only now >beginning to recover from over a decade of depressed economy and hard times. >Patrick From owner-gene-linkage@net.bio.net Wed Feb 15 22:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.gene-linkage Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 16 Feb 1995 02:00:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 338 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502161000.CAA03250@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. 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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 ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs 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 BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses 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 MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish 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: From owner-gene-linkage@net.bio.net Wed Feb 15 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!tome From: tome@ebi.ac.uk (Patricia Rodriguez-Tome) Subject: Re: GAS and CEPH Database Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Thu, 16 Feb 1995 12:23:22 GMT Lines: 90 Reply-To: tome@ebi.ac.uk (Patricia Rodriguez-Tome) References: Organization: European Bioinformatics Institute (EMBL) - UK X-Newsreader: mxrn 6.18-16 Hello, In article , dean@lenti.med.umn.edu (Dean Flanders) writes: >Where can I get GAS, which is an affected pedigree member program I >believe. You can find this information in the BioCatalog maintained at the EBI. (URL http://www.ebi.ac.uk/biocat/biocat.html) Here is the corresponding entry : AC BC00116 NAME GAS DOMAIN Genetic tools DESCRIPTION This package provides facilities for reading, writing, DESCRIPTION sectioning and performing statistical analyses on DESCRIPTION phenotypic and genotypic data. AUTHOR Alan Young RT - ADDRESS Department of medicine at Oxford University (UK) CONTACT ayoung@vax.oxford.ac.uk SITE ftp anonymous well.ox.ac.uk SITE Directory /pub/genetics/gas SITE-CONTACT - OS DOS,SUN/Solaris, SunOS,DecAlpha(OSF1), Dec5000(ULTRIX) LANGUAGE C VOLUME - REQUIRES - In addition does anyone know where I can get the Unix version >of the CEPH database, I can only find the PC version. I believe the Unix >version is Sybase orientated. There is a Unix (Sybase) version of the database, but I don't know exactly how it is distributed (I am enquiring). The contact for the ceph database is : cephdbm@cephb.fr The ascii files for the ceph db can be found at the ceph ftp server: ftp.cephb.fr directory : /pub/ceph_genotype_db/ceph_db/UNIX here is part of the readme file > - ceph_db/UNIX/asc/ contains text files that represent all the concatenated markers and their genotypes for each chromosome. Read the ceph_db/UNIX/asc/Readme file to know what each line of these files represents. To decompress these files use the following command: uncompress chrii.asc.Z or uncompress *.asc.Z ( to decompress several ...asc.Z files) - In ceph_db/UNIX/link/ you will find for all markers in DB 7.1 the files in LINKAGE format. There is a chrii.pdi (for pedin.dat) and chrii.dti (for datain.dat) for each chromosome. To decompress these files, use the uncompress command. uncompress chrii.pdi.Z chrii.dti - ceph_db/UNIX/mkr/ contains the list of all the markers in DB 7.1. This list is useful because it lets you know which marker number corresponds to which marker name. To decompress these files, use the uncompress command. uncompress mk71.ii.Z - In ceph_db/UNIX/lods/ you have the lod score table files (lod scores for all marker pairs) for each chromosome. To decompress them use the uncompress command. uncompress chrii.lods.Z >Thanks! > >Dean > Regards, Pat -- ======================================================================= Dr. Patricia Rodriguez-Tome | Email:tome@ebi.ac.uk EBI - European Bioinformatics Institute | URL: http://www.ebi.ac.uk Hinxton Hall, Hinxton | Tel: +44 (0)223 494 413 Cambridge CB10 1RQ, UK | Fax: +44 (0)223 494 468 ======================================================================== From owner-gene-linkage@net.bio.net Thu Feb 16 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!pipex!uknet!bcc.ac.uk!dac159!dcurtis From: dcurtis@hgmp.mrc.ac.uk (David Curtis) Subject: Re: THE BELL CURVE Sender: news@ucl.ac.uk (Usenet News System) Message-ID: Date: Fri, 17 Feb 1995 14:03:58 GMT References: <60.354.3898.0N1CFD8E@canrem.com> Organization: Institute of Psychiatry X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 37 >- What is intelligence defined as? Does it have multiple >definitions? As a general factor underlying performance on tests, or just the performance on the tests. >- What methods exist of measuring intelligence? How accurate are >they? Can I obtain copies of these tests or test questions? There are a number of standardised tests which have reasonable reliability and which are published and generally available. >- Is Intelligence generally considered to be due to genetics or >environment? What evidence is there supporting either? There is good evidence for a contribution of both. It would be extremely naive to think that either completely determines intelligence. One kind of evidence comes from comparing identical to non-identical twins - the identical ones score more closely than non-identical. >- What do you people see as the consequences of the revelation that >intelligence may differ ON AVERAGE by racial group? Most experts believe this is unlikely to be true, and certainly that there is not sufficient evidence currently to say that it is true. >- Have scientists found an 'intelligence gene'? No. >- How does the brain function to form thought? Is it just a reaction >to various chemicals being shifted around? If that is true, can we >accurately predict every thought of the mind? The system is far to complex to envisage being able to do anything like that. From owner-gene-linkage@net.bio.net Sat Feb 18 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!charnel.ecst.csuchico.edu!olivea!news.bu.edu!gw1.att.com!princeton!hedgehog.Princeton.EDU!news From: "Lee M. Silver" Subject: Re: RE: pedigree analysis software Message-ID: <1995Feb17.154022.15427@Princeton.EDU> Originator: news@hedgehog.Princeton.EDU Sender: news@Princeton.EDU (USENET News System) Nntp-Posting-Host: molecular17.princeton.edu Organization: Princeton University References: <1995Feb14.092523.1@max.u.washington.edu> Date: Fri, 17 Feb 1995 15:40:22 GMT Lines: 18 > > > A graduate student in Jeff Walter's lab here is in need of a source of > > pedigree analysis software for her studies of birds. She has roughly 6000 > > individuals and wants to put them all in a pedigree. Any suggestions for > > public domain or commercial software that could do this would be > > appreciated. If you (or anybody else) would like information on a Macintosh software package that is able to keep track of the inter-relationships between animals in a large pedigree, please send me an E-mail message (LSILVER@Molbiol.princeton.edu) or a FAX (1-609-258-1703 or 1-609-258-3345). The software package that I have developed (and is now commercially available at a modest cost) is specifically designed for the purpose of tracking pedigrees rather than do linkage analysis (for which there are numerous other packages). Happy breeding From owner-gene-linkage@net.bio.net Sun Feb 19 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!EU.net!uknet!bcc.ac.uk!dac159!dcurtis From: dcurtis@hgmp.mrc.ac.uk (David Curtis) Subject: Re: THE BELL CURVE Sender: news@ucl.ac.uk (Usenet News System) Message-ID: Date: Mon, 20 Feb 1995 11:03:14 GMT References: <60.354.3898.0N1CFD8E@canrem.com> <1995Feb14.182030.1@leif> Organization: Institute of Psychiatry X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 10 >> - What do you people see as the consequences of the revelation that >> intelligence may differ ON AVERAGE by racial group? > About the same consequence as the revelation that skin colour or >height differs, ON AVERAGE, between "racial groups". (Not sure how you define >"racial groups"). In other words, it's hardly surprising. Just to say that I, and I believe many others, vehemently disagree that intelligence differs on average between racial groups. It is certainly absurd to suggest that the magnitude of the effect (if it exists at all) is at all comparable with the way that skin colour differs between races. From owner-gene-linkage@net.bio.net Mon Feb 20 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!gatech!howland.reston.ans.net!pipex!uknet!comlab.ox.ac.uk!oxuniv!ayoung From: ayoung@vax.oxford.ac.uk (Geordie +1865 740 011) Newsgroups: bionet.molbio.gene-linkage Subject: course in genetic analysis Message-ID: <1995Feb21.144756.29103@oxvaxd> Date: 21 Feb 95 14:47:56 GMT Organization: Oxford University VAX 6620 Lines: 105 WELLCOME SUMMER SCHOOLS FOURTEENTH ADVANCED COURSE 16th - 21st July 1995 The Wellcome Trust Centre for Human Genetics, University of Oxford Windmill Road, Headington, Oxford, OX3 7BN All email inquiries to: wss@umds.ac.uk. HUMAN GENOME ANALYSIS: GENETIC ANALYSIS OF MULTIFACTORIAL DISEASES An intensive computer-based course aimed at scientists actively involved in genetic analysis of multifactorial traits. The following topics will be covered: Programme 1. Gel analysis Operation of GENESCAN software for defining tracks and checking size standards on the ABI fluorescent 373A DNA sequencer. Including sample sheet set up, installation of matrix files, analysis and pre-process parameters. 2. Genotyping Scoring of microsatellite results using GENOTYPER and GAS software, including setting up of macros files, export of data, allele binning and format conversions. 3. Linkage Introduction to basic concepts of linkage analysis, in particular, those related to non-Mendelian diseases. 4. Sibpair Analysis Comparison of identity-by-descent, identity-by-state and maximum likelihood methods of affected sib-pair analysis. Analysis of quantitative traits. 5. Lodscore analysis Use of LINKAGE program to calculate likelihoods for general pedigrees, including construction of locus linkage maps, error checking and analysis of marker locus linked to disease. 6. Affected Relative Methods General non-parametric tests aimed at detecting linkage by examining correlation between the affected members of a pedigree. 7. Associated Tests Use of tests for linkage disequilibrium between markers and disease, construction and analysis of haplotypes. Teaching will take the form of lectures by invited speakers, informal tutorials, hands-on computer sessions and analysis of disease family data sets. There will also be an opportunity to analyse and discuss participants' own data sets. Course Instructors SUMIT BHATTICHARYYA, HEATHER CORDELL, JUNE DAVIES, SIW DANIELS, TONY MERRIMAN, LYNN PRITCHARD, PETER REED, JOHN TODD, JOE TERWILLIGER, MARGARET TOWN, DAN WEEKS, ALAN YOUNG. Confirmed speakers include: MIKE BOEHNKE (Ann Arbor), ARAVINDA CHAKRAVARTI (Case Western), DOUG EASTON (Sutton), MARTIN FARRALL (Oxford), MARK LATHROP (Oxford), MARGARET PERICAK-VANCE (Duke). Participants Applicants should be scientists at an advanced level of research (post-doctoral or equivalent). Documentation verifying that the applicant is actively engaged in a linkage or family-based association study (animal/human) must be provided with the application, as well as evidence of access to a fluorescence-based automated genotyping system. The course is subsidised by the Wellcome Trust for scientists based in academic institutions anywhere in the world. This is a residential course, without exception, and there is a charge of 350 pounds Sterling towards board and lodging. Applications There are no formal application forms, but applicants should send a hard copy of their full CV together with a 300 word outline of their research plans and supporting documentation, to Dr Pelin Faik, Course Co-ordinator, Division of Biochemistry & Molecular Biology, UMDS, Guy's Campus, London Bridge SE1 9RT. Tel: 0171 403 6998 Fax: 0171 407 5281 Email: wss@umds.ac.uk. Closing date for applications is 14th April 1995 -- ------------------------------------------------------------------------------- ___ / \ / | / Alan Young @ uk.ac.ox.vax /____/ / ___ __ |___/ / / / / | / | / "The bigger they are, / \_/\__\__/|_/ /_________/ the harder they fall on you." From owner-gene-linkage@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!WELCHLINK.WELCH.JHU.EDU!dmeyers From: dmeyers@WELCHLINK.WELCH.JHU.EDU (Deborah Meyers Phd) Newsgroups: bionet.molbio.gene-linkage Subject: subscribe Date: 22 Feb 1995 12:40:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502222039.AA05767@welchlink.welch.jhu.edu> NNTP-Posting-Host: net.bio.net Please add my address to the subscription list for this bulletin board. Thanks, Deborah Meyers dmeyers@welchlink.welch.jhu.edu From owner-gene-linkage@net.bio.net Tue Feb 21 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!cs.utexas.edu!swrinde!pipex!uknet!festival!leeds.ac.uk!news From: gen6ads@sun.leeds.ac.uk (A D Stewart) Subject: Re: What is the Genome-Project? Message-ID: <1995Feb22.093704.23648@leeds.ac.uk> Reply-To: gen6ads@sun.leeds.ac.uk Organization: University of Leeds, U.K. Date: Wed, 22 Feb 1995 09:37:03 +0000 (GMT) References: <3hjhnt$eae@maze.dpo.uab.edu> Lines: 33 In article eae@maze.dpo.uab.edu, Mpsy0l3@uabdpo.dpo.uab.edu (Flammable) writes: >Please send me some E-Mail to Mpsy013@uabdpo.dpo.uab.edu and in it please >tell me what the Genome project is about, what it entails, who's involved, >or any other information you have availible. ANYTHING you can give me >would be incredibly apperciated. Thank you. This is a common request from high schools all over. It would be nice if teachers would teach ... To be more positive, an easy starting point is on the WWW: http://www.gdb.org/Dan/DOE/intro.html This outlines the USA HGP - of course there are significant programmes in other countries too, including France, Germany, Britain ... Best wishes, Alistair Stewart a.d.stewart@leeds.ac.uk Department of Genetics University of Leeds Leeds LS2 9JT England FAX (+44) 113 244 1175 PHONE (+44) 233 3108 From owner-gene-linkage@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!TEOSINTE.AGRON.MISSOURI.EDU!byrne From: byrne@TEOSINTE.AGRON.MISSOURI.EDU (Patrick Byrne) Newsgroups: bionet.molbio.gene-linkage Subject: Journal of Quantitative Trait Loci Date: 21 Feb 1995 16:04:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502220003.SAA02692@teosinte.agron.missouri.edu> NNTP-Posting-Host: net.bio.net ANNOUNCING THE JOURNAL OF QUANTITATIVE TRAIT LOCI The Journal of Quantitative Trait Loci (JQTL), sponsored by the Crop Science Society of America (CSSA), will provide a peer-reviewed, fully electronic forum in which articles dealing with the theory and practice of QTL analysis will be published. The publication format will facilitate links to related publications and databases, and will permit the inclusion of more complete analyses than is generally feasible in bound media. Improved publication speed, easy and inexpensive access, and flexibility should make JQTL a preferred journal for the publication of papers dealing with the analysis of the inheritance of quantitative traits. PURPOSE OF THE JOURNAL 1. JQTL will publish articles relevant to the analysis, manipulation, and use of genes modifying quantitative characters in any species. We are defining quantitative characters as those for which the phenotypic variation among genotypes is continuous and cannot be separated into discrete classes. This definition of QTL makes no assumptions regarding the number of genes controlling such characters, nor the magnitude of genetic effects. When appropriate, authors will be encouraged to include datasets upon which their analyses depend. 2. JQTL will serve as a medium for announcing, describing, and storing new software developed for QTL analysis. 3. JQTL will publish secondary analyses of primary datasets when such analyses prove novel and illuminating. 4. JQTL will publish worthy editorial commentaries and review articles as space and interest warrant. GENERAL STANDARDS Papers will be submitted either electronically or on diskette. They will consist of ASCII text, with .gif files holding images. Papers will be written in general accordance with style standards of CROP SCIENCE (Publications Handbook and Style Manual, 1988, American Society of Agronomy, Madison, WI). Papers will be submitted to the Editor, who will then request review by two Technical Editors. INFORMATION TO BE INCLUDED IN ARTICLES SUBMITTED All articles should contain a) title, b) affiliation, phone number, and e-mail addresses of all authors, c) abstract briefly summarizing the work, d) introduction, methods, results and discussion sections in accordance with ASA guidelines, and e) literature cited. For all articles containing datasets authors must supply a data dictionary (description of data fields) and a description of how the data was gathered. Software submission: All software described in a JQTL article should be, if at all possible, available for JQTL readers. Ideally, an anonymous ftp site would already exist from which software could be downloaded. If this is not the case, and the software was developed by the authors, then the software should be uploaded to hordeum.oscs.montana.edu. All executable software should be accompanied by source code, if available, as well as a user manual. Acceptable formats are Unix: a compressed tar file (compressed with either the compress program or by gzip) DOS/Windows: a zip file MacIntosh: a StuffIt archive (.sit) file ORIGINALITY AND NOVELTY To be considered for publication, neither data nor analyses should have been published previously in any peer-reviewed journal, book, or bulletin. While updates (i.e., second year datasets or datasets gathered in new environments using lines already characterized) may be considered for publication, they will generally be accepted as appendices to prior articles. New analyses of previously published datasets will be accepted if they provide novel insights into the data. PEER REVIEW AND COMMENT Each submitted article will be reviewed by two scientists familiar with the area of research. They will be asked to review the manuscript for compliance with the above criteria, to judge suitability of the article for inclusion in JQTL, and to write brief critiques of the manuscript to be returned to the author. The editors will attempt to evaluate the performance of submitted software. SUBMISSION PROTOCOL Articles may consist of text, tables, and data sets (all in ASCII format) and figures (in .gif format). Other acceptable formats may be announced in the future. There are no size limitations. Prior to submission, authors should e-mail the Editor (current address: blake@hordeum.oscs.montana.edu) to request a submission number. Files should then be renamed to include the submission number (e.g., text##.asc, fig1##.gif, fig2##.gif, tabl##.asc, data##.asc, etc.). This will avoid the problem of one submission over-writing another. Submit files via ftp to hordeum.oscs.montana.edu Login as jqtlsubm Password: your e-mail address. The Editor will scan each submitted article for gross compliance with standards, then will send all appropriate articles to two Technical Editors. They will review the paper, suggest modifications if necessary, and return the files to the Editor, who will in turn send them to the author as files appended to a letter describing the Technical Editors' recommendations. For manuscripts dealing with re-analysis of previously published data, the Editor will invite the corresponding author of the original publication to submit a review. This will provide the original authors an avenue for direct feedback prior to publication of the new analyses. After receiving the Technical Editors' recommendations, the author may revise (if necessary) and resubmit the paper with "r" appended to each file name (e.g., text##r.asc, fig1##r.gif, tabl##r.asc). Each accepted manuscript will then be sent to CSSA headquarters for HTML formatting, and thence to the U.S. National Agricultural Library for immediate publication. JQTL will be continuously updated with new articles. JOURNAL ACCESS Beginning April 1, 1995, JQTL will be available for public on-line access from the National Agricultural Library via World Wide Web at http://probe.nalusda.gov:8000/ under the heading Newsletters, Journals, and Other Publications. No charge will be levied for publication or for journal access during 1995, although nominal fees may be assessed at a later date. JQTL will be indexed in the AGRICOLA bibliographic database and by other biological indexing services. JOURNAL ANNUAL By the end of the first year of publication we hope to have the capacity to make annual CDs of the journal available for a nominal fee. JQTL Editor: Thomas Blake, Montana State University JQTL Technical Editors: Jim Anderson, North Dakota State University Doug Bigwood, USDA, National Agricultural Library Cynthia Bottema, Waite Institute (Australia) Pat Byrne, USDA, Agricultural Research Service Rebecca Doerge, Cornell University Jon Geadelmann, Holden's Foundation Seeds, Inc. Dave Matthews, Cornell University Phil McClean, North Dakota State University Laura Oberthur, Montana State University Andrew Paterson, Texas A&M University Mark Sorrells, Cornell University CSSA Editor-in-chief: P. Stephen Baenziger, University of Nebraska CSSA Board of Directors: R.C. Shearman, President A.B. Maunder, President-Elect V.B. Cardwell, Past President R.F. Barnes, Executive Vice President From owner-gene-linkage@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!WELCHLINK.WELCH.JHU.EDU!fmcm From: fmcm@WELCHLINK.WELCH.JHU.EDU (Francis McMahon) Newsgroups: bionet.molbio.gene-linkage Subject: subscribe Date: 22 Feb 1995 12:04:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Please add my address to the subscription list for this bulletin board. Thanks, Francis McMahon fmcm@welchlink.welch.jhu.edu From owner-gene-linkage@net.bio.net Wed Feb 22 22:00:00 1995 Path: biosci!NS.UNIVET.HU!pkabai From: pkabai@NS.UNIVET.HU (Kabai Peter) Newsgroups: bionet.molbio.gene-linkage Subject: Re: pedigree analysis software Date: 23 Feb 1995 02:58:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199502090720.XAA12774@net.bio.net> NNTP-Posting-Host: net.bio.net To Jeff Walter! Hi, you may wish to contact Dr. Joseph K. Kovach at the Menninger Foundation. He has run a genetic experiment on quail for decades and developed a program to trace anything back to any generation. His e-mail address is: 72073.3147@compuserve.com Good luck, Peter Kabai, Budapest, Hungary On 8 Feb 1995 fishgen@vt.edu wrote: > > > ----------------------------Original message---------------------------- > A graduate student in Jeff Walter's lab here is in need of a source of > pedigree analysis software for her studies of birds. She has roughly 6000 > individuals and wants to put them all in a pedigree. Any suggestions for > public domain or commercial software that could do this would be > appreciated. > > From owner-gene-linkage@net.bio.net Thu Feb 23 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!ix.netcom.com!netnews From: bryan6@ix.netcom.com (Bryan Thornberg) Newsgroups: bionet.molbio.gene-linkage Subject: Re: DNA/Electrophoresis...I Would Like Some Input Date: 24 Feb 1995 00:31:14 GMT Organization: Netcom Lines: 13 Distribution: world Message-ID: <3ij9ci$g14@ixnews1.ix.netcom.com> References: <3ij94h$fvq@ixnews1.ix.netcom.com> NNTP-Posting-Host: ix-pit2-19.ix.netcom.com In <3ij94h$fvq@ixnews1.ix.netcom.com> bryan6@ix.netcom.com (Bryan Thornberg) writes: > >I am currently in the process of putting a college course onto the >Internet relating to electrphoresis . This will be a hands-on course to >allow students to see DNA (fingerprinting), proteins, lipoproteins, and >specific unique features and benefits of the gels themselves. I would >like some additional input on what could be added t