Published by Jürg Ott, Columbia University, New York
(support through grant HG00008 from the National Center for Human Genome Research is gratefully acknowledged)
Postal address:
The purpose of this newsletter is to foster communication among researchers active in the analysis of human genetic linkage. The following three paragraphs are quotes from the first issue in 1987:
The fourth linkage course at Columbia University will be an Introductory Course held from May 15-18, 1991 (Wednesday through Saturday). The previously scheduled dates of April 3-6 had to be changed because the microcomputer classroom was unavailable then. Registration is now open and applications will be accepted until February 28, 1991. An application form is attached to this newsletter. Please pass on copies of the attached announcement to anyone interested. There is presently no possibility for travel stipends or for reduced admission fees. In the fall of 1991, the usual Advanced Linkage Course will be taught at Columbia University (date not yet set). The topics will include estimating and testing for heterogeneity; linkage disequilibrium; linkage with pseudoautosomal loci; risk calculations (also under linkage disequilibrium and locus heterogeneity).
Linkage courses will also be given in Europe on a more regular basis. The next European course (an introductory course) will be held July 9-12, 1991, at the Association Francaise contre les Myopathies (AFM) in Paris. Tuition is FR 6 000 and the language of instruction is English. Participants (maximum 24) must meet the following criteria: (i) be currently affiliated with an European laboratory, (ii) be familiar with a PC (i.e. word processing), and (iii) be able to exhibit an immediate need for linkage mapping. For further information and application forms, please contact:
Dr. Lynn Davis; AFM; 1 rue de l'Internationale
BP 59 - 91002 EVRY cedex, FRANCE;
telephone: (33)(1) 69 47 28 28, FAX: 60 77 12 16.
University of Pittsburgh
Department of Human Genetics
130 DeSoto Street, A300 Crabtree Hall
Pittsburgh, PA 15261
Tel. (412) 624-5388 FAX: (412) 624-3020
WEEKS@PITTVMS.BITNET WEEKS@VMS.CIS.PITT.EDU
1/7/91
To: All users of the SLINK package
From: Daniel E. Weeks
Re: a bug in MSIM, ISIM, and LSIM
Instructions for correcting MSIM, ISIM, and LSIM:
We have discovered another bug in three programs of the SLINK
package. In order to correct this bug, one line in the PROCEDURE
readspseg has to be changed in each of the programs MSIM, ISIM,
and LSIM:
IF j>0 THEN
has to be changed to
IF (j > 0) AND (i <= segperson) THEN
Using a text editor, find the appropriate line in each of your
three source code files (as indicated below) and then change it.
Then you must recompile each corrected program before you use it.
If you have any problems, please feel free to contact me.
Old version:
************************************************
PROCEDURE readspseg;
{Reads from the speedfile in appropriate segments}
VAR
i, j, a, b, sys: integer;
ch : char;
BEGIN {readspseg}
{ Note that each person[]^.unknown is set to FALSE as the
person is read in}
i:=lastspeed;
j:=lastspeed-lastseg;
IF j>0 THEN
BEGIN
person[j]^.unknown:=TRUE;
NEW(person[j]^.store);
{ person[j]^.store:=infoptr(NewPtr(SizeOf(information)));}
WITH person[j]^.store^ DO
FOR sys:=1 TO nlocus DO
FOR a:=1 TO maxall DO
FOR b:=1 TO maxall DO
possible[sys, a, b]:=FALSE;
END;
************************************************
Corrected version:
************************************************
PROCEDURE readspseg;
{Reads from the speedfile in appropriate segments}
VAR
i, j, a, b, sys: integer;
ch: char;
BEGIN {readspseg}
{ Note that each person[]^.unknown is set to FALSE as the
person is read in}
i := lastspeed;
j := lastspeed - lastseg;
IF (j > 0) AND (i <= segperson) THEN
BEGIN
person[j]^.unknown := TRUE;
NEW(person[j]^.store);
{ person[j]^.store := infoptr(NewPtr(SizeOf(information)));}
WITH person[j]^.store^ DO
FOR sys := 1 TO nlocus DO
FOR a := 1 TO maxall DO
FOR b := 1 TO maxall DO
possible[sys, a, b] := FALSE;
END;
************************************************
A particular version of the LINKAGE programs is now available, which allows for two loci to be jointly responsible for occurrence of a disease (DISK22 in list of programs). To receive a list of all our programs please write, fax, or send an e-mail message.
We are planning on making our programs available by e-mail. One possibility of doing this would be to install a file server on our IBM mainframe running under VM/CMS, which is a Bitnet node. However, we have no file server available and might have to write one. Does anyone have experience with such programs? The other possibility is to run a microcomputer under Kermit in server mode so that people can call up and download information and program files. The latter solution would be relatively easy to implement but requires people to pay telephone tolls.
The course will be taught by myself and my collaborators. It will take place in the computer classroom of the Health Sciences Library (701 West 168th Street) which is equipped with 20 microcomputers of type IBM PS/2 (3-1/2" diskette drives). Due to space limitations, course attendance is limited to 30 participants. Participants should plan on arriving in New York on the evening of Tuesday, May 14, 1991.
Your name: Affiliation: Address: Tel. number: FAX number: Bitnet: Interested in staying at Bard Hall? YES / NO DOUBLE / SINGLE If yes, which nights? Tue Wed Thu Fri Sat Sun What size diskettes do you use? 3-1/2" 3-1/2"HD 5-1/4"HD (we prefer 3-1/2"; we have no easy way of writing to low-density 5-1/4" disks) For applicants from abroad: Do you want us to make hotel reserva- tions? What accommodations? Below, please describe which linkage programs you have used if any, how many families you have analyzed, and other experience in linkage analysis you might have: Signature: Date: Katherine Montague, Course Coordinator Tel. (212) 960-2507 FAX +1 (212) 568-2750 or 960-5624 Bitnet: OTT@NYSPI