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To: Multiple recipients of list HUM-MOLGEN <HUM-MOLGEN@NIC.SURFNET.NL>
Subject: Linkage Newsletter
From: Jurg Ott <ott@linkage.cpmc.columbia.edu>
Date: Thu, 9 Nov 1995 12:31:36 -0500

                      Linkage Newsletter
                Vol. 9   No. 3   November 1995

Published by Jurg Ott, Columbia University, New York
        Email:  jurg.ott@columbia.edu
        WWW:    http://linkage.cpmc.columbia.edu

Postal address:
        Columbia University, Unit 58
        722 West 168 Street
        New York, NY 10032

Editorial Assistant:  Katherine Montague
        Email:  km165@columbia.edu or kath@linkage.cpmc.columbia.edu
        Fax:    212-568-2750
        Tel:    212-960-2507


LINKAGE COURSES

        The next four linkage courses have been scheduled as fol-
lows:

        January 8-12, 1996, at Columbia University, New York (ad-
vanced course, maximum of 20 participants, deadline for applica-
tion is Nov. 10).
        February 26 - March 1, 1996, at the University of Zurich,
Irchel Campus Computer Center,  Switzerland (basic course,
maximum of 18 participants).
        June 10-14, 1996, at Columbia University, New York (basic
course, maximum of 30 participants).
        June 24-28, 1996, at Columbia University, New York (basic
course, maximum of 30 participants).

        To obtain information on these courses, please write to
Katherine Montague, course coordinator, by email (preferred) or
fax.
        We will use our book (Terwilliger and Ott, "Handbook of
Human Genetic Linkage," Johns Hopkins University Press, 1994),
with supplemental handouts for advanced courses.  Participants
are expected to buy the book and bring it to the course;  in case
of problems please contact Katherine Montague in advance of the
course.  A list of corrections for the book may be downloaded
from our anonymous ftp site, linkage.cpmc.columbia.edu (file
corr_ter.txt in directory book).


SOFTWARE NEWS

     Bug in FastLINK

Rita Kruse, Bonn Germany, made me aware of the following problem
in FastLINK:  For a pedigree with seven loops, the lod score was
different depending on the order in which "loop individuals" were
defined.  For one order, a maximum lod score of 6.50 was obtained
while under another order, with the same data, the maximum lod
score was only 0.66.  This difference occurred only with FASTLINK
while the LINKAGE programs consistently furnished a lod score of
6.50.  Dr. Alejandro Schaffer confirmed this bug and has already
corrected it in version 2.3P of FASTLINK.


     SIMLINK and RHMAP on the Web

The following announcement was contributed by Dr. Michael Boehn-
ke, Ann Arbor:

For some time, I have been distributing two programs for genetic
analysis:  RHMAP and SIMLINK.  RHMAP is a program package for the
statistical analysis of radiation hybrid mapping data.  SIMLINK
is a program for evaluating the statistical power of a proposed
linkage study.  Both RHMAP and SIMLINK are written in FORTRAN 77,
and both previously were distributed free of charge on floppy
diskettes after completion of a user agreement.

Beginning October 31, 1995, the primary method of distribution
for RHMAP and SIMLINK will be via the World Wide Web (WWW).  To
access the current versions of RHMAP and SIMLINK (2.01 and 4.11,
respectively), you will need a WWW browser such as Mosaic or
Netscape.  Using a browser, you can download the software packag-
es from http://www.sph.umich.edu/group/statgen/software.

Both analysis packages, containing source code and manuals, are
available as archives for Unix and DOS systems.  Once you down-
load the program package archives, you will need to dearchive the
files.  On Unix computers the "tar" utility should be used, e.g.,
"tar -xvf filename".  (For other computer systems, e.g., VMS,
etc., one can usually obtain public-domain utilities which can
read "tar" files.  Links to several such utilities are provided
on the web page.)  Simply compile the FORTRAN 77 code on your
computer to obtain an executable.  For DOS computers the archives
are self-extracting and contain DOS executables of the programs.
Simply issue the name of the archive as a DOS command, e.g.,
rhmapzip.exe, and all the files in the package, including the
executable(s), will be extracted.

Also beginning October 31, the primary method for notification of
software updates for RHMAP and SIMLINK will be via e-mail.  If
you already have or do in the future obtain one or both of the
programs, I urge you to add yourself to the appropriate mailing
list by sending a short e-mail note to me at boehnke@umich.edu
indicating which package(s) you use and your preferred e-mail
address for notification.  This will insure that you continue to
get program updates, and will be helpful for me at grant renewal
time.

For those who lack Internet access, I will continue to distribute
RHMAP and SIMLINK by floppy diskette.  However, I ask you to make
use of this option only if it truly is necessary.  In this case,
you will need to request a user agreement which you will need to
fill out and send back.

Please feel free to contact me if you have any questions.

-----------------------------------------------------------------
Michael Boehnke                  Phone:         313-936-1001
Department of Biostatistics      FAX:           313-763-2215
University of Michigan           E-Mail:        boehnke@umich.edu
-----------------------------------------------------------------


     Announcement of GenoCheck program

The following announcement was contributed by Dr. Margaret Gelder
Ehm, Houston:

                  GenoCheck, version 1.0

                     Meg Gelder Ehm
                    Rice University
                 Department of Statistics
                   Houston, Texas  USA
                  gelder@stat.rice.edu

New error detection capabilities are available for genetic
linkage data!

GenoCheck, 1.0 is an error checking program designed to identify
individuals and loci that are likely to contain errors.  The
statistical method was designed to identify typing error, but is
general enough to pinpoint any unlikely genotype still consistent
with Mendelian inheritance.

GenoCheck was developed using FASTLINK 2.2 (modified version of
LINKAGE 5.1) and uses a similar file configuration and installa-
tion procedure.  The code contains checkpointing facilities that
allow users to recover from crashes without having to rerun the
program and comes with documentation.

The instructions for retrieving the code are given below:

ftp softlib.cs.rice.edu

Login as anonymous and leave your full e-mail address as the
password.

cd pub/GenoCheck

In that directory you will find various files.  You can get
everything at once by retrieving:

genocheck.tar.Z

and then (outside of ftp) doing the commands:

uncompress genocheck.tar.Z
tar xvf genocheck.tar

If you prefer to get the files piecemeal, instead of getting
genocheck.tar.Z start by getting README*.  The file README (with
no extension) will describe all of the documentation.

The statistical algorithm implemented in GenoCheck, version 1.0
is described in the papers:

M. G. Ehm, R. W. Cottingham Jr., and M. Kimmel.  Error Detection
in Genetic Linkage Data Using Likelihood Based Methods.  Journal
of Biological Systems, Vol. 3, No. 1 (1995) 13-25.

M. G. Ehm, R. W. Cottingham Jr., and M. Kimmel.  Error Detection
in Genetic Linkage Data Using Likelihood Based Methods.  American
Journal of Human Genetics, Vol. 58, No. 1 (1996) (to appear).

Please e-mail any questions or suggestions about GenoCheck to
gelder@stat.rice.edu.


     INFOBIOGEN server on the Web

        Dr. Lucien Bachner (bachner@infobiogen.fr) requested that
information about his server be included in this newsletter.
Here is a brief description:  The server may be accessed at URL
http://www.infobiogen.fr/vjf/server_vjf.html.  Academic users may
obtain an account at Infobiogen (after returning a form) which
enables them to access a large number of programs and databases
useful for gene mapping and DNA analysis.  Interaction with the
server is in French.
        Dr. Bachner is also organizing linkage training courses at
the beginners level.  The first was held October 24-25, he is
planning the second for end of May 96 or June.  Language is
French.  The same course is also scheduled at Institut Pasteur,
December 19-20.


     New version of ANALYZE package

        A new version of the ANALYZE program package has been
released.  It simplifies the performance of a large array of
parametric and nonparametric tests for linkage and association on
data entered in LINKAGE format pedigree and parameter files.  The
programs are distributed at two different sites.  You can obtain
them either from

        ftp.well.ox.ac.uk             in directory software/analyze

or from

        linkage.cpmc.columbia.edu     in directory software/analyze.

Users are advised to download and study the README files.  A DOS
version of the whole package is in preparation and should be
available on the latter ftp site by the end of November.


SURVEY

        We occasionally hear from people that they are having
problems obtaining our books through book stores.  Typically
these books are not stocked in regular book stores but those
outlets designated by the Johns Hopkins University Press should
always have books on stock.  Readers who had problems obtaining
our books (either through a book store or directly from the
publisher) are invited to let us know;  please also indicate the
date when you had problems.  We would like to have customer
service improved in this area.

Support through grant HG00008 from the National Center for Human
Genome Research is gratefully acknowledged.


   
 
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