Published by Jürg Ott, Columbia University, New York
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).
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 packages 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 download 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 -----------------------------------------------------------------
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 installation 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.eduLogin as anonymous and leave your full e-mail address as the password.
cd pub/GenoCheckIn that directory you will find various files. You can get everything at once by retrieving:
genocheck.tar.Zand 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.
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.
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.
Support through grant HG00008 from the National Center for Human Genome Research is gratefully acknowledged.