Published by Jürg Ott, Columbia University, New York.
We started using the NDP Pascal compiler from Microway (see advertisements, for example, in BYTE magazine, Feb. 1993, page 160) and are impressed with its potential. It has none of the restrictions that plague users of Turbo Pascal and, to some degree, also of Prospero Pascal. The company is very responsive to inquiries, which unfortunately seems less the case for the makers of Prospero Pascal in England. Currently, only a beta test version of NDP Pascal is available for OS/2 but the full version might be on the market by the time you read this.
We are also in the process of porting the LINKAGE programs to Windows under Borland Pascal version 7. However, Borland Pascal has restrictions similar to those of Turbo Pascal except that presumably, much more memory can be allocated under Windows than under DOS. On the other hand, arrays still cannot exceed 64KB in size, etc.
Among other developments at Columbia, we are working on setting up an anonymous ftp site for program distribution. Also, programs will be available not only for DOS but also for Unix and VMS machines (see below for some existing ftp sites).
Registration is open for both of these courses. For information and application forms please write to the address above, preferably by fax. The Columbia University Advanced Course for the academic year 1993/4 will be held in January of 1994 but a date has not been fixed yet.
On many machines other than IBM's, it is preferable to make changes to the BIOS before installing OS/2. In our experience the most important point is that an external disk cache be disabled (OS/2 provides its own disk cache, which works well). Also, installation is easiest when you allow the installation program to format the hard disk while it installs OS/2. If you want to install OS/2 without reformatting the hard disk, the following steps are recommended: 1) Make a boot disk (floppy) for DOS and try it out; that is, you must be sure you can boot DOS from the floppy drive. 2) Delete any unneeded files. 3) Remove all file fragmentation and make all files contiguous on the disk by using, for example, the Norton SpeedDisk program (use full optimization). 4) Turn off your computer, insert the OS/2 installation disk, and turn your computer on again.
The program will ask you whether you want to install every- thing or only a selection of features. I would choose the latter. For example, I would NOT install fonts or games. This way you only require approximately 25MB of disk storage for the system. As you select and deselect features, the program displays how much space is available on your disk and keeps a running tally of how much disk space is required for the current selections.
A major decision is whether you want to use the high perfor- mance file system (HPFS) or the old-fashioned file allocation table (FAT) system. For compatibility with other programs, particularly when you want to boot native DOS, FAT is preferable although it suffers from the well-known problem of file fragmentation. Once you use OS/2, you may occasionally encounter a problem with extended file attributes that OS/2 uses but DOS does not. For example, you may be unable to delete a file because it is cross- linked with another file's extended attribute. There is an easy solution: just run OS/2's chkdsk program as often as is required to get rid of the problem. Some of these problems cannot be fixed by chkdsk if OS/2 was booted from the hard disk (as is usually the case). Then, shut down OS/2 (keep the cursor on a free space of the Desktop and press the right mouse button), put the OS/2 installation disk into the A: drive, and reboot. After you insert the second floppy (disk no. 1), press Esc when the program asks whether you want to continue installing. You are then left with a working version of OS/2 and should see the prompt, [A:>]. Now, enter, for example, C:\OS2\CHKDSK D: if your OS/2 system resides on the C: drive and you want to check problems on the D: drive. Alternatively, insert disk no. 2 of the installation package (it contains chkdsk.exe) into the A: drive and enter A:CHKDSK D:. You may need to issue this command repeatedly until chkdsk no longer reports a problem (it seems to fix only one problem at a time).
You may switch between various DOS and OS/2 windows. However, be aware that whatever windows are open consume a certain amount of RAM, which is lost to other windows. Also, the DOS windows by default have 2MB of extended and expanded memory each, which is usually much too much. To adjust these settings for a given DOS window, first exit from this window (it must not be active), then click on its icon using the right mouse button. A small window appears, which says "Open" at the top. With the left mouse button, click on the arrow in that row (be sure it's the arrow). Then click on Settings, then on Session, and then on DOS Settings. The most important DOS settings to change are EMS_MEMORY_LIMIT and XMS_MEMORY_LIMIT. Also, if you want to operate a modem from this window (it is best to reserve one window for running your communi- cations program such as Kermit), set IDLE_SENSITIVITY to 100; this will ensure smooth operation of your communications program. Note that these changes cannot be made on a window while it is open.
Under OS/2, one has even more control over programs running in a DOS window than when they run under native DOS. For example, if a program is caught in a loop and you are unable to interrupt it, you can simply close the window in which it is running. Under DOS or Windows 3.1, one must reboot the machine.
In our experience, there are very few DOS programs that do not work properly in DOS windows of OS/2. Some of the newest Norton Utilities do not work properly (but FileFind and FileSize work fine). To occasionally use such programs, one simply boots the machine under DOS from a floppy disk.
While OS/2 emulates DOS version 5 very closely, we have found one difference thus far: Backup and Restore are different enough that files backed up in a DOS window under OS/2 cannot be restored under native DOS, and vice versa.
The current OS/2 version supports Windows 3.0. We have successfully installed several Windows programs in this "Windows" version. One program, SYSTAT, does not work properly this way although it works fine under regular Windows 3.1.
Incidentally, we also ran the benchmark data set using the MENDEL program. It was compiled with Microsoft Fortran 5.1 such that it ran under DOS or OS/2. Because of the array sizes, which are required by MENDEL for the given data set, MENDEL was unable to run under DOS. Under OS/2, it required approximately 12MB of RAM to run and took 1298 seconds to complete (run on an 80486 with 16MB RAM to prevent usage of virtual memory). The MENDEL program can thus be quite slow in the presence of many untyped individuals. On the other hand, it is more flexible than LINKAGE in the problems that a user can address.
In this context, the time requirements for the benchmark data set on three other machines are of interest (reported by Iain Fenton, Cardiff). The following times represent elapsed time, not CPU time:
SENSEN and SENPED are short Fortran programs designed to facilitate
basic sensitivity analyses of families, as described in Hodge and
Greenberg [1].
SENSEN takes a standard LIPED input file with data for one family
and prepares equivalent LIPED input files, reversing the affect-
edness status at the main trait for each family member, one at a
time.
SENPED takes the lod file output of LIPED runs on all the sensi-
tivity files for a single family (and a single marker) and creates
an input file for the Pedigree/Draw program [2], showing the
original lod score and the difference in lod score caused by each
change in affectedness status.
SENSEN and SENPED are available from
David A. Greenberg, Ph.D.
Department of Psychiatry, Box 1229
Mt. Sinai Medical Center
1 Gustave Levy Place
New York, NY 10029
e-mail: miriam@onion.salad.mssm.edu
----------------------------------------------
[1] Hodge SE and Greenberg DA (1992): Sensitivity of lod scores to
changes in diagnostic status. Am. J. Hum. Genet. 50:1053-1066.
[2] Pedigree/Draw is a set of shareware programs for the Apple
Macintosh used to prepare genetic pedigrees. For further infor-
mation about this program (and how to obtain a copy), contact:
Paul Mamelka
Department of Genetics
Southwest Foundation for Biomedical Research
P.O. Box 28147
San Antonio, TX 78284
Internet: paul@darwin.sfbr.org
TypeNext implements a special version of the SLINK program. For a number of untyped individuals in a pedigree, it estimates which individuals should be typed next to gain the most informa- tiveness for linkage analysis (Am J Hum Genet 51 (suppl), A197).
VaryPhen varies the phenotype (affected/unaffected) for each individual and reports the change in maximum lod score (Am J Hum Genet 47, A205, 1990).
LOOPS checks for undetected loops remaining in the data after a pedigree file has been processed by the MAKEPED program. The LOOPS program is now part of the LINKAGE package and is automati- cally invoked whenever one calls MAKEPED (Am J Hum Genet (suppl) 51, A206, 1992).
ftp corona.med.utah.edu or ftp 128.110.231.1
When prompted to provide a user name, enter "anonymous". As the
password, give your last name. Then, issue the commands
cd pub/linkage/sun
binary
get linkage.tar.Z
quit
This ends your ftp session. On your Sun machine, issue the
commands
uncompress linkage.tar.Z
tar xvf linkage.tar
rm linkage.tar
We also keep getting requests for information about pedigree drawing programs for the PC. Several programs exist, some have been discussed in this newsletter. As an example, the PEDRAW program by Dr. David Curtis (dcurtis@crc.ac.uk) may be obtained from various anonymous ftp sites such as ftp.embl-heidelberg.de or ftp.bio.indiana.edu.