Program Syntax

There are two general versions of GENBLIS. The first runs on UNIX systems (e.g., AIX, HP-UX, LINUX) and the binary is called genblis. The second version is a 32 bit Windows 95/98/NT application. The Windows binary is called genblis.exe. The Windows version of GENBLIS runs in a DOS window (and currently has only a command-line interface), but it is not a DOS application. It is a true 32 bit Windows application.

The GENBLIS program is a command line program which reads a model specification (modelspec) file and produces output to files specified in the modelspec file and to standard output. The name of the model specification file is expected by GENBLIS on the command line. For example,

unix> genblis files/example1
windows dos shell> genblis c:\files\example1

In either case GENBLIS will read the file named example1 which is located in the files directory.

GENBLIS can take two command line options. The first, as described above, names the model specification file. The second names the file to which GENBLIS will send its output. If this second option is not given, GENBLIS sends its output to standard out. It is advised that on UNIX systems one use the redirection capabilities of the shell to redirect this output to a file or to wherever else one wishes. In Windows, however, GENBLIS handles the redirection to a file better than the OS does. Several versions of Windows will buffer the redirected output until the GENBLIS process ends. This can be extremely annoying because GENBLIS will not produce any output while the process is running to inform the user of its current status. Therefore, in Windows it is highly suggested that one provide the second command line option naming the output file. In UNIX and particularly in Windows it is not recommended that GENBLIS be allowed to send output to the screen. Screen output comes at a significant performance cost. Therefore, it is best to redirect standard output to a file either by providing a second command line option naming the output file (in Windows) or by redirecting the output (UNIX).

In addition to the output which GENBLIS by default sends to standard out, GENBLIS creates a list file which contains a summary of the results. The list file provides a description of the estimated model, the options chosen, and the results requested. The list file does not provide the details of program execution. By default GENBLIS sends this list output to a file it creates with the same name as the model specification file plus the extension .lst. For example, if the specified model specification file is entitled 1run the default list file will be 1run.lst and it will be created in the directory from which GENBLIS is executed. The name of the list file can be chosen using the listfile option--please see the General Setup section.

All error messages are sent to general output and to standard error. One may, therefore, see an error message displayed in duplicate if both standard error and standard out are being directed to the same location.

The modelspec file has five different parts the first three of which are required: general setup; linear structure model definition; parameter bounds; starting values; and genetic operator controls.

 Comments are allowed in the model specification file. Comments begin with # and continue until the end of the line. Lines must be no longer than 4096 characters. Comments are not allowed to appear between a variable name and its setting. For example, when the name of the data file is being set, a comment cannot appear between datafile and the filename--see datafile description. Only white space may appear between a variable name and its setting. White space includes space, tab, and end-of-line characters.

GENBLIS is case sensitive. With the exception of a few special commands, the model specification file must be written completely in lower case.

Setting up a GENBLIS model specification file is not as difficult as the following text may lead one to believe. There are a large number of options, but they need not be used. It is probably best to look at the provided example model specification files. Four example model specification files are provided with the binary distribution of GENBLIS. Please see the Example Files section for more details.