Simple text output

To view the results of data analysis performed in this example, select 'Results' from the 'Edit' menu.

This will start the Windows text editor "WordPad" which is distributed as a part of the operating system. The "WordPad" application displays the contents of a simple ASCII text output file named index.txt located in the output directory.

The output file contains the summary of the results of fit in simple text format, suitable for export or cut-and-paste to any word processing or typesetting software. In particular, the output file contains:

• Name of the input script file.
• The given task (simulation or fit of experimental data).
• The presumed reaction mechanism.
• A mathematical model derived from the symbolic description of the reaction mechainsm.
• A quick summary of the least squares fit (number of iterations, residual sum of squares, etc).
• Best-fit values of adjustable parameters and the associated formal standard errors.
• Covariance matrix.
• Eigenvalues and eigenvectors of the Fisher information matrix.
• Name and location of tab-delimited text files containing data for input into third-party plotting programs.

HTML output

DynaFit produces the same output in several different formats, one of which is HTML (the HyperText Markup Language) recognized by web browsers. To view DynaFit output in a web browser, select Browse Results from the View menu. The HTML output file is named index.html and it is located in the same directory where the simple text output file (index.txt) is located.

Depending on your system, there may be a short delay (between five and ten seconds) after the menu selection is made, and before the browser starts showing the results of analysis. In the intervening time, the computer displays a console window (this is not an error).

LaTeX output

LaTeX is a powerful computer system for scientific and mathematical typesetting. There are several freely available software package for processing LaTeX files. We use the package PC-TeX from  Personal TeX, Inc. .

DynaFit produces LaTeX output files suitable for direct typesetting. The master LaTeX file is named index.tex and it is located in the designated output directory (in this example problem it is the directory C:\Program Files\ BioKin\ DynaFit\ examples\ reductase\ output\ substrate\ simple\). Additional files, internally linked to the master file, are located in the subdirectory tex.

When the LaTeX file generated by DynaFit is processed by a LaTeX typesetting program, such as PC-TeX, the output can be directly distributed in the Adobe PDF format.  This PDF file was generated by the LaTeX typesetting system directly from DynaFit output. The LaTeX file is shown   here for illustration. The figures in this PDF file were generated automatically from the PostScript output (see explanation below).

PostScript output

PostScript is a page description language invented and owned by  Adobe . Files in the PostScript format can be printed in high resolution on any PostScript enabled printer. PostScript files also can be viewed on the computer screen by using special viewer software such as the  GhostView freeware.

DynaFit generates PostScript files in the EPS format ("Encapsulated PostScript") and stores them in the subdirectory eps (see above). To view or print these high-resolution graphic files, open any of the EPS files by using "GhostScript" which is available for most major computer platforms including Windows and Macintosh.

Tab-delimited output

Many users of DynaFit will want to produce their own graphic output by using specialized third-party graphic software. For this reason, each graph produced by DynaFit is automatically exported into the subdirectory tab in a tab-delimited text format suitable for importing into any third-party software package.