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Sykes NMR Software Centre

Funding for this software has been provided by the
Canadian Institutes of Health Research (CIHR Group)

Overview

This software was developed to integrate a series of spectral data files. Our data was obtained on the fluorimeter, however any two column coordinate data input is all that is required. The impetus for this software arises from the lack of our spreadsheet programs to provide the required functionality.

The advantage of the program is that one can load all the data files simultaneously, integrate over boundaries chosen by user, and then step through plots quickly and easily to verify data integrity. The ease of doing this should be worth the effort in learning the software.

Granted that our spectral analysis consists of integration only, but the possibilities of adding other mathematical calculations are interesting. This software provides a good template for other adhoc data analysis.

Download and Installation

1. Make sure you have the program wish on your system.

   Wish is an interpreter that takes Tcl/Tk scripts and creates the GUI widgets. You can type whereis wish or which wish to verify that you have the program. If you cannot find wish, you may have to download and install tcl/tk which is public domain software.

2. Click here to download the latest version of this software (www.bionmr.ualberta.ca/download/nic-1.0.tar).

3. Un-tar the download file if your browser didn't do it. You should end up with a directory called nic-1.0

   	> tar xvf nic-1.0.tar
   	> ls
   		nic-1.0
   

4. Arrange to have your related data input files in one directory (eg, data). The data files from the fluorimeter look like this, but more simple data files like this are acceptable.

   	> cd data
   	> ls
   		BLANK001.SP     BLANK004.SP     BLANK007.SP     BLANK010.SP
   		BLANK002.SP 	BLANK005.SP     BLANK008.SP     BLANK_P.SP
   		BLANK003.SP 	BLANK006.SP 	BLANK009.SP
   

5. Start the program by typing the following. The GUI for nic should start up.

   	> cd nic-1.0
   	> wish nic.tcl
   

6. Optional: Make an alias for "nic" in your .tcshrc file.

Using the program

1. Select the browse button and locate your directory of data files.

2. Propose a name for the results file in the field provided.

3. Determine the upper and lower bounds for the x coordinate value in the data files. If you want to use all the points, then enter values which include all x coordinates.

4. Click the Calculate button. The software will then calculate the volume of the curve underneath the points in the specified interval and display those volumes in the Results window below. The results also go into the user supplied text file.
   

   The area calculation begins at the first point which is >= the lower bound. The area calculation ends at the last point which is <= the upper bound. If this is problematic, I will leave it to you to change it in the nic.tcl file.

5. Click on any line in the Results window shows a plot of the data. This is a good way to see if the data looks correct and that the limiting bounds for area are chosen appropriately.
   

   The Next Graph and Prev Graph buttons allow the user to quickly parse each graph. The Save Postscript saves the plot in a user specified file which the user can send to the printer.

   The user can re-size the graph to any size and comparing multiple plots is accomplished by clicking on a second line in the Results window. Multiple plots in the same window is currently not supported.

Changing the Software

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