A2 General Information and Advice

Five different programs can be obtained by sending an email to David Mitchell <[email protected]>. Each program is available in a zipped format (Table A.1):

Table A.1. The program files

Related to

File (.zip)

The program simulates:

Chap. 22


A well-mixed bioreactor

Chap. 23


A rotating drum bioreactor

Chap. 24.2


A traditional packed-bed bioreactor

Chap. 24.3


A Zymotis packed-bed bioreactor

Chap. 25


An intermittently-mixed forcefully-aerated bioreactor

Each of these zipped files contains the two files that you need to run the corresponding program. These two files are:

• an input file that specifies the values of some of the parameters and operating variables that the program will use. A default input file (named "input.txt" in all cases) is provided for each program.

These programs should run on IBM-compatible PCs with Microsoft Windows®. The general procedure for running each program is to:

• save the ".zip" file to a directory on your hard disk;

• extract the zip file, which will produce an .exe file;

• edit the input file (changing values of parameters and variables as appropriate);

• run the program by clicking twice on the executable file. A DOS window will appear. It will ask you for the input and output file names. Answer with file names in DOS format, pressing RETURN after each file name. If you make a mistake, it is not possible to go back and change file names. In this case, press CTRL-C to close the DOS window and then open another one by clicking twice on the executable file). Please make sure that you type the input file name exactly, otherwise you will get an error message. After entering the last file name the program will run. Also, the input file must be in the same directory as the executable file that you are running. As the program runs, it will show within the DOS window the time of fermentation. When the program has finished a message will appear saying "Press any key to continue". After pressing a key the DOS window will disappear. The output files should have appeared in the directory (the same directory as the executable program file);

• inspect the output files that appear in the directory, importing them into a spreadsheeting program if you wish to make graphs.

More detail about running each program is provided in the following subsections for each of the individual bioreactor programs. When prompted for file names, you should use DOS-type filenames (i.e., a filename of eight letters or numbers followed by a point and an extension of three letters), without using any special characters. Note also that you can save various input data files containing different information with different file names. When you run the program you can then give, when prompted, the name of any one of the saved input files.

Each input file contains the following instructions within it "The program reads one number per line before skipping to the next line. (That is, it doesn't even see the text that is to the right of each number). So please leave this input file with exactly the appearance that it has now. It would be a good idea to save a copy of this as "backup.dat", so that you always have a file in the correct format to come back to, if it becomes necessary! Also, please put decimal points in all numbers EXCEPT those marked as integers." Note that scientific notation is used for very large or very small numbers. For example, "23245000" would be written as "2.3245D7", while "0.000023245" would be written as "2.3245D-5".

The various output files are text files, designed to be easily read by a spread-sheeting program. Most spreadsheeting programs can be used for the rapid construction of graphs, which will help you to visualize the trends in the data. In most cases you will need to open your spreadsheeting program and then, once within the spreadsheet, you should import the ".txt" file. Note that there may potentially be a problem if your spreadsheeting program uses commas as the decimal separator, since the output of the bioreactor will have the decimal point. Some of the most recent spreadsheeting programs allow you to specify whether the file that you are importing uses the comma or decimal point, at the time that you import the data. If there are problems, one strategy is to open the ".txt" file in a text editor or word processor and then use the "substitute all" function to substitute all the decimal points with commas. You should make sure that you save the file as a simple "text only" file before exiting the text editor/word processor.

The remaining sections assume that you have followed the above instructions and have already extracted the ".zip" file for each bioreactor program to different directories on your hard disk.

Please note that all the figures and tables in this appendix show the variables, parameters, and explanations in the format that they appear in the text files that either accompany or are generated by the corresponding computer program (i.e., in normal font and without superscripts or subscripts).

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