-------------------------- INSTALLATION OF MFI ----------------------------- Attention! Being unaware of the following design principle for the use of MFI is the most common source of user frustration. Copy MFI.EXE into a directory on your DOS PATH. Place the listmode data files for each experiment in a unique subdirectory created for each experiment (and not on the path). Run MFI from the directory containing the current experiment's listmode files. Thus, for each new experiment, MFI should be run from a different directory. If you are upgrading from an earlier version of MFI, it is recommended that you consult the document files MFIENHAN.DOC and MFICHRON.DOC. These files are not necessary for using MFI and may be deleted. -------------------- END OF INSTALLATION INSTRUCTIONS ---------------------- If the above instructions are clear to you, you need not read further. For those who want a more detailed explanation, here it is. You should probably print this document to refer to it. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PLACING MFI ON YOUR DOS PATH What the DOS PATH is. The DOS PATH is a list of subdirectories containing programs you use frequently. When you give the name of a program to DOS by typing it at the DOS prompt, DOS looks in all directories on the PATH to find it. If the program is present anywhere on the PATH, it can be run from any disk or subdirectory on your computer. If the program is not on the PATH, it can be run only from the single directory in which the program itself sits. Otherwise, you'll get that frustrating "bad command or filename" message. To find out what your DOS PATH is, type the command "PATH" at the DOS prompt (without the quotes) and press Enter. If this does not elicit a list of subdirectories, or reports "No path", then you need to create a path. If it does elicit a list, then you need only edit the PATH, and may skip the section "Creating a DOS PATH", resuming at the section "Including MFI on your PATH". Creating a DOS PATH. DOS commands, Wordperfect, Xtree, and MFI are programs you should be able to run from any place in your hard disk subdirectory tree, so they should be on your PATH. You may have other, specialized, rarely used programs which need not be on your PATH. To create a path, edit your C:\AUTOEXEC.BAT file, inserting a path command. Before doing this, it would be an excellent idea to make sure you have a bootable diskette to use in case you inadvertantly modify AUTOEXEC.BAT so as to make your computer non-bootable! Use a DOS ASCII file editor program; or, if you use a word processor such as Wordperfect or MS Word, be sure to save the edited file in the DOS TEXT file or ASCII mode (do not save it in the usual way as a document file). N.B.: After changing AUTOEXEC.BAT, you must reboot your computer to make the new path take effect. A typical PATH command for a computer containing DOS 6.2 in directory C:\DOS, Wordperfect 5.1 in the directory C:\WP51, Xtree Pro Gold 3 in D:\XTG3, and miscellaneous utilities in D:\UTIL would be: PATH C:\DOS;C:\WP51;D:\XTG3;D:\UTIL Including MFI on your PATH. When you type the command "PATH" at the DOS prompt, DOS will display any path that is already set. Typically, there will be a directory for miscellaneous utility programs on your path. Often it is named \UTIL or \BIN (for binary programs). If such a generic directory is already on your path, copy MFI.EXE into it. Do not put MFI.EXE into a directory reserved for a particular group of programs, such as \DOS or \WP51. This will make it hard to find MFI.EXE when you want to upgrade it, or MFI.EXE may get thrown away with an obsolete version of DOS or WP. If you have copy MFI.EXE into a directory already on your path, you don't need to modify the PATH statement in AUTOEXEC.BAT. If you create a new directory such as C:\UTIL in which to put MFI.EXE and other such programs, then be sure that directory is included in your DOS PATH (follow the above instructions for editing AUTOEXEC.BAT). Suppose that C:\UTIL is on your PATH, and you have copied MFI.EXE there, so it is C:\UTIL\MFI.EXE. To verify that the PATH is working, change to another directory and run MFI. If you get "bad command or filename", this is DOS' way of telling you it could not find the program file MFI.EXE on the PATH. If you get an offer to display or print a document called "How to run MFI for the first time", you succeeded in running MFI from the PATH. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - USING DOS SUBDIRECTORIES TO ORGANIZE YOUR FLOW DATA The best way to organize your listmode data files is to put those belonging to each experiment in a different subdirectory. The subdirectories can be grouped by the name of the investigator, the project, or whatever is appropriate. For example, the directory C:\FLOWDATA might contain a branched subdirectory tree containing all flow cytometry data. Under it could be major branches for different principal investigators, for example: C:\FLOWDATA\MARTZ C:\FLOWDATA\OSBORNE Under C:\FLOWDATA\MARTZ could be branches for each person in the Martz Lab team, for example: C:\FLOWDATA\MARTZ\TOM C:\FLOWDATA\MARTZ\ERIKA C:\FLOWDATA\MARTZ\JUSTIN Under C:\FLOWDATA\MARTZ\TOM could be subdirectories for each experiment done by Tom, for example: C:\FLOWDATA\MARTZ\TOM\TOM-001 C:\FLOWDATA\MARTZ\TOM\TOM-002 C:\FLOWDATA\MARTZ\TOM\TOM-003 Often, it is simplest for an experiment-level subdirectory such as TOM-001 to contain all listmode files for this experiment. If the experiment is especially large or complicated, it may make sense to break the listmode data files into further subdirectories. For example, if samples were excited by a single argon laser at either 488 or 514 nm, there will never be a need to directly compare files with different excitations. Moreover, both FL1 and FL2 may be needed with 488 nm excitation, but FL1 may be useless at 514 nm excitation. So it helps to separate the two categories of files: C:\FLOWDATA\MARTZ\TOM\TOM-003\488 C:\FLOWDATA\MARTZ\TOM\TOM-003\514 Suppose you are ready to use MFI to analyze the data for excitation at 488 nm. Use the DOS command CHDIR (or CD) to change to the appropriate subdirectory. After you do so (provided your DOS is configured to display the current directory as part of the prompt), the DOS prompt should be: C:\FLOWDATA\MARTZ\TOM\TOM-003\488 > _ Where _ represents the cursor. (If your prompt does not display the current directory, edit the following command into your C:\AUTOEXEC.BAT disk file: "PROMPT $P$G" [without the quotes]). Now that you are in the subdirectory containing the relevant listmode files, run MFI. If you are not familiar with the DOS commands MKDIR, RMDIR, CHDIR (or their short forms MD, RD, CD) you should practice using them. Even better, you should learn how to use a directory management program such as Xtree, 1Dir, the File Manager in Windows, or any of several other excellent programs available commercially for this purpose. These programs make much easier the creation of subdirectories, copying or moving of files, and general housekeeping of files in a large DOS directory tree. ------------------ END OF MFI INSTALLATION HELP DOCUMENT --------------------