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BIOLOGY
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STAGES.DOC
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1992-08-06
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Stage Predictor Program
Latest revision: AUGUST 1991 Version: V1.4
Direct correspondence to:
Dr. Rex A. Hess
Veterinary Biosciences
University of Illinois at Urbana-Champaign
2001 S. Lincoln Avenue
Urbana, IL 61801
Phone: 217/333-8933 or 333-2506
FAX: 217/333-4628 or e-mail: r-hess@uiuc.edu
Program written by:
Paul P. Chen
Coordinated Science Laboratory
University of Illinois at Urbana-Champaign
Urbana, IL 61801
Stages was created using Turbo C, copyright Borland 1987, 1988.
Description:
Given a list of initial cells of observation, the program
calculates, for any given number of days, the cells reached
from the first third, second third, and end of each initial
cell's stage.
To determine in what stage a cell was x days ago,
use -x days (negative number of days) as input;
to determine in what stage a cell will be x days hence,
use x days (positive number of days) as input.
I. Required input files:
The program requires the following 5 input files for each animal.
1/ Stage information file format:
(example: "sdrat.stg")
This file contains information about the stages of the
cycle of spermatogenesis for the particular animal.
cycletime (in units of days)
number of stages (integer)
length of stage 1 (in % of cycletime)
length of stage 2 (in % of cycletime)
... ...
length of stage n (last stage)
epididymis transit time (in units of days)
2/ Cell sequence file format:
(example: "sdrat.seq")
This file contains a sequential list of all the cell names
in the cycle of spermatogenesis for the particular animal.
cellname (text)
cellname (text)
cellname (text)
... etc.
3/ Stage/Cell association printout file:
(example: "sdrat.fil")
This file contains the formatted text of cellular associations
within stages; this file gets printed out verbatim whenever
the user requests to see the "cell sequence data."
4/ Multi-cell file format:
(example: "sdrat.mcl")
This file contains a table of cells for stages in which more
than one cell may exist. For example, in the Sprague-Dawley
rat, cells I-4 and B-4 can both be found in Stage 4. I-4
cells are typically found in the first 2/3 or so of the stage;
B-4 cells may be found in the latter 1/3 of the stage. The
format of this file groups cells of the same stage in rows;
there are 3 cells in each row, corresponding to what cell
type is found in the first 1/3, the second 1/3, and the third
1/3 of the stage.
Example: sdrat.mcl
3 (# of multicell stages: integer, required)
I-4 I-4 B-4
B-6 B-6 PL-6
M1-14 SS-14 M2-14
II. Input may be interactive or batch mode, using input from a batch file.
1) In interactive mode, Stages is menu-oriented. The user
simply types responses to questions from menus, thereby
selecting choices from menus and moving among the menus.
2) A batch file has the following format:
(example: "sdrat.bat")
initcell (string) days
initcell (string) days
... etc.
See "IV. Running the Program" on using batch input files
to the program.
III. Output can be directed to the file <stages.out> or to a line
printer, using one of the options in the General Menu.
IV. Running the program:
-------------------------------------------------------------
program uses
mode: you type: input from:
-------------------------------------------------------------
interactive stages terminal
batch stages <file> <file>
-------------------------------------------------------------
If a specified input file does not exist,
the program will ask the user to re-enter the name of the
file, or to simply hit <return> if the user has decided
not to use input from a file.