EPA/600/R-94/035
.1994
GENETOX MANAGER SYSTEM -
BACTERIAL MUTAGENESIS ASSAYS;
USER'S GUIDE
Prepared by:
Larry D. Claxton, Ph.D. and John Creason, Ph.D.
Health Effects Research Laboratory
U.S. Environmental Protection Agency
Research Triangle Park
North Carolina 27711
and
Joe Nader, Way Poteat, and John Orr
Computer Sciences Corporation
4401 Alexander Driive
Research Triangle Park
North Carolina 27711
Prepared Under
Contract # 68-WO-4W43
Delivery Order # 507
Task Officer: Larry B. Claxton
June 1993
Version 2.21
Printed on Recycled Paper
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PREFACE
This user's guide is the reference manual describing use of the EPA Genetox
Manager System. GeneTox Manager is a data capture, data management, and statistical
analysis program used for microbial mutagenicity data. Its main purpose is to provide
a homogeneous environment for the collection, organization, and analysis of data
generated in the laboratory while also supporting a quality assurance program. The
complete system consists of both a personal computer (PC) system and a minicomputer
(VAX) system, although the PC system can be used as a stand-alone system. The system
controls the data collection and management through a user-friendly, menu-driven system
that requests specific information and provides uniform methods for data and information
entry. GeneTox Manager is capable of performing specialized statistical analysis of the
data and creating tabular and graphical summaries. Two versions of the PC system exist:
a stand-alone PC only version, and a VAX version. The VAX version of the system is
designed to function with VAX FOCUS databases so that the VAX can be used for long-
term storage, archiving of files, and the analysis of large groups of data.
GeneTox Manager was developed by the U.S. Environmental Protection Agency.
This software is public domain software; therefore, you are free to use and to distribute
this software free of charge. You may not market this software, however, without prior
consultation with and acknowledgement of the U.S. EPA and its developers.
We only make a few REQUESTS OF THE USERS. First, we request that you
provide to the creators of this software proper acknowledgement. [See the title page to
the software and to the User's Guide. Also in the near future, we hope to have
references that you may cite.] Secondly, realizing that the software is provided free of
charge, please understand that we cannot service this software. [Because the source code
is available, many consultants and companies that use Clipper® could provide additional
help and programming options for you.] Follow the installation and distribution
instructions very carefully. If you have problems, first read the section of the User's and
Programmer's Guides that deal with problems before contacting us. Most problems that
we have seen are due to either not following installation instructions completely (especially
in regard to autoexec.bat and config.sys files) or to memory allocation problems. Most
all of the memory allocation problems are due to other "resident programs" - please see
the guides. If you receive and especially if you distribute the software, be sure to do that
in the proper manner. Be sure that you understand the statistics and proper
interpretation of the statistical programs. Also understand that statistics do not replace
sound scientific judgment and that statistics on a single test does not replace replication
of an experiment. Lastly, be sure to read the "readme.lst" file.
We sincerely hope that this software will be useful to you and will aid you in your
scientific endeavors.
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Acknowledgements
We would like to acknowledge those individuals who used prototype versions of
this software and gave us useful, productive comments. Without their suggestions, this
product could have not been done. In this regard, we give our thanks to Sarah Warren,
Erica Perry, Virginia Ilouk, Sam Schalkowsky, Mary Beth Lawhorn, and Maria Taylor.
We also want to thank those who gave us permission to use the statistical analysis
programs that they developed. These include Dr. L. Bernstein, Dr. D. Krewski, and Dr.
A. Stead. If you use information from these statistical programs, we hope that you will
give proper acknowledgment to the authors of the statistical manuscripts.
We also want to thank Mr. Ken Laws for providing administrative support that
made this project possible, and Drs. Lawrence W. Reiter and Michael D. Waters for
creating the scientific support that made our endeavors a joy.
Notice
The software and the user documentation are provided "as is". CSC and EPA make no warranty,
express or implied with respect to the software and/or user documentation and specifically disclaims the
implied warranties of merchantability and fitness for a particular purpose. EPA and CSC do not warrant
that the software will be uninterrupted and/or error free. You are solely responsible for the selection of
the software to achieve your intended results and for the results actually obtained.
This document has been reviewed in accordance with U.S. Environmental Protection Agency policy and
approved for publication. Mention of trade names or commercial products does not constitute endorsement
or recommendation for use.
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Contents
Preface i
Acknowledgements ii
Notice ii
Document Organization . v
Chapter 1: Introduction „ 1
User Interface 1
Initiation 3
Termination . 3
Error Message . 3
Chapter 2: Using the GeneTox Manager System 5
GeneTox Manager Main Menu 6
Enter/Modify Menu 8
Enter New Experiment Menu 10
Experiment Description 12
Assay Type Selection 14
Final Strain Entry 16
Neg/Pos Control Entry 18
Activation System Information 21
Sample Specific Data 23
Strain and Activation Selection 25
Quality Assurance Checks 27
Dose Data Entry 29
Experimental Remarks 32
Continuation 34
Modify Existing Experiment .37
Change Existing Samples ' 40
Instructions for Experiment Menu 40
Utilities Menu 41
Vax Functions Menu . . „ . 41
Execute VAX GeneTox Program 42
Upload New Data to VAX 43
Upload Modified Data to VAX 44
Download Data from the VAX 45
PC Functions Menu 47
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List Experiments in Database 49
Reindex Databases 50
Retrieve Backup Experiment Data 51
Import/Export Experiment Data 53
Export Experiment Data to File 53
Import Experiment from File 55
Delete Read Only or Download Experiment 56
Archive/Dearchive Experiment Data 57
Archive Experiment Data 58
Dearchive Data to Databases 60
~ Dearchive Data to Disk File . 62
Accept Archived Data From File 64
Import Spiral Systems Data 65
Reports Menu 67
Defaults Menu 71
Special Options Menu 73
Change Password 73
Suggestion Box Modifications 75
Principle Investigator List Modifications 77
Reindex/Clear Databases 78
Assay Type Modification 79
Modify Iteration Count For Plates 80
Enable Help Text Modifications 81
Reset Experiment Status 82
List Archived Experiments 83
Delete Experiment 84
Quit Menu 85
Appendix A: Installation Instructions 87
Appendix B: GeneTox Manager Troubleshooting 91
Appendix C: System Upgrade to Version 2.2 93
Version 2.2 Changes 93
Upgrade Procedure 94
Restoration Procedure 94
Cleanup Procedure 94
Upgrade From Version 1.x or 2.0 95
Appendix D: Colony Counter Interface 97
Appendix E: Known Problems and Limitations . 99
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Document Organization
Chapter 1 provides an overall introduction to the GeneTox Manager system,
conventions, and operation.
Chapter 2 provides a discussion of each menu in the GeneTox Manager system
including the following:
A brief description of the menu
A representation of the screen
User Input
Processing
Outputs
Quality Control
Appendix A provides installation information as well as hardware configuration
requirements for execution of the application.
Appendix B (GeneTox Manager Troubleshooting) covers various problems that
may occur using GeneTox Manager and how they might be solved.
Appendix C covers system upgrade to version 2.2 from earlier versions using the
GeneTox Manager Upgrade utility.
Appendix D covers interfacing GeneTox Manager with an Artek Colony Counter.
Keyboard Notations
The following special terminal keys are referenced:
refers to special keys indicated by inclusion within left and right angle
brackets ( <> ). Examples: , .
refers to the carriage return, or RETURN, key. concludes all
operator responses.
refers to the escape key, which will quit the current transaction and
return to the previous menu.
Representation of Screen Displays
In this manual, the screen displays produced by GeneTox Manager are shown in the form
seen by the user.
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CHAPTER 1
INTRODUCTION
Overview
The GeneTox Manager system is a U.S. EPA system for the collection, organization, retrieval,
and analysis of microbial mutagenicity data. Although the system was designed primarily for
the Salmonella typhimurium plate-incorporation assay, it will accept data and information for any
mutagenicity assay where similar information is obtained.
Microbial assays, especially Salmonella bioassays, are the most common type of mutation tests.
These tests determine whether or not a substance interacts with the DNA of the organism hi such
a way as to create permanent, heritable changes within the DNA. These tests are important
because they can be used to screen for both mutagens and genotoxic carcinogens. The
Salmonella assay has been reported to have been used by over 2000 laboratories. In comparison
to other genotoxicity assays, these microbial assays are relatively rapid and inexpensive. These
tests, therefore, generate very large databases.
In order to collect, manage, and analyze microbial mutagenicity data hi an orderly and rapid
manner, the U.S. EPA (through the services of Computer Sciences Corporation) developed the
GeneTox Manager system. Using this system, investigators can use a PC to collect information
and data, to provide short-term storage of the information, and to provide selected types of
statistical analysis. The complete GeneTox Manager system also includes a VAX FOCUS
system that can be used for the archiving of databases and for the analysis of large groupings
of data. The total system is designed to achieve compatibility between the PC and VAX system
environments. The GeneTox Manager system is designed to be user friendly through the use
of a structured menu system, screen entry helps, and other help screens. Reports are both
tabular and graphical hi nature, and they can be seen on the computer screen, sent to a printer,
or winfteato a PC file. Technical aspects of the GeneTox Manager software (e.g., data field
descriptions) are addressed hi the Programmer's Guide.
It is the hope of EPA that GeneTox Manager, will not only be of benefit to the Agency but will
also be of constructive use to others outside of the EPA.
User Interface
The GeneTox Manager system provides a series of high-level menus that guide the user
through execution of the application. Menu items are identified by highlighted fields, one for
each accessible function. For each function, a submenu is provided with options to perform
subsequent subfunctions.
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Input screens allow the user to enter GeneTox Manager data. The screens have been
implemented with the following design standards:
("HELP") may be entered at any screen. "HELP" displays basic information
about the screen input and returns to the current screen.
("suggestion") may be entered if a selection can be made from a list provided
in the suggestion box. If a selectable list is not available, a general help
message will appear telling the user that no suggestion list is available.
< Shift-F2 > ("expand suggestion text window") may be used to allocate a broader area of the
screen for review/selection of data entry field selection values.
< F5 > ("enable instrument interface)" may be used to request transmission of data from
the colony counter when in the appropriate data entry field.
("review protocol text") may be used to scroll protocol text entered by research
scientists.
("switch current value") may be used on certain screens to switch the current
value for a sample or experiment strain.
("edit expanded text field") may be used to edit text in an expanded window for
certain descriptor fields.
("save expanded text field") may be used to save expanded text window
information.
("save modified information") may be used from the modify environment to
save data/text changes to application databases.
affirms a field entry and moves the cursor to the next entry field. At the last
entry on the screen, the key accepts the entries on the entire screen
and begins validation procedures.
will move the cursor to the previous field during data entry.
< UP-ARROW > and < DOWN-ARROW >
keys will navigate the user through fields on the screen.
key cancels a transaction and returns the user to the previous screen. The
current process is aborted.
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may be entered to go to the previous screen. If editing the first screen, a
message will appear informing the user of this.
may be entered to go to the next screen. If editing the last screen, a message
will appear informing the user of this.
Initiation
To start the GeneT.ox Manager program, type GTM at the DOS prompt. If the GeneTox
Manager System is not in the DOS path, then move to the subdirectory containing the GeneTox
Manager application and execute GTM using the following three commands:
dos prompt > d:
where < d > is the drive containing the application
dos prompt > CD \subdir < RET >
where is the directory for the application
dos prompt > GTM < RET >
Termination
There is only one acceptable method to end a GeneTox Manager session, which is to select the
QUIT option on the MAIN MENU. Using the < ESC > key on all GeneTox Manager menus
will return the user to the previous menu. The key will also allow a system abort,
but this will not reset many of the necessary internal system variables. If a session is
aborted, restart the system, select the QUIT option and quit the system to properly initialize
these internal variables. The only viable exit from the entire system is from the MAIN MENU.
Error Messages
Although there are a variety of error messages that can be encountered, they fall into 3
categories (PC-Clipper generated, VAX-Focus generated, and GeneTox software generated).
The GeneTox error messages deal primarily with user input errors (e.g., asking to upload from
the PC to the VAX an experiment that does not exist on the PC). To understand these error
messages, refer to the portions of the User's Manual that applies to the action being performed.
The software also creates a record of certain types of errors in transaction files. In the PC,
these transition files fall into one of two categories: *.TRN files and *.*T files. The *.TRN
files (e.g., PCDOWN.TRN) record error messages when transferring files from one format to
another. The *.*T files are used to record errors encountered during a retrieval/transaction
process. The actual format for these files is eeeeeeee.fft where the eeeeeeee.ff corresponds to
the experiment name and the "T" is a literal value added to the experiment name to indicate that
this file is a "transaction" file. See the Programmer's Guide for further explanations.
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The PC-Clipper error messages are messages generated by the Clipper® run-tune software.
These messages usually allow the user to "continue", "retry", and/or "quit". Most often these
messages occur if (1) a program file is missing or (2) not enough memory is available for the
program to run. See Appendices B and E and/or a Clipper® manual if these errors occur.
For those having a system that takes advantage of the VAX interface, errors that occur during
the transport of data are logged hi *.TRN files. See the VAX User's Guide and VAX
Programmer's Guide.
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CHAPTER 2
USING THE GENETOX MANAGER SYSTEM
Upon startup, the system will verify that all necessary files are present and display any error
messages that occurred during the initialization. After the system has successfully verified that
all necessary files are present, the following welcome message will be displayed:
Uelcone To
GENETOX NANAGEIl uZ.Z
Deueloped by
Dr. Larry Claxton, and
Dr. John Creason
Health Effects Research Laboratory
U.S. Environmental Protection Agency
Research Triangle Park, HC
&
J, Uay Poteat, Joseph A. Nader,
Daniel G. Husser, John D. Drr, '
Duyian Dauisj and Dauid L. Owens
Applied Technology Diuision
Computer Sciences Corporation
Press Any Key To Continue
After pressing a key, the MAIN MENU for the GeneTox Manager system will be displayed.
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GENETOX MANAGER MAIN MENU
The desired option can be selected by either entering the first letter of the option name or by
using the arrow keys to highlight the particular function. Each function has an associated
submenu and/or input screen(s).
EnterxModify Utilities^
GeneTox Manager Main Menu
EPA Uersion
enu|
Ji>__
Reports
Defaults
Quit
Add Hew Experiment, Modify Existing Experiment, Modify Existing Samples
User Input
Five options may be selected from the MAIN MENU. To select an option, use the left and
right arrow keys to select (highlight) one of the options. After selecting an option, press
to continue with that selection. An alternate selection method is to enter the first
letter of the desired option - this method will invoke the requested option without a
or any other keystrokes. Either of these methods can be used on all selection menus in the
application.
The five options that can be selected from the main menu are:
Enter/Modify - allows the user to Enter new experiment information, Modify existing
experiment information, Change existing sample information, and Maintain Experiment
Instructions.
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Utilities - allows the user to List the experiments in the PC database, Upload and Download
Experiments (VAX Version), Import/Export Experiments, and Archive/De-archive Experiments.
Reports - allows the user to Execute a Raw Data report, or one or more of the Statistical
Model reports: Bernstein, Histidine, Stead, and Quasi-Stead.
Defaults - allows the user to change the default settings for: Communication Setup, Colors,
Protocol File Name, Reindex Databases, Set Location of Application DataBases and Archive
Files, and Special Options.
Quit - allows the user to exit the GeneTox Manager system and return to DOS or to continue
using the system. The < ESC > key will also allow a system abort, but this will not reset
many of the necessary internal system variables. DO NOT use the key to quit
unless absolutely necessary (see pg. 3, Termination).
Processing
The MAIN MENU is the main selection area. It allows the user to select the various options
for manipulating data.
Output
None.
Quality Control
Only keystrokes pertaining to specific menu selections are permitted from this screen.
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ENTER/MODIFY MENU
After selecting the ENTER/MODIFY option from the MAIN MENU, the following screen will
appear. This screen will allow the user to enter new experiments, modify existing experiments,
modify existing sample data, and update the online experiment instructions.
GetieTox Manager Main Menu
—i EPft Uersion
Enter/Modify Utilities
enur
Jihan
Reports
Defaults
Quit
Enter Hew Experiment
Modify Existing Experiment
Change Existing Samples
Instructions For Exprant
Enter New Experiment Data Into The DataDase
User Input
The following fields are input for the ENTER/MODIFY menu:
Enter New Experiment - allows the user to enter new experiment information.
Modify Existing Experiment - allows the user to modify current experiment information.
Change Existing Sample - allows the user to enter new sample information into the database.
Modify Existing Samples - allows the user to modify existing sample data in the database.
Instructions for Experiment - allows the user to Select, View, Print, or Modify experiment-
specific instructions that are accessible from any point in the GeneTox Manager system.
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Processing
The ENTER/MODIFY function provides the general data entry needs for the entire GeneTox
Manager system. For both PC only and VAX Versions, all initial data entry as well as data
modifications must be performed oh the PC, not on the VAX. Updated information must then
be uploaded to the VAX as a separate step. This approach is taken to ensure that databases on
the PC are current with the master databases stored on the VAX.
Outputs
None.
Quality Control
Only keystrokes pertaining to specific menu selections are permitted from this screen.
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ENTER NEW EXPERIMENT MENU
To invoke the Data Entry phase of GeneTox Manager, select ENTER NEW EXPERIMENT
from the ENTER/MODIFY option. Upon selection, the following screens will appear in the
order hi which they are listed below. A more detailed explanation of each screen follows.
User Input
Experiment Description - allows the user to enter general, descriptive information about the
experiment.
Assay Type Selection - allows the user to enter the Assay Type for the experiment.
Final Strain Entry - allows the user to enter the Final Strain information into the system.
Neg/Pos Control Entry - allows the user to enter the Positive and Negative Control information
for the experiment.
Activation System Information - allows the user to enter metabolic Activation System
Information for the experiment.
Sample Specific Data - allows the user to enter Sample Specific Data information. This is the
first screen where unique experiment data can be entered; therefore, it is the first place the user
is allowed to save data and exit the system.
Strain and Activation Selection - allows the user to enter the dose units to be used with the
sample.
Quality Assurance Checks - allows the user to enter the Quality Assurance Checks for the
experiment.
Dose Data Entry - allows the user to enter the Dose Data specific to the experiment.
Experimental Remarks - allows the user to enter the Experimental Remarks that pertain to the
experiment.
Continue Screen - allows the user to continue entering dose response data or to return back to
the Enter/Modify menu.
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Processins
The ENTER NEW EXPERIMENT function provides the user with the capability to enter new
experiment information into the system according to the sequence of screens described on the
following pages.
Outputs
None.
Quality Control
All fields are validated. If an invalid entry occurs, the system will display an error message
and allow the user to correct it.
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EXPERIMENT DESCRIPTION
After selecting the ENTER NEW EXPERIMENT option from the ENTER/MODIFY menu,
the user will be presented with the following screen. This screen allows the user to enter
descriptive information about the experiment into the database.
GeneTox Manager
L
Experiment Description
Entry Date : 66x05x92
Experiment Date.: / /
Research Lab :
Lab Book Number.:
Data Entered By.
Lab Technician..
P Inuestigator..
Experinent
Suggestion Box:
DATE OF DATA ENTRY
The date the experiment is being entered into
the computer (usually today's date)
Fi- Help F2- Suggestion TF3- Uieu Instr ESCr Abort
User lAput
The following fields are input for the EXPERIMENT DESCRIPTION screen:
Entry Date - date sample data is entered into the PC.
Experiment Date - date the experiment was conducted.
Research Lab - unique four character code representing the Lab responsible for conducting the
experiment.
Lab Book Number - lab notebook number associated with the experiment, up to 25
alphanumeric characters.
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Data Entered By - initials of technician entering the sample data into the PC, up to four
characters.
Lab Technician - initials of technician who performed the experiment, up to four characters.
Principal Investigator - initials of principal investigator responsible for the experiment, up to
four characters.
Experiment - unique experiment name, up to 10 characters.
EPA has limited this somewhat to fulfill EPA laboratory needs. The EPA format is
AAAAYYNNNN where AAAA is an alphanumeric code for a project, YY is numeric indicator
of the year in which the project started, and NNNN is a sequential numeral indicating a specific
experiment or test. The system, however, will allow a user to enter only the AAAA portion or
the AAAA portion plus any numeral. NOTE: This identifier must not conflict with any previous
entry because it is one of the key identifiers by which data is retrieved. We suggest that you
order you experiment numbering in some very logical manner and that you keep a log of that
numbering system.
Processing
The EXPERIMENT DESCRIPTION function allows the user to enter descriptive information
about the experiment into the database. The option of SAVE/EXIT is not available at this point,
as all of the information is considered header information and can be duplicated for many
experiments.
Outputs
No data is saved at this point. The data is held in temporary variables until the user elects to
save it at the CONTINUATION screen.
Quality Control
All fields are validated. If an invalid entry occurs, the system will display an error message
and allow correction.
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ASSAY TYPE SELECTION
The user will be presented with the following screen. At this point the user will select an assay
type that applies to the experiment being conducted. If an assay type does not fit the
experiment, exit the data entry phase by pressing < ESC > and select the DEFAULTS menu.
This menu will allow the user to change, add, or delete assay types.
. [_ I
Assay Type Selection
Sel Cd Test Type Description Hin Hour Tenp'C Tenp'F
AJ 1 Stands
BJ 17 Kado t
CD 5 Preint
D) 3 Plate
E) 19 Plate
FD 22 Spiral
G3 IB ICC/An
ird Plate Incorporation Assay 0 0.0 37.0
licroassay 90 1.5 37.0
:ubation assay - standard 90 1.5 37.0
test - Billips-Rothenberg Ch. 0 0.0 25.0
test - Tedlar Bag 0 0.0 37.0
[ Assay 0 0.0 37.0
IBS Plate Test 0 0.0 37.0
Suggestion Box:
SELECTION OF THE TVPE OF ASSAV
Use the up and down arrow keys to select the
type of assay performed then press the
enter key .
98.0
98.0
98.0
77.0
98.0
98.6
98.0
Fl- Help F2- Suggestion Enter- Continue
To select an assay type, press the letter that designates the type desired or use the arrow keys
to highlight the selection and press .
User Input
The following field is input for the ASSAY TYPE SELECTION screen:
Assay Modified - changes to the standard assay type that was used. The default value will be
"NONE". If a change was made, the user has 35 characters to enter a description of the change.
Additional information can later be entered into the REMARKS screen.
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Processing
The ASSAY TYPE SELECTION performs no validation on the assay types that were entered
from the DEFAULTS menu. The user cannot change any information contained in this menu;
changes can only be made from the DEFAULTS menu.
Outputs
No data is saved at this point. The data is held in temporary variables until the user elects to
save it at the CONTINUATION screen.
Quality Control
All fields are validated. If an invalid entry occurs, the system will display an error, message
and allow correction.
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FINAL STRAIN ENTRY
The user will be presented with the following screen. At this point the user will enter
the strains, strain date, activation level and culture density used within the experiment.
1) Strain:
23 Strain:
3) Strain:
43 Strain:
53 Strain:
63 Strain:
73 Strain:
83 Strain:
93 Strain:
J r~ T « 1
Final Strain Entry
Str Date: Leuel: Cul Density:
Str Date: Leuel: Cul Density:
Str Date: Leuel: Cul Density:
Str Date: Leuel: Cul Density:
Str Date: Leuel: Cul Density:
Str Date: Leuel: Cul Density:
-Str Date: Leuel: Cul Density:
Str Date: Leuel: Cul Density:
Str Date: Leuel: Cul Density:
Suggestion Box:
The Selectable List of Salmonella typhinurium
strains is as follows:
CUse to see expanded list 3
TA98
TA100
Fl- Help F2- Suggestion ESC- Abort
User Input
The following fields are input for the FINAL STRAIN screen:
Strain - strain associated with the sample being used hi the experiment. The user will be limited
to 20 strain/activation combinations per experiment.
Strain Date - date the master plate or culture was prepared.
Level - metabolic activation level to be used with this strain. This should be either 0 (no
activation), 1 (first activation level), or 2 (second activation level).
Culture Density - cells per milliliter of overnight culture or other appropriate designation, up
to 11 characters.
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Processing
The FINAL STRAIN ENTRY function validates that the items being entered are valid
as defined in the data dictionary and through lookup tables.
Outputs
No data is saved at this point. The data is held in temporary variables until the user
elects to save it at the CONTINUATION screen.
Quality Control
All fields are validated. If an invalid entry occurs, the system will display an error
message and allow correction.
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NEG/POS CONTROL ENTRY
After completing the previous screen successfully, the user will be presented with the
NEG/POS CONTROL ENTRY screen. This screen will allow the user to enter the positive and
negative control information for the experiment. Control data for all strains being used should
be entered at this time.
1 1
Negatiue/Positiue Control Entry
Strain: Tfl98 Str Date: 06/05/92 Leuel: 0 Cul Density: 1
Cd Control Name Amount Unt Pltttl PltttZ Plttl3 I
15 0 0.000 -Is -Is -Is
2)
3)
4)
Suggestion Box:
Select CONTROL CODE AND CONTROL NAME
CUse shift-F2 to see expanded list)
Negatiue CSoluent) Controls:
50 - Negatiue (No Solvent)
51 - Distilled uater
52 - Normal Saline
Fl- Help F2- Suggestion F6- Change Strains ESC-
x 10 e9
•lt«4 PLTttS
-Is -Is
- Abort
User Input
t
The following fields are input for the NEG/POS CONTROL ENTRY screen:
Control Code - two-digit code that indicates negative or positive control. Positive control
numbers range from 1-49. Negative control numbers range from 50-99.
Control Name - name of control that corresponds to code, up to 20 characters.
Amount - amount delivered per plate.
Units - units for amount per plate.
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Plate Counts 1-5 - actual plate counts. If an automatic colony counter is directly attached to
your PC on the serial line, you may take advantage of the automated instrument interface for
collecting plate counts. A laboratory is responsible for obtaining and establishing its own
hardware and connections for interfacing the colony counter with the PC. The instrument
interface is enabled by pressing , whereupon a highlighted window will be displayed hi
the upper, left-hand corner of the screen indicating that the instrument is enabled. The < F5 >
is a toggle function key, such that pressing it will alternately enable and disable the instrument
interface. If is entered in a field other than Plate Count, the instrument is enabled so
that as soon as the user moves to a Plate Count field, control passes to the instrument.
Alternatively, pressing in a plate count field to enable the instrument interface will
immediately pass control to the instrument.
Data is passed from the instrument to the PC through the following process:
Either 1, 3, or 5 readings will be taken from the instrument per plate depending
on the iterative reading setting in the application. (The default iterative count is
3. The median value is accepted as the plate count of record.) The iterative
count can be set to a different value via the Special Options menu of the Defaults
function.
When control is passed to the instrument, the number of counts to be taken per
plate will be disp^ed hi the suggestion window in the lower, middle portion of
the screen. Data is accepted to the PC by pressing the < PRINT > button on the
Omni-Interface box. Then, an additional instrument reading of the sample can
be taken by pressing the < COUNT > key on the Artek Counter. Each iterative
reading will be displayed in the suggestion window, and .the median value will be
displayed in the current plate count data entry field.
To enter a -1 in the current plate count field, press < ENTER >. To cancel the
current plate count reading from the instrument, press < ESC >. To disable the
instrument interface and return to manual mode, press < F5 >.
Code - code that appears after the plate count has been entered indicating the condition of the
plate (eg, s, satisfactory; c, contaminated; etc.). May be changed if needed, but not necessary.
To change this field, move to the Plate Count following the Code to edit. Then press the
< TAB > key to move back to the Code field.
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Processing
The NEG/POS CONTROL ENTRY function allows all positive and negative controls to
be entered from one location and used throughout the system. There is a limit of 20
strain/activation combinations that may have positive and negative controls.
Outputs
No data is saved at this point. The data is held in temporary variables until the user
elects to save it at the CONTINUATION screen.
Quality Control
The code field is validated from a lookup table. The other fields are validated as numeric
only.
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ACTIVATION SYSTEM INFORMATION
The user will be presented with the following screen. At this point, the user will enter a code
for the S9 type and lot number, amount of activation mixture used per plate, QA information,
and the S9 type and lot description.
J
GeneTox Manager
L
Actiuation System Information
89 Type And Lot Number.
QQO
Level 1 Units
Leuel 2 Units
Actiuation Mixture Per Plate.
S9 Sterility Check (BeiPore)..
S9 Sterility Check CAfter)...
S3 Lot Description
Suggestion Box:
FIRST CHARACTER INDICATES ANIMAL TVPE:
M = MOUSE
H = HAMSTER
R = RAT
G = GUINEA PIG
B = RABBIT
Fl- Help F2- Suggestion FB- Expand Des F9- Saue Des ESC- Abort
User Input
The following fields are input for the ACTIVATION SYSTEM INFORMATION screen:
S9 Type - type of metabolic activation system (S9 type) that is being used for the experiment.
Each character is validated from a lookup table. For example MLA091 indicates that the ninety-
first lot of mouse liver Aroclor-induced S9 activation batch was used.
S9 Lot Number - unique three-digit code representing the specific lot of S9 that is being used
for the experiment.
Activation Mixture Per Plate - activation mixture per plate for levels 1 and 2. The user may
enter an activation amount per plate for each level.
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Units - respective units for the activation mixture per plate. This item will default to microliters
and does not requke an entry unless the user desires to change it.
S9 Sterility Before - one-digit code representing the sterility of the S9 before the experiment.
The codes are presented to the user hi the suggestion box.
S9 Sterility After - one-digit code representing the sterility of the S9 after the experiment. The
codes are presented to the user in the suggestion box.
S9 Description - description for the S9 type and lot number. To exit from the description field
press or . Pressing will allow an expanded description to be
entered and pressing will save the description.
Processing
The ACTIVATION SYSTEM INFORMATION function defines the information associated
with the S9 type and lot for the experiment.
Outputs
No data is saved at this point. The data is held hi temporary variables until the user elects to
save it at the CONTINUATION screen.
Quality Control
Only the S9 type will be validated; the other information will be left to the user's discretion.
If the S9 type is not entered, a warning message will be displayed telling the user that the
information entered will not be retained if the S9 type is left blank.
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SAMPLE SPECIFIC DATA
After successfully completing the NEG/POS CONTROL ENTRY screen, the user will be
presented with the following screen. This screen allows the user to enter sample information
specific to its analysis under an experiment into the database.
GeneTox Manager
Sanple Specific Data
Sample Id :
Sanple Description...:
Source/Batch/Lot :
CDS Number :
Suggestion Box:
SIMPLE IDENTIFICATION NUMBER
The format of the Sanple Identification Nunber
is: flftftftyVNNNN
where AiBAA is a four letter identifier
of the source for the sanple,
VV identifies the year the sample
uas receiuedj and
NfiNN is a sequentially assigned
Fl- Help F2- Suggest F8- Expand Bes F9- Saue Des ESC- Abort
User Input
The following fields are input for the SAMPLE SPECIFIC DATA screen:
Sample ID - unique field that identifies the sample, up to 10 characters. The first four
characters can be alphanumeric but the remaining six must be numeric. NOTE: If you have
entered a sample previously and are returning to this screen from the Continue screen by
choosing "Change Sample ID", this sample ID will be automatically incremented by GeneTox
Manager (i.e., if sample IARC930001 was the last sample entered, the new sample ID will be
IARC930002). If you do not wish to number your samples consecutively, you may change the
sample ID.
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Sample Description - description for the sample that is being used hi the experiment, up to 51
characters. Pressing will allow an expanded description to be entered and pressing
will save the description.
Source/Batch/Lot - identification for the source, batch, and lot number of the sample, up to 51
characters.
CAS Number - CAS number associated with the substance being tested, up to 15 characters.
Processing
The SAMPLE SPECIFIC DATA function allows the user to enter sample information specific
to an experiment into the database. Each field uniquely identifies the experiment and lists some
of the aspects of the sample.
Note: When entering a sample id which has been previously defined to the system, the remaining
fields on this screen will be filled with current values for the sample. Any changes to these
values WILL NOT be stored in the database. To change general sample information, see the
Change Existing Sample function described later in this document.
Outputs
No data is saved at this point. The data is held hi temporary variables until the user elects to
save it at the CONTINUATION screen.
Quality Control
The system will check for the existence of a duplicate sample ID. If one exists, the system
Will display the information associated with that sample. Solvent units will be checked against
a lookup table. If an error is detected, the user will be notified and allowed to correct the entry.
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STRAIN AND ACTIVATION SELECTION
After successfully completing the SAMPLE SPECIFIC DATA screen, the user will be
presented with the following screen. The current strain is listed.
GeneTox Manager 1
Strain ft Actiuation Selection
Current Strain —
Strain Date
Actiuation Leuel.
Culture Density..
Dose Units
IA96
06/85/92
0
1 x 10 e9
Cug )
Suggestion Box:
Enter in the following format or select:
ug - nicrograns
ng - milligrams
ul - microliters
nl - nilliliters
n3 - cubic meters (gases, air samples)
uH - micromoles
Fl- Help F2- Suggestion F6- Change Strains ESC- Abort
User Input
The only input at this screen is the DOSE UNITS to be used for the sample when this strain
is being used. Press < F6 > to change the strain.
Processing
The STRAIN AND ACTIVATION SELECTION function allows the user to select what
sample dose units to associate with the individual strains.
Outputs
A dose unit is associated with each strain.
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Quality Control
All fields are validated. If an invalid entry occurs, the system will display an error message
and allow correction.
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QUALITY ASSURANCE CHECKS
After successfully completing the STRAIN AND ACTIVATION SELECTION screen,
the user will be presented with the following screen. A header will appear from this point on
to allow the user to identify the sample that is being worked on.
1 1- T " 1
Quality Assurance Checks
Samp Id: SAHP920001 Strn: TA98 Strn Date: 12/12x12 fit
So luent Description..:
Solvent Amount/Plate.: 0 PhenoCopy Check Code
Hours Of Incubation..: 0.00 Sample Sterility After...
Suggestion Box:
SOLUENI DESCRIPTION
Enter the name of the solvent for the sample.
Fl- Help F2- Suggestion ESC- Abort
:t Leul: 0
1
•i
1
User Input
The following fields are input for the QUALITY ASSURANCE CHECKS screen:
4
Phenocopy Check - one-digit code representing the phenocopy check code. The user is
presented with appropriate codes within the suggestion box.
Sample Sterility Before - one-digit code representing the sterility of the sample before the
experiment. The user is presented with the appropriate codes within the suggestion box.
Sample Sterility After - one-digit code representing the sterility of the sample after the
experiment. The user is presented with the appropriate codes within the suggestion box.
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Solvent Description - description of solvent used for the test substance.
Solvent Amount/Plate - amount of solvent used per plate.
Solvent Units - units to be associated with solvent.
Hours of Incubation - hours that the plates were incubated.
Processing
The QUALITY ASSURANCE CHECKS function allows the user to enter codes that
represent the state of the bacteria and the sterility of the sample being used.
Outputs
No data is saved at this point. The data is held in temporary variables until the user
elects to save it at the CONTINUATION screen.
Quality Control
All fields are validated from a lookup table. If an invalid entry occurs, the system will
display an error message and allow correction.
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DOSE DATA ENTRY
After successfully completing the QUALITY ASSURANCE CHECKS screen the user will be
prompted with the following screen. This screen will allow the user to enter the actual test data
into the computer.
1 1
Dose Data Entry
Sanp_Id: SAHP Strain: TA98 Strn Date: 12/12/12
Dose CJ ) Flttl Cd Plt82 Cd Plt83 Cd Plttt4 Cd
Zero Dose Not Entered .....
1) 0.000
2)
3)
4)
Suggestion Box:
DOSE AMOUNT
Enter the numeric indication of the dose amount.
Be sure to note the units at the top of the
column.
Fl- Help F2- Suggestion F5- Colony Counter ESC- Abort Pgl
Ac: 0
Plt35 Cd
In- Continue
The following fields are input for the DOSE DATA ENTRY screen:
Dose - amount of the dose for each level used during the experiment, up to 20 doses.
Plate#l - 5 - actual colony count (by the technician or the colony counter). If an automatic
colony counter is directly attached to your PC on the serial line, you may take advantage of the
automated instrument interface for collecting plate counts. The mstrument interface is enabled
by pressing < F5 >, whereupon a highlighted window will be displayed in the upper, left-hand
corner of the screen indicating that the mstrument is enabled. The is a toggle function
key, such that pressing it will alternately enable and disable the mstrument interface. If < F5 >
is entered hi a field other than Plate Count, the instrument is enabled so that as soon as the user
moves to a Plate Count field, control passes to the mstrument. Alternatively, pressing
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in a plate count field to enable the instrument interface will immediately pass control to the
instrument.
Data is passed from the instrument to the PC through the following process:
Either 1, 3, or 5 readings will be taken from the instrument per plate depending on the
iterative reading setting in the application. (The default iterative count is 3. The median
value is accepted as the plate count of record.) The iterative count can be set to a
different value via the Special Options menu of the Defaults function.
When control is passed to the instrument, the number of counts to be taken per plate will
be displayed in the suggestion window in the lower, middle portion of the screen. Data
is accepted to the PC by pressing the < PRINT > button on the Omni-Interface box.
Then, an additional instrument reading of the sample can be taken by pressing the
< COUNT > key on the Artek Counter. Each iterative reading will be displayed in the
suggestion window, and the median value will be displayed in the current plate count
data entry field.
To enter a -1 in the current plate count field, press < ENTER >. To cancel the current
plate count reading from the instrument, press < ESC >. To disable the instrument
interface and return to manual mode, press .
NOTE: A -1 indicates to the software system that a plate count was not recorded. It is
the system's way of determining the number of plates per dose.
Cd (Code) - one character code representing the type of plate reading that was taken. This field
does not have to be entered. The system will default to "s" as values are read in. To change
this field, move to the Plate Count following the Code to edit. Then press the < TAB > key
to move back to the Code field.
Processing
The DOSE DATA ENTRY function allows the user to enter experiment specific data that
represents the results of the experiment.
Outputs
No data is saved at this point. The data is held in temporary variables until the user elects to
save it at the CONTINUATION screen.
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Quality Control
The system will validate each code from a lookup table. If an invalid entry occurs, the system
will display an error message and allow correction. Dose and plate counts are verified only as
numeric values.
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EXPERIMENTAL REMARKS
After successfully completing the DOSE DATA ENTRY screen the user will be prompted with
the following screen. The remarks screen will allow the user to enter text about the experiment.
1
1- - M 1
Experimental Remarks
Jarap Id: SAHP920091 Strn: Tft98 Strn Date: 12/12/12 ft
Suggestion Box:
REMARKS (Press sF2 for information)
Fl- Help F2- Suggestion F7- Dose Screen F9- Saue DCS ESC
:t Leul: (
:- Abort
)
User Input
The following field is input for the EXPERIMENTAL REMARKS screen:
Remarks - text to explain the results or some other point about the experiment. When finished
entering the remark press < F9 >. This will terminate the data entry phase and bring up the
next screen.
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After entering the remarks text and pressing , the user will be asked if they wish to
append an instruction set to the remarks text. If the user answers yes, they will be presented
with another prompt which asks if they wish to append the currently selected instruction set.
Answering yes appends the instruction set currently selected for this experiment. Answering no
allows the user to select a particular instruction set that has been previously entered and saved.
After appending, the user is returned to editing the remarks text and may make changes to the
appended instruction text. Pressing a second tune causes the remarks text plus the
appended instruction set to be saved.
Processing
The EXPERIMENTAL REMARKS function allows the user to enter experiment-specific
remarks about the way the experiment concluded or any text that the technician believes is
pertinent to the experiment. Up to 700 characters may be entered for the remarks.
Outputs
No data is saved at this point. The data is held hi temporary variables until the user elects to
save it at the CONTINUATION screen.
Quality Control
No validation is made on the remarks. The user may enter any valid character represented by
the PC.
NOTE: Any special characters used may not be represented correctly on the VAX since the
VAX does not support DOS's extended character set.
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CONTINUATION
After successfully completing the EXPERIMENTAL REMARKS screen the user will be
prompted with the following screen. This screen will allow the user to continue entering dose
response data, change sample ID and description, save data and exit, return to the remarks field
to continue editing or exit without saving.
——'GeneTox Hanager*—•
Experimental Remarks
Samp Id: TEST920001 Strn: TA9B Strn Date: 06/05/92 Act Leul: 0
Continue Entering Dose Response Data
Change Sample Id II Description
Saue Data And Exit
Resume Editing The Remarks Field
Exit Without Sailing Data
Suggestion Box:
REMARKS (Press sF2 for information)
Fl- Help F2- Suggestion F9- Saue Des ESC- Abort
User Input
The following fields are input for the CONTINUATION screen:
Continue Entering - allows the user to continue entering dose response data for any remaining
strains for the present sample. All previously entered data is saved. User is returned to the
Strain and Activation Selection screen and the next strain is selected.
Change Sample ID - allows the user to change samples and enter dose response data for the
new sample while remaining in the same session (i.e., none of the General or Control
information is changed). All previously entered data is saved. User is returned to the Sample
Specific Data screen and the sample ID is incremented (i.e., if sample IARC930001 was the last
sample entered, the new sample ID will be IARC930002).
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Save Data and Exit - allows the user to save all data entered and exit to the main menu.
Resume Editing - allows the user to return to the remarks field to continue editing.
Exit without Saving - aborts the data entry sequence for the current sample. Any data entered
prior to reaching this screen is saved from this screen by choosing "Continue Entering",
"Change Sample", or "Save And Exit". General experiment data is saved when continuing from
this screen after entering the dose response data for the first sample. Dose response data for
each sample is saved when continuing from this screen or choosing "Save Data and Exit".
Therefore, choosing "Exit without Saving" will only abort saving data for the current sample,
unless this sample is the first sample entered for the experiment.
Processing
The CONTINUATION function allows the user to continue entering dose response data or to
exit back to the MAIN MENU.
Outputs
All data is saved at this point unless the user chooses EXIT WITHOUT SAVING DATA or
presses to abort. If the user chooses to EXIT WITHOUT SAVING or presses
< ESC >, no data will be saved and the MAIN MENU will appear. If data is saved at this
point, an output file is also generated which contains all of the information for the experiment
in condensed form. This file serves as a back-up file of experiment data in addition to the data
loaded directly to the PC databases.
The naming convention for this output file is as follows:
eeeeeeee.fffi where
eeeeeeee are the first 8 characters of the experiment name,
ff are the 9th and 10th characters of the experiment name, and
B is a literal value appended to the experiment name to
indicate that this file contains backup experiment data.
Note: If an experiment name is less than 10 characters, the filename will be shortened
accordingly with a "B" still appended to the end (e.g., an experiment name of CSCT910001 will
yield a back-up filename of CSCT9100.0IB, while an experiment name of TEST will yield a
back-up filename of TESTB).
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Quality Control
If CONTINUATION OF DOSE DATA ENTRY is chosen, there is a check for any strains for
which no data has been entered. If no more of these strains remain, the PC will not allow this
option to be selected. Conversely, if SAVE DATA AND EXIT is chosen and there still remain
unentered dose responses for strains, the PC will prompt the user for verification to exit without
completing the data entry for this session.
If the user chooses to CHANGE SAMPLE ID, as in the SAVE AND EXIT option, the PC will
check for remaining unentered dose data for strains and prompt accordingly. This option will
"rewind" to the SAMPLE SPECIFIC DATA screen and allow additional samples to be added.
NOTE: No data hi the Experiment Description, Assay Type Selection, Final Strain
Entry, Neg/Pos Control Entry, or Activation System Information screens will be
displayed or changed when the CHANGE SAMPLE ID OPTION is selected.
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MODIFY EXISTING EXPERIMENT
After selecting the MODIFY EXISTING EXPERIMENT option from the ENTER/MODIFY
menu, the user will be prompted with other screens to specify exactly which data is to be
modified. These screens will allow the user to modify existing experiment data in the database.
After choosing what data is to be modified, the user will be presented with the screens associated
with the data. Each screen is defined in the ENTER NEW EXPERIMENT section of this
manual. Please refer to that section for instructions.
After selecting either Modify Existing Experiment or Change Existing Samples, the user is
presented with the following screen:
GeneTox Manager Main Menu
—i EPfl Uersion
Enter/Modify lit i 1 it ies
Reports Defaults Quit
Enter Mew Experiment
Modify
Change
Instru
Date:
Initials:
Reason:
03/08/93
FB - Expanded Reason F9 - Saue Expanded Reason
Modify Experiment Data Contained In the Database
The user is required to enter their initials and a reason for the modification before they are
allowed to continue. This feature was implemented hi accordance with the Good Laboratory
Practices standard, and provides a method of tracking user modifications to experiment and
sample data. Modification information is appended to the S9 Description for Experiment data
modifications; for sample modifications, the information is appended to the Sample Description.
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EnterxModify Utilities
GeneTox Manager Hain Menu
EPA Uersion •—
Reports Defaults
Quit
Enter Hew Experiment
Mo
Ch
In
General Exper. Data
Control Exper. Data
Existing Sample Data
Dose Response Data
New Sample Data
Delete Sample Data
Modify Experiment Data Contained In the Database
User Input
The following options are available from the MODIFY EXPERIMENT screen:
General Experiment Data - allows modification of the following: Experiment Description,
Assay Type Selection, Final Strain Entry and Activation System. After selecting one of these
options, the user is required to enter the experiment name and research laboratory associated
with that experiment.
Control Experiment Data - allows modification of the control data. The user is required to
enter the experiment name.
Sample Specific Data - Under the modify experiment function, sample information can be
modified that applies to analysis of a sample under a given^experiment. Sample specific data,
however, cannot be changed in this environment and is displayed for information only. To
change sample specific data, see the Change Existing Sample function described later in this
document.
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In the modify experiment environment, the following sample information can be
modified: Sample Specific Data, Current Strain Selection, Quality Assurance Checks and
Experimental Remarks. After selecting one of these options the user is required to enter
the experiment name and the sample ID of the sample to be modified.
Dose Response Data - allows modification of the Dose Response Data. The user is required
to enter the experiment name and sample ID of the sample to be modified.
New Sample Data - allows the registration of additional samples to an existing experiment.
Delete Sample Data - allows deletion of a sample from its association with an experiment strain.
User is required to enter the experiment name and sample ID, and to choose the strain from
which to delete. If the sample is not used for any other experiment strains, it is permanently
deleted from the database.
Processing
The MODIFY EXISTING EXPERIMENT function provides the user with the capability to
change data contained in the database. The MODIFY routine allows modifications to categories
of previously entered data: General Data, Control Data, Sample Specific Data, Dose Response
Data, and New Sample Data. This simplifies the process for making minor modifications. Each
section is modified individually, with modifications saved/aborted separately.
NOTE: .The screens have been defined in the ENTER NEW EXPERIMENT section of this
manual. Please refer to the appropriate section to obtain help on these screens.
Outputs
None.
Quality Control
Search Criteria (Experiment Name, Sample ID) are validated. If an invalid entry occurs, the
system will display an error message and allow correction. All other fields are validated in
similar fashion to their counterparts in the ENTER NEW EXPERIMENT function.
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CHANGE EXISTING SAMPLES
After selecting the CHANGE EXISTING SAMPLES option, the user will be prompted for a
sample id for an existing sample. After validation, the system will present the user with a
screen of sample specific data (equivalent screen to the one under ENTER NEW EXPERIMENT
for sample specific data). Refer to the SAMPLE SPECIFIC DATA description under the
ENTER NEW EXPERIMENT section for details on the sample fields that may be modified.
Modification tracking is also done on Sample Data (see Modify Existing Experiment).
INSTRUCTIONS FOR EXPERIMENT MENU
The following options will be available to the user upon selecting the INSTRUCTIONS menu:
Add - allows the addition of new instruction sets to the instruction database.
View - prompts for the path and allows inspection of the available instruction sets.
Modify - prompts for the path and allows the modification of any available instruction sets.
Delete - prompts for the path and allows the removal of available instruction sets.
Select - prompts for the path and allows for the selection of an instruction set to be used during
the GeneTox Manager session or until a new set is chosen.
Transfer - prompts for the source path and permits the transfer of an instruction set to another
disk or path.
Print - prompts for the path and generates a printout of the selected instruction set.
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UTILITIES MENU
After selecting the UTILITIES option from the MAIN MENU, the user will be presented with
two options: PC FUNCTIONS and VAX FUNCTIONS.
VAX FUNCTIONS MENU (Accessible to VAX Version Only)
The communications programs are driven by predesigned script files that are specific to the
VAX setup at the U.S. EPA Laboratory in Research Triangle Park, North Carolina. Using a
VAX .version of GeneTox Manager at another site may require some modifications to these files.
This applies to all functions under the VAX FUNCTIONS menu.
The following menu lists VAX functions:
GeneTox Manager Main Menu
—i EPfl Uersion i—
Enter/Modify Utilities
Reports
Defaults
Quit
Execute UAX GeneTox Program
Upload New Data To VAX
Upload Modified Data To UAX
Download Data Fran The UAX
Upload To Uax, Download From Uaxj Logon to Uax
Execute VAX GeneTox Program - Allows user to connect to the VAX as if logged hi at a
VAX Terminal. Provided to allow user to access VAX GeneTox Manager programs without
exiting PC system. Users may also access the VAX without using the PC GeneTox Manager
Program.
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Upload New Data To VAX - Extracts all data for the specified experiment to a file on the PC,
transfers the file to a VAX and loads the data to master Focus databases.
Upload Modified Data To VAX - Performs an equivalent function to the one above for new
experiment data, but in this case applies to modified data for an existing experiment.
Download Data From The VAX - Extracts data for an experiment from the VAX Focus
databases, downloads the file to the PC and loads the information into PC databases.
Downloaded experiments are in "Read Only" status and cannot be modified.
EXECUTE VAX GENETOX PROGRAM
This Function is provided to allow the user to run the VAX FOCUS version of the GeneTox
Manager without leaving the PC Application. The user is logged on to their VAX account
through PathWorks using the DEC SetHost communications program and the VAX GeneTox
upload program is executed.
User Input
User must provide the SetHost script program with the user name and password of the VAX
account they are logging in under. User exits by typing "lo " (logout) at the VAX $
prompt and then using Control-FlO to exit SetHost and return to the PC GeneTox program.
Processing
User is logged in by SetHost (assuming user name and password are correct) and the VAX
GeneTox program is executed.
Output
Behaves as if the user were logged on to the VAX through a DEC Terminal.
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UPLOAD NEW DATA TO VAX
This function allows the user to extract all data for an experiment to a file and subsequently
upload the data to VAX master databases. The user is logged on to their VAX account through
PathWorks using the DEC SetHost communications program and a VAX GeneTox upload
program is executed.
The SetHost program is driven by a predesigned script file that is specific to the VAX setup
at this laboratory. Using a VAX version of GeneTox Manager at another site may require some
modifications to this file.
User Input
Experiment name for which to upload data. User name and Password for the VAX account
they wish to login under.
Processing
This function will search application databases for the requested experiment name. If the
experiment name does not exist, the user will be notified hi an error message and allowed to try
again. This function will only extract data for an experiment which has NOT already been
uploaded to the VAX previously. To upload revised experiment information, use the UPLOAD
MODIFIED DATA TO VAX function.
If incomplete or invalid data is found for the experiment requested, the user is notified via a
message to the screen and the processing of this data file to the VAX is terminated. If, on the
other hand, a clean extract file is generated, the system will then attempt to establish
communications to the VAX using SetHost.
If appropriate communication to the VAX can be established, the extracted file is transferred to
the user's VAX account and a Focus upload procedure is invoked to load the extract file to
Focus master databases. A verification message is displayed to the user at the end of this
process to indicate successful completion of the upload or an abnormal abort situation.
A log file which provides further information on the VAX database upload results is also
generated to the user's VAX account.
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Outputs
• A file containing all experiment data for the experiment name requested on the PC.
• Updated VAX master databases containing new information based on the experiment
requested.
• Resetting of a flag in the PC databases which indicates that the experiment has now been
uploaded to the VAX. A log file which provides detailed information on the VAX database
upload. The file is named as follows:
mmddhhuu.LOG- where
mm is a 2 character code for the current month
dd is a 2 character code for the current date
hh is a 2 character code for the current hour
uu is a 2 character code for the current minute
For purposes of this file name, CURRENT is defined as the point in time that the log file was
opened (i.e., when loading of data to the'VAX began).
Quality Control
The experiment name field is validated. If the experiment does not exist in the application
databases, an error message to that effect is displayed to the user. In addition, the extraction
file is validated for completeness before attempting to transfer it to the VAX. And, finally, the
upload of VAX databases is validated with results documented in a log file and in a display
message to the user at the completion of the process.
GeneTox expects the PathWorks network software to be loaded in order to make the connection
to the VAX. Uploading will not be possible if the PC is booted without the network. If user
name or password are entered incorrectly, the login will not be completed. To exit sethost,
press to exit and return to GeneTox Manager.
UPLOAD MODIFIED DATA TO VAX
This function is very similar to the function described immediately above, UPLOAD NEW
DATA TO VAX. The difference hi this function is that the user may extract "data
modifications" for a specified experiment to a file and subsequently upload the data to VAX
master databases. Note that modified data may represent only a portion of the total information
available for a given experiment.
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DOWNLOAD DATA FROM THE VAX
This function allows user to download data previously uploaded by another user with NEW or
MODIFIED UPLOAD. The user is logged on to their VAX account through PathWorks using
the DEC SetHost communications program and the VAX GeneTox download program is
executed. Downloaded data is stored in the databases in "Read Only" status. Downloaded
Experiments may NOT be modified, re-uploaded, or archived.
The SetHost program is driven by a predesigned script file that is specific to the VAX setup
at this laboratory. Using a VAX version of GeneTox Manager at another site may require some
modifications to this file.
User Input
User must provide GeneTox Manager with the user name and password of the VAX account
they wish to login under. User must also provide the experiment name of the experiment to
download. Users may only download data that does not currently exist on their PC. The system
will inform the user of any conflicts with existing experiment names of experiments currently
stored on their PC and may require the user to rename their current experiment or the download
experiment depending on the circumstances.
Processing
User is logged on to the VAX through the specified account and a download program is run.
The specified experiment data is extracted from the VAX databases and a file containing the
experiment data is created. This File is called "PCDOWN.VAX". PCDOWN.VAX is
transferred to the PC., Downloaded data is then loaded into the PC databases.
Output
GeneTox informs user of current status throughout the process (i.e. when running VAX extract
program, transferring file, processing downloading file, and saving data to the databases). If
any errors occur the user is informed. A transaction file PCDOWN.TRN is created on the PC
in the same directory as the GeneTox Manager Databases which will contain specific information
on any errors encountered. This file can be viewed by the user with the DOS TYPE command
or with a text editor of the user's choice.
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Quality Control
Downloaded data is validated before saving it to PC databases. User is notified of success or
failure of download attempt. Specific errors are written to transaction log file PCDOWN.TRN
on the PC. Errors encountered when extracting data from VAX FOCUS databases are written
to the PCDOWN. VAX download file. This file can be viewed by the user with the DOS TYPE
command or with a text editor of the user's choice.
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PC FUNCTIONS MENU
After selecting the PC FUNCTIONS option from the UTILITIES menu, the following screen
will appear:
r T u u • M
- PP A 1 Iiawo -i nn
Ini-nnTn-ff-C
1 '
1 List Experiments In Database
1— Re index GeneTox Manager Databases
Hetrieue Backup Experiment Data
Import/Export Experiment Data
Delete Read Only or Download Exp
Archiue/Dearchiue Experiment Data
Import Spiral Systems Data
5 Defaults Quit
List Experiments, Extract Files, Use Uax Files, Reindex Databases
Functions available from this menu include the following:
List Experiments In Database - Provides a list of all experiments defined to the PC system.
Reindex GeneTox Manager Databases - Reindexes PC based databases to ensure data integrity.
Retrieve Backup Experiment Data - Allows user to reload backup copies of previously entered
experiment data should the original data become corrupted.
Import/Export Experiment Data - Allows user to share experiments between different PC
copies of GeneTox Manager. Imported experiments are in a "Read Only" status and cannot be
modified.
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Delete Read Only or Download Experiment - Allows user to delete experiments that are in
"Read Only" status from the database. (Imported or Downloaded Experiments Only)
Archive/Dearchive Experiment Data - Allows user to archive/dearchive old experiment data
to reduce size of databases.
Import Spiral Systems Data - Allows user to import data collected by a Spiral Biotech's laser
scanner/counter using the Spiral Biotech data collection program.
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LIST EXPERIMENTS IN DATABASE
This function allows the user to review a list of all experiment names logged to the system.
User Input
The following input field is provided for this function:
Experiment Name - defines the experiment name(s) to be listed. A partial definition of the
name will generate a list of all experiments meeting the defined letters. A response of a blank
field will generate a list of all experiments logged to the system.
The following selection criteria are supported: (1) all experiments; (2) experiments that have
been previously uploaded; (3) experiments that have not been previously uploaded; (4) read only
experiments.
Processing
This function will search application databases for all experiment names hi the system meeting
the character mask provided by the user.
Outputs
A list of the experiments hi the PC database is generated to the terminal, printer, or file, based
upon the user's choice.
Quality Control
The experiment name field is validated. If the experiment does not exist hi the application data
bases, an error message to that effect is displayed to the user.
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REINDEX GENETOX MANAGER DATABASES
»
This function allows the user to reindex PC based databases to ensure data integrity. It is most
advisable to use this function whenever it is suspected that an index file has been corrupted.
User Input
No user input is required for this function.
Processing
This function will select each application database and regenerate defined indices for each.
*
Outputs
A set of new indices for application databases is generated. As each database is selected and
indexed, a notification message is displayed to the user on the screen.
Quality Control
Each database is indexed according to key fields defined hi the application code.
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RETRIEVE BACKUP EXPERIMENT DATA
A backup copy of experiment data is saved every time you enter or modify an experiment.
This Function is provided to retrieve this backup data should experiment data hi the databases
become corrupted. Backup data will normally reside in the same directory as the GeneTox
Manager databases.
The naming convention for this backup data file is as follows:
eeeeeeee.ffB where
eeeeeeee are the first 8 characters of the experiment name.
ff are the 9th and 10th characters of the experiment name.
B is a literal value appended to the experiment name to
indicate that this file contains backup experiment data.
Note: If an experiment name is less than 10 characters, the filename will be shortened
accordingly with a "B" still appended to the end (e.g., an experiment name of CSCT910001 will
yield a back-up filename of CSCT9100.01B, while an experiment name of TEST will yield a
back-up filename of TESTB).
User Input
User enters the experiment name for which to retrieve backup data, and optionally the drive
and DOS path where the backup file is located if the backup file is not found in the default
directory.
Processing
If the backup file is found, data is restored to the databases. If any data for the experiment
currently exists hi the databases, the user is warned that data will be over-written as part of the
retrieval process.
Output
A transaction log is created with a DOS filename similar to the backup file, but with the letter
"T" as the third letter of the extension. This file contains error messages describing any errors
encountered hi the retrieval process. The user is also informed of the success or failure of the
retrieval attempt.
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Quality Control
System checks for existence of a backup data file first in the directory containing the GeneTox
Manager Databases (where they are located when generated), and then in a user specified
directory, and informs the user if the data cannot be located. System also informs user if backup
file is in invalid format. Specific errors noted in backup file will be recorded in the transaction
log.
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IMPORT/EXPORT EXPERIMENT DATA
The following menu is displayed when selecting IMPORT/EXPORT EXPERIMENT DATA.
Enter/Modify Utilit
1
_ VPft 1 In-nt- i nn
1
1 List Experiments In Database
*— Re index GeneTox Manager Data Bases
n_f .
Imp
Del
Import Experiment Data from File
Export Experiment Data to File
,
List Experiments j Re Index
, Retrieve Backups j Import/Export, Archiue/'Dearchiue
EXPORT EXPERIMENT DATA TO FILE
This function allows user to share experiment data with*bther GeneTox users. Data is exported
in "Read Only" status - receivers cannot modify the data. An output file of experiment data is
generated. The naming convention for this file is as follows:
eeeeeeee.ffR where
eeeeeeee are the first 8 characters of the experiment name.
ff are the 9th and 10th characters of the experiment name.
R is a literal value appended to the experiment name to
indicate that this file contains exported experiment data.
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Note: If an experiment name is less than 10 characters, the filename will be shortened
accordingly with a "R" still appended to the end (e.g., an experiment name of CSCT910001 will
yield an export filename of CSCT9100.01R, while an experiment name of TEST will yield an
export filename of TESTR).
User Input
Experiment Name for which to export data; and Drive/DOS Path location for exported
experiment file.
Processing
.' fT'
Creates export file of experiment data. Any errors noted will be recorded hi the export file.
Output
Export file containing experiment data.
*
Quality Control
User informed of any errors in drive or pathname specified, and of any errors encountered hi
generating the export file. Specific error information is written to the export file.
NOTE - If errors occur hi generating export file, export file will NOT have the correct format
and may NOT be subsequently imported by another user. Cause of the error must be fixed and
a new export file generated.
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IMPORT EXPERIMENT DATA FROM FILE
This function allows user to bring data exported by another user into their databases. Imported
experiments have "Read Only" status and cannot be modified, re-uploaded, or archived. Import
data files have the following format:
eeeeeeee.ffR where
eeeeeeee are the first 8 characters of the experiment name.
ff are the 9th and 10th characters of the experiment name.
R is a literal value appended to the experiment name to
indicate that this file contains exported experiment data.
Note: If an experiment name is less than 10 characters, the filename will be shortened
accordingly with a "R" still appended to the end (e.g., an experiment name of CSCT910001 will
have an import filename of CSCT9100.01R, while an experiment name of TEST will have an
import filename of TESTR).
User Input
Experiment Name; Location of import file - drive and DOS path. Users may only import data
that does not currently exist on their PC. The system will inform the user of any conflicts with
existing experiment names of experiments currently stored on their PC and may require the user
to rename then: current experiment or the import experiment depending on the circumstances.
Processing
Experiment added to databases in "Read Only" status.
Output
Displays messages when processing import file and saving data. Errors are written to a
transaction log file. Transaction file has DOS filename similar to the import file, but with the
letter "T" as the third letter of the extension.
Quality Control
User notified if import file cannot be found, or if specified drive and path are incorrect. User
notified if import file has incorrect format. Specific format errors are recorded in the transaction
log.
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DELETE READ ONLY OR DOWNLOAD EXPERIMENT
This function allows user to delete experiments imported from other users or downloaded from
the VAX databases. Experiment data is permanently deleted.
User Input
Experiment name of experiment to be deleted.
Processing
Deletes all data associated with the experiment from the databases.
Output
None.
Quality Control
Informs user if experiment does not exist. Will NOT allow deletion of experiments that have
not been either imported or downloaded. A function Ło delete ANY experiment is provided
under the password protected options hi SET SPECIAL OPTIONS under the DEFAULTS menu.
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ARCHIVE/DEARCHIVE EXPERIMENT DATA
The following menu will be displayed after selecting ARCHIVE/DEARCHIVE EXPERIMENT
DATA:
1 . T?PA Ur»v«
-------
needs to know only the experiment name and the location of the file hi this case, not the
password. To bring this data into then* databases, the receiver uses "Accept Archived Data
From Disk" and provides the experiment name and location (DOS drive and path) when
prompted.
Transfer Ownership (from Shared Archives): To transfer ownership of data that has been
archived to a shared archive (an archive file to which bofy. users have access, on a shared file
service, for example), you will merely need to provide the receiving user with the location and
password for the experiment. The receiving user can dearchive the data using "Dearchive To
Databases" by specifying the password an location when prompted.
ARCHIVE EXPERIMENT DATA
This function allows the user to remove experiment data from the PC databases. Archived data
will be compressed using the PKZIP compression utility and stored hi a specified archive file
in a user specified location. Experiment data must be in Inactive status (uploaded to VAX
databases) before archiving on the VAX version of GeneTox Manager. Archiving experiment
data will reduce the size of the GeneTox databases and increase the speed of reports. Archiving
data will also save disk space. Experiments are archived using a specified password, and may
not be dearchived without that password.
User Input
User enters name of experiment to archive, password for archive file, and location and name
of archive file. Default location values are set at. system installation or changed with LOCATE
ARCEDTVES hi the DEFAULTS menu. The default archive file has the filename
"GTMARCHV.ZIP". The user may override any of these default values.
Processing
Experiment data is generated hi the same format as exported experiment data. The naming
convention for this output file is as follows:
eeeeeeee.ffX where
eeeeeeee are the first 8 characters of the experiment name.
ff are the 9th and 10th characters of the experiment name.
X is a literal value appended to the experiment name to
indicate that this file contains archived experiment data.
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Note: If an experiment name is less than 10 characters, the filename will be shortened
accordingly with an "X" still appended to the end (e.g., an experiment name of CSCT910001
will yield a filename of CSCT9100.01X, while an experiment name of TEST will yield a
filename of TESTX).
This file is then compressed using the PKZIP compression utility and added to the specified
archive file. Data is then deleted from the databases and a database containing information
concerning archived experiments is updated with experiment name, password, location, and date
for this archive file (See LIST ARCHIVED EXPERIMENTS under the SPECIAL OPTIONS
of the DEFAULTS menu).
Output
Experiment data is compressed and placed in the user specified archive file. Any specific
errors encountered in generating the output data file are written to the file. If an error occurs
archiving of the experiment data will be aborted. This file can be viewed by the user with the
DOS TYPE command or with a text editor of the user's choice.
NOTE - because the location for the archive file is specified using a DOS drive and path name,
the actual archive file can be generated on the PC hard disk, on floppy diskette for transfer to
another user, or on a network file service by specifying the proper drive and path names.
Quality Control
User is informed if experiment does not exist, drive and path are incorrect, or not enough
space is left on disk for archive file. If an error occurs during archiving, data is NOT deleted
from the databases.
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DEARCfflVE DATA TO DATABASES
This function allows the user to dearcMve previously archived experiment data from a
compressed archive file.
User Input
Experiment name and password of file to dearchive. The password must be the same password
used to archive experiment (If the password has been forgotten, use LIST ARCHIVED
EXPERIMENTS function under SET SPECIAL OPTIONS of the DEFAULTS menu).
Optionally, a user specified drive, path, and archive filename if a record of this experiment is
not stored in the user's archived experiments list.
Processing
Archived experiments database is searched for an entry indicating that this experiment was
archived. If found, the drive, path, and filename information stored in the database is used to
retrieve the archived data. If the entry does not exist, or the file is not found, the user is
prompted for the location of the archived experiment (drive, path, and archive filename). This
allows the user to dearchive experiments that have been archived by another user if they know
the experiment name, password, and location.
The PKUNZIP decompression utility is used to decompress the requested experiment and the
data is then restored to the databases. The entry for the archived experiment is then deleted
from the archived experiments list.
Output
GeneTox Manager informs the user when decompressing and saving data, and when errors
occur during processing decompressed data file. A transaction log file is created during the
dearchival attempt. Any errors noted in processing the dearchived data are written to this log
file.
The naming convention for this transaction log is as follows:
eeeeeeee.ffT where
eeeeeeee are the first 8 characters of the experiment name.
ff are the 9th and 10th characters of the experiment name.
T is a literal value appended to the experiment name to
indicate that this file contains transaction data.
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Note: If an experiment name is less than 10 characters, the filename will be shortened
accordingly with a "T" still appended to the end (e.g., an experiment name of CSCT910001 will
yield a log filename of CSCT910Q.01T, while an experiment name of TEST will yield a log
filename of TESTT).
Quality Control
The user is informed of any errors - incorrect password, drive, path or archive file not found,
experiment data not found hi archive file, decompression unsuccessful, or problem processing
decompressed data. Specific errors are reported in the transaction log.
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DEARCfflVE DATA TO DISK FILE
This function is provided to allow users to place dearchived data into a disk file which may be
given to other users and added to their databases using ACCEPT ARCHIVED DATA FROM
FILE. This function is similar to IMPORT EXPERIMENT DATA, but data is not restricted
to "Read Only" status.
PLEASE NOTE:
The receiving user may modify the experiment data. DEARCHIVING TO DISK FILE by one
user followed by ACCEPTing ARCHIVED DATA FROM FILE by another user effectively
transfers ownership of the experiment data from one user to another.
User Input
Same inputs as for DEARCHTVE DATA TO DATABASES. The user also specifies output
drive and path for the dearchived data.
Processing
Same as DEARCfflVE DATA TO DATABASES, but an output file similar to the one created
when exporting data is created and placed on the user specified drive and path. Data is NOT
added to dearchivmg user's databases, but is deleted from archive file and from archived
experiments list. The created output file has the only data for the dearchived experiment. The
naming convention for this output file is as follows:
eeeeeeee.ffX where
eeeeeeee are the first 8 characters of the experiment name.
ff are the 9th and 10th characters of the experiment name.
X is a literal value appended to the experiment pame to
indicate that this file contains archived experiment data.
Note: If an experiment name is less than 10 characters, the filename will be shortened
accordingly with an "X" still appended to the end (e.g., an experiment name of CSCT910001
will yield a filename of CSCT9100.01X, while an experiment name of TEST will yield a
filename of TESTX).
Output
GeneTox Manager informs the user when decompressing data, and if errors occur. An output
disk file containing experiment data is created.
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Quality Control
The user is notified of any errors - invalid password; drive, path or filename or archive file
incorrect; output drive or path incorrect; experiment data not found in specified archive file; or
error during decompression.
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ACCEPT ARCHIVED DATA FROM FILE
This function allows the user to accept data into their databases that has been dearchived by
another user using DEARCHTVE TO DISK FILE.
PLEASE NOTE:
The accepting user effectively gains ownership of this experiment. The user may subsequently
modify the data for this experiment.
User Input
The user enters the experiment name, drive, and path for experiment data file. Data file will
have a filename of the format:
eeeeeeee.ffX where
eeeeeeee are the first 8 characters of the experiment name.
ff are the 9th and 10th characters of the experiment name.
X is a literal value appended to the experiment name to
indicate that this file contains archived experiment data.
Note: If an experiment name is less than 10 characters, the filename will be shortened
accordingly with an "X" still appended to the end (e.g., an experiment name of CSCT910001
will have a filename of CSCT9100.01X, while an experiment name of TEST will have a
filename of TESTX).
Processing
Experiment data file processed and data added to databases if format correct.
Output
The user is informed when processing data, saving data, or errors occur. A transaction log
is created. The transaction log has a DOS filename similar to the experiment data file but with
a "T" as the third letter of the extension.
Quality Control
User informed of errors hi drive, path, experiment data not found, or errors processing data
file. Specific errors are written to the transaction log.
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IMPORT SPIRAL ASSAY DATA
This function allows users who may be collecting data using a Spiral Biotech laser counter to
"import'1 this data into GeneTox Manager for statistical analysis. User must make the necessary
files available to GeneTox Manager. Two files are necessary for the data to be imported into
GeneTox Manager. Both files will have a filename equal to the name of the sample being
analyzed. The extension of the first file will be .ID; the extension of the second will be .PRN.
The first file is created automatically by the spiral program when the sample is entered; the
second must be explicitly generated by choosing Export Data from the spiral program menu.
Both must be available to GeneTox Manager before the import can proceed.
User Input
User enters the drive, path, and filename (minus extension) of the Spiral sample they wish to
import into GeneTox manager. User is then prompted for an experiment name and a sample ID
for the spiral data (along with other data required by GeneTox but not provided by the spiral
program) on the following screen:
GeneTox Experiment/Sample Data
Exper inert
Research 1
Sample ID
P Inuestic
Lab Book t
i
,ab :
fator. . :
lumber . :
Suggestion Box:
EXPERIMENT NAME
Format for Experiment Names is
AAAAVVNNNN
where A = any character,
!? = denotes the year, and
11 = is a unique number identifier
Fl:Help F2: Suggestion PgDn: Do Conversion ESC: Abort
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Processing
The spiral data is saved to the GeneTox Manager databases.
Output
N/A
Quality Control
GeneTox Manager verifies that the necessary files exist in the specified drive and directory
location. User is forced to enter data required by GeneTox Manager but not supplied by the
spiral data files. The experiment is added as a newly entered experiment, and the user has full
control of the imported data.
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REPORTS MENU
After selecting the REPORTS option from the MAIN MENU, the user will be presented with
the following screen. This function will allow the user to generate a Raw Data, Bernstein,
Histidine, Stead, or Quasi-Stead Model report.
(ieneTox Manager Main Menu
—i EPA Version i—
Enter/Mod ify Ut i1 ities
First Experiment Name..
Last Experiment Name...
First Experiment Date..
Last Experiment Date...
First Sample ID Number.
Last Sample ID Number..
Research Lab .
/ /
/ /
PgDn-To Continue uith Report Esc-Exit Reports
Gen Reports For The Genefox Manager System
User Input
The following fields are input for the REPORTS menu (at least one but any combination or
all of these fields can be used as selection criteria for the report):
First Experiment Name - first or only Session ID. As the first Session ID, the database is
searched from this ID, including any identical match.
Last Experiment Name - second Session ID, or the Session ID to search up to, including any
identical match.
First Experiment Date - first or only Experiment date. As the first Experiment date, the
database is searched from this date, including any identical match.
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Last Experiment Date - second Experiment date, or the Experiment date to search up to,
including any identical match.
First Sample ID Number - first or only Sample ID. As the first Sample ID, the database
searches from this ID, including any identical match.
Last Sample ID Number - second Sample ID, or the Sample ID to search up to, including any
identical match. '• *
Research Lab - Research Lab to match on.
After the first REPORTS screen has been completed, the following REPORTS screen will
appear:
Enter/Modify Utilities
:neTox Manager Main Hem
-1 In,
jports
Firs
Last
Firs
Last
Firs
Last
Rese
RAU REPORTS
Paw Data
STATISTICAL REPORTS
Bernstein Model
Histidine Model
Stead Model
Quasi-Stead Model
All Reports
/
/
Defaults Quit
—
1 i i
i i
Contains All Information
The following fields are input to this screen:
Raw Data - allows the user to execute a report based on the raw data contained in the database.
A new database query will be performed when this option is selected.
*** See Note Below ***
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Bernstein Model - allows the user to extract data from the PC database to execute the PC-based
Bernstein Model report. The report generates a point rejection/linear regression model The
query has already been performed for the databases.
Reference: Bernstein, L., Kaldor, J., McCann, J. and Pike, M.C. (1982) "An empirical
approach to the statistical analysis of mutagenesis data from the Salmonella test "
Mutation Research, 97, 267-281.
*** See Note Below ***
Histidine Model - allows the user to extract data from the PC database to execute the PC-based
Histidine Model report. The report generates a non-linear regression graph based on the dose
response data. The query has already been performed for the databases.
Reference: Krewski, D., Leroux, E.G., Bleuer, S.R. and Broekhoven, L.H (1993)
'Modeling the Ames Salmonella/Microsome Assay," Biometrics, 49, 499-510.
*** See Note Below ***
Stead Model - allows the user to extract data from the PC database to execute the PC-based
Stead Model report. The report generates a non-linear regression graph based on the natural log
of the dose response data. The query has already been performed for the databases
Reference: Stead, A.G., Hasselblad, V., Creason, J.P. and Claxton, L.D (1981)
Modeling the Ames test," Mutation Research, 85, 13-27.
*** See Note Below ***
Quasi-Stead Model - allows the user to extract data from the PC database to execute the PC
based Stead Model report. The report generates a non-linear regression graph based on the
natural log of the dose response data in a slight variation to the Stead model The auerv has
already been performed for the databases.
Reference: Creason, J.P. [personal communication].
*** See Note Below ***
All Reports - allows the user to execute every statistical report automatically Only the
statistical reports will be executed by this option. The selected data set is submitted to the
models and executed in consecutive order.
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*** NOTE ***
• Once a report type has been requested, the system will generate an output file containing
formatted information. The user will then be prompted for a desired output device. The
user may respond by pressing for the Screen, or by pressing the letter "S";
the Printer by pressing the letter "P"; or a File by pressing the letter "F" or by
highlighting the desired selection and pressing < RET >. If a File is chosen for output,
the user will be prompted for the appropriate filename(s).
• If Screen output is chosen, the information will be scrolled across the screen one page
at a time. Press < ENTER > to continue display of additional information to the
screen.
After directing output to the requested device, the user will be prompted again for the
destination of the output (Screen, Printer, or File). Thus, the user may continue to direct the
same output to other devices until pressing to exit the report function.
Processing
The REPORTS function provides the user with the ability to view the information contained
in the database. The. user has the option to direct the output to the Printer, the Screen or a File.
All queries are made against the PC databases, including the execution of statistical model
reports. The Bernstein and Stead models may also be executed on the VAX using data extracted
from the VAX FOCUS databases.
Outputs
Each report is output to the Printer, Screen, or a File.
Quality Control
All fields are validated. If an invalid entry occurs, the system will display an error message
and allow correction.
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DEFAULTS MENU
After selecting the DEFAULTS option from the MAIN MENU the user will be presented with
the following screen. This screen will allow the user to change the default settings for
Communication Setup, Screen Colors, Protocol File Name, Locate Databases, and other Special
Options. Each function is intended to allow the user to customize the system to individual
needs.
| Gen
i__L
GeneTox Manager Maim Menu
EPA Uersion i—
Enter/Mod ify Uti1 ities
Reports Defaults Quit
Connunication Setup
Modify Colors
Beset Colors
Protocol File Name
Locate Databases
Locate Archives
Set Special Options
Modify The Communications Setup
User Input
The following fields are input for the DEFAULTS menu:
Communications Setup - allows the user to select which type of communication option will be
used: 1200- or 2400-baud modem, terminal server, or PCSA.
Modify Colors - allows the user to customize any or all of the screen colors.
Reset Colors - resets the screen colors to the original colors.
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Protocol File Name - allows the user to choose which protocol file to use while entering an
experiment.
Locate Databases - allows the user to reset the location of application databases to a drive
and/or subdirectory other than the default.
Locate Archives - allows the user to reset the location of archive files to a drive and/or
subdirectory other than the default.
Special Options - password-protected options including: Password Changes, Suggestion box
Modifications, Principal Investigator List Modifications, Add or Modify Assay Type Selections,
Modify Iteration Count for Plates, and Help Text Modifications.
Processing
The DEFAULTS function provides the user with the ability to customize the system to
individual needs.
Outputs
Each function saves the default data to a file named XXXXXXXX.DFT, except for the
suggestion and location of databases functions. The suggestion box listing will be saved to a file
named SUGGEST.LST and the suggestion box help will be saved to an ASCII file named
SUGGEST.HLP.
For resetting the database locations, the system maintains a file called DRVPATH.MEM (hi the
application directory - normally \GENETOX) which defines the database locations. The user
has two options to reset the database location. The user can either use the Locate Databases
function under the Defaults menu pick or, if a database find error is occurring at start-up, the
user can erase the DRVPATH.MEM file and the system will re-prompt for the location of
databases. The same applies to the archive location, stored hi the file GTM ARCH V.MEM.
Quality Control
All fields are validated. If an invalid entry occurs, the system will display an error message
and allow correction.
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SPECIAL OPTIONS
The SPECIAL OPTIONS function of the DEFAULT menu allows the user to modify other
defaults. .This option is password-protected; when it is selected, the user is required to enter the
correct password before changes are allowed. After entering a valid password, the following
menu is displayed:
Enter/Modify U1
ly. _ u U • 1
« — | EPA Version
-llities1—
lenu
-I HfM
nej
torts Defaults Quit
Connunic
Modify C
Change Password
Suggestion Box Modifications
Principle Investigator List Hods
Re index/Clear Databases
Add/Hod if y flssay Type Selections
Modify Iteration Count for Plates
Enable Help Text Modifications
Flag Reset for Experiment Status
List flrchiued Experiments
Delete Experinent
:ation Setup
Colors
lors
File Name
atabases
rchiues
ial Options
Password Protected Options
CHANGE PASSWORD
After selecting the CHANGE PASSWORD option from the SPECIAL OPTIONS menu, the
user is allowed to change the GeneTox Manager system password.
User Input
The following fields are input for the CHANGE PASSWORD option:
New Password - the new password, at least six characters.
Verify Password - enter the new password again to verify.
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Processing
The CHANGE PASSWORD option allows the user to change the password needed to get to
the SPECIAL OPTIONS menu. This is a security measure against unauthorized changes being
made to the system. This password is also used to allow yAX version users to obtain statistical
model reports for data that has not been uploaded.
Outputs
The password needed for entry after choosing SPECIAL OPTIONS from the DEFAULTS
menu is changed.
Quality Control
The password must be at least six characters long. If the new password entered is not of this
length, an error message will result and the user will be prompted to enter it again. Also, the
password will be verified. If the same password is not entered hi the verification process, an
error will result.
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SUGGESTION BOX MODIFICATIONS
After selecting the SUGGESTION BOX MODIFICATIONS option from the SPECIAL
OPTIONS menu, the user will be allowed to make changes to any of the suggestion boxes that
appear on the screen.
User Input
The following fields are input for the SUGGESTION BOX MODIFICATIONS option. After
selecting a screen to edit, a message will appear informing the user that information for that
screen exists. The user will then be required to enter " Y" to continue editing the suggestion box
or to press any other key to return to the menu without editing. If "Y" is entered the next
prompt will be "Is this a selectable list?". Enter "Y" if it is or any other key to begin entering
the help text.
Experiment Description - allows changing suggestion boxes for: Entry Date, Experiment Date,
Research Lab, Lab Book Number, Experiment, Data Entered By, and Lab Technician.
Assay Type Selection - allows changing suggestion boxes for: Assay Selection and Modification
to Assay Type.
Final Strain Entry - allows changing suggestion boxes for: Strain, Strain Date, Activation
Level, and Culture Density.
Neg/Pos Control Entry - allows changing suggestion boxes for: Control Code, Control Name,
Amount for Plate, Control Unit, Plate Count 1-5, and Background Plate 1-5.
Activation System Information - allows changing suggestion boxes for: Characters 1-6 of the
S9 type, S9 Level 1, S9 Level 1 Units, S9 Level 2, S9 Level 2 Units, S9 Sterility Before, S9
Sterility After, and S9 Description.
Sample Specific Data - allows changing suggestion boxes for: Sample ID, Sample Description,
Source/Batch/Lot, and CAS Number.
Current Strain Selection - allows changing suggestion box for: Dose Units.
Quality Assurance - allows changing suggestion boxes for: Solvent Description, Solvent
Amount/Plate, Solvent Units, Hours Of Incubation, Phenocopy Check, Sample Sterility Before,
and Sample Sterility After.
Dose Data Entry - allows changing suggestion boxes for: Dose Amount, Plate Count 1-5, and
Background for Plates 1-5.
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Experimental Remarks - allows changing suggestion box for: Experimental Remarks.
Processing
The SUGGESTION BOX MODIFICATION option allows the user to modify all of the
suggestion boxes that appear on the screen. This allows very specific information and help to
be shown at the entry screen.
Outputs
The suggestion boxes on the screens will reflect the changes that have been made using this
option.
Quality Control
None.
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PRINCIPAL INVESTIGATOR LIST MODIFICATION
The PRINCIPAL INVESTIGATOR LIST MODIFICATION option allows the user to^add new
Pi's to the list or modify the ones already in the database.
User Input
The following fields are input for the PRINCIPAL INVESTIGATOR option:
Add Pi's to the List - allows the user to enter new PI names to the list.
Modify PI Listing - allows the user to edit the PI names already hi the list.
Processing
The PRINCIPAL INVESTIGATOR LIST MODIFICATION option allows entering new PI
names to the list or modifying the names currently hi the list. The MODIFY option brings up
the list of names already entered and allows the user to make changes to these names.
Outputs
The list of Pi's is modified and the changes are reflected during the data entry phase.
Quality Control
None.
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REINDEX/CLEAR DATABASES
The REINDEX/CLEAR DATABASES option will delete all experiment and sample records
from application databases and reindex these databases. Given the impact of this feature on
application data, the user is prompted with an ARE YOU SURE YOU WANT TO ERASE ALL
RECORDS message, which must be responded to with a Y for the function to continue. The
primary use for this feature would be to reset the environment after initial testing of the system
with test data or to reset databases that have become corrupted and the contents are non-
recoverable.
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ASSAY TYPE MODIFICATION
After selecting ASSAY TYPE MODIFICATION from the SPECIAL OPTIONS menu, the user
will be allowed to make changes to the Assay Type Selections.
User Input
The following fields are input to the ASSAY TYPE MODIFICATION screen:
Test Type Code Test Type Description
Time in Minutes Time in Hours
Temperature in Degrees C Temperature in Degrees F
Processing
To modify an existing assay, highlight the correct assay to modify by using the arrow keys and
then press < SHIFT > . This will bring up the existing data and allow modifications.
To add a new assay, press < F4 > and the same fields will be brought up, ready for new data
to be entered.
Outputs
The new assay types will appear on the ASSAY TYPE SELECTION screen.
Quality Control
All fields except for Test Type Description must be numeric. No other characters are allowed.
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MODIFY ITERATION COUNT FOR PLATES
The MODIFY ITERATION COUNT FOR PLATES option allows the user to redefine the
number of iterative plate count readings to be taken automatically from the Artek Colony
Counter, before calculating a median value and assigning that value in a plate count data entry
field. The default value is set to 3; other allowable values are either 1 or 5.
Note that the iteration count set by this option is only applicable when the user intends to
automatically collect plate count readings from the Artek Colony Counter (i.e., enabled by
having pressed and moving the cursor to a plate count data entry field).
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ENABLE HELP TEXT MODIFICATIONS
The ENABLE HELP TEXT MODIFICATIONS option allows the user to modify the help text
that appears on the screen when is pressed. The help text is brought up on the screen
and the user can make modifications.
User Input
The existing help screen is shown on the screen and the user can enter whatever is needed to
modify the existing screen.
Processing
The help text screen is modified.
Outputs
After successfully editing and saving the help text, the modified version will be shown on the
screen the next tune the key is pressed for help.
Quality Control
None.
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FLAG RESET FOR EXPERIMENT STATUS
This function applies only to the VAX Version of GeneTox Manager. Allows user to reset
status flags of experiment to "A" (Added, not yet uploaded) or "I" (Inactive, has been uploaded)
Status. Flags are automatically reset (to I) after a successful upload, but this function is
provided in case of unforseen errors.
User Input
Experiment name to reset and status code (A or I).
Processing
Status flags reset for all data associated with the experiment.
Output
None.
Quality Control
User informed if experiment does not exist or if flags cannot be reset. Status flags cannot be
reset on imported or downloaded experiments.
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LIST ARCHIVED EXPERIMENTS
This function allows users to view a list of experiments that have been archived from their
databases. The list contains experiment names and passwords, and can reveal additional
information including .archived location (drive, path, and filename) and archive date. Entries
are automatically added to the list as experiments are archived and deleted as they are
dearchived.
The following screen is a sample display of additional information for an archived experiment:
Enter
Lis
Exper
TESTS
(PgDn>
p
Archive List
Exit
Previous Experiment
lltext Experiment
i
Setup
Name
ases
es
ptions
Password Protected Options
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DELETE EXPERIMENT
This function allows users to delete an experiment similar to the PC FUNCTIONS option
DELETE READ ONLY OR VAXDOWN but deletes regardless of the status of the experiment.
User Input
Experiment name to delete.
Processing
All data associated with the experiment is deleted from databases.
Output
None. .
Quality Control
User informed if experiment does not exist.
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QUIT MENU
After selecting the QUIT option from the MAIN MENU, the user will be presented with the
following screen. This screen will allow the user to Quit the GeneTox Manager system and
return to DOS or to Continue using the GeneTox Manager system.
GeneTox Manager Main Menu
—i EPA Uersion
Enter/Modify Utilities
'Reports
Defaults
Quit
Continue
Quit To Dos
Continue Using The GeneTox Manager System
User Input
The following fields are input for the QUIT option:
Continue - do not quit the GeneTox Manager system, continue with the established session.
Quit - quit the GeneTox Manager system and return to DOS.
Processing
The QUIT function provides the user with the ability to exit the system logically by closing all
files, databases, and indexes and by releasing all variables in memory. This is the only viable
way to exit the system.
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Outputs
None.
Quality Control
All fields are validated. If an invalid entry occurs, the system will display an error message
and allow correction.
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APPENDIX A
INSTALLATION INSTRUCTIONS
This appendix provides installation instructions for the GeneTox Manager system and describes
hardware configuration requirements for execution of the application. This appendix or similar
information is also included on installation diskettes as the README. 1ST file.
Please carefully read the instructions below before attempting to install the GeneTox Manager
system or executing it for the first time. This information is provided as a supplement to the
GeneTox Manager System Users Guide. If you have any questions on the installation process,
or on execution of the system, contact your local PC support service (or your local PC guru).
As a last resort you may contact Dr. Larry Claxton at MD-68A, HERL, U.S. Environmental
Protection Agency, Research Triangle Park, NC 27711.
1. This system will execute on AT-class, 386-class, 486-class (or compatible) PCs with the
following minimum hardware and software configuration:
i) 640 KBytes Random Access Memory (RAM)
*,** Note: At least 440K must be available for GeneTox Manager to execute
properly (i.e., any memory resident programs plus DOS must not take up any more
than 200K). The DOS CHKDSK command will identify how much free RAM you
have available on your system.
ii) A hard disk (or Bernoulli type removable disk) .with at least 1.55 Mega-bytes of available
memory to accommodate system and data files.
iii) MS-DOS version 3.3 or higher.
iv) The following additional hardware and software is recommended to increase GeneTox
Manager system performance:
a) Expanded Memory - The availability of expanded memory for use by GeneTox
Manager will greatly increase system performance. The memory manager used
must conform to LIM EMS 3.2 or higher specifications.
b) Math Coprocessor - A math coprocessor is recommended to decrease the
execution time of the statistical models included with GeneTox Manager.
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Unless you provide a special justification, the installation diskette will be a 3 1/2" High
Density (1.44 Mbyte) diskettes (Quantity 1).
With special justification and depending on your PC configuration, the following
installation diskettes are available to you in one of three forms as listed below:
i) 5 1/4" High Density (1.2 Mbyte) diskette, s (Quantity 1)
ii) 5 1/4" Low Density (360 Kbyte) diskettes (Quantity 3)
iii) 3 1/2" Low Density (720 Kbyte) diskettes (Quantity 2)
Installation Process: Loading Files From Installation Disks
Your installation diskettes contain an automated, self-install program which you must
execute to load GeneTox Manager to your PC. DO NOT ATTEMPT to install this
application manually using DOS copy commands, as certain support files in specific sub-
directories will not be appropriately established with this method.
Rather, insert the installation diskette labelled Disk 1 into your PC and type INSTALL
to initiate the installation process. The system will notify you that it is loading
installation parameters and then prompt you for your preferred location for application
executables and for application databases. Note that default locations are \GENETOX
for application executables and \GENETOX\DBASE for application databases. If you
enter a sub-directory location that does not currently exist, the program will attempt to
create it for you. If it cannot create it, and you have trouble creating the desired sub-
directories yourself using DOS, contact your local PC support person.
Note that at least 1.5 MBytes must be available for loading application executables and
500 KBytes for loading application databases.
Once sub-directory locations are established, the program will copy the contents of Disk
1 to your hard disk. At the conclusion of this step, the program will prompt you to
remove Disk 1, insert Disk 2 into the drive and press < ENTER> to continue. Upon
copying the contents of Disk 2, you will follow a similar procedure for Disk 3 if
necessary. Finally, you will be instructed to re-insert Disk 1 to handle installation
program close-out.
At the conclusion of the installation, the program will place you in the application sub-
directory in preparation for execution of GeneTox Manager.
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Installation Process: Setting DOS attributes for GeneTox Manager
I
Two of the DOS related files on PCs which control system operation are the
AUTOEXEC.BAT file and the CONFIG.SYS file. For proper execution of GeneTox
Manager, minor additions/modifications must be made to both of these files as listed
below:
i
CONFIG.SYS- files and buffers must be set to at least the following values for
execution of GeneTox Manager
FILES = 55
BUFFERS = 20
If the above two lines are not already in your current CONFIG.SYS file, add them.
If the two lines are already in your CONFIG.SYS file, make sure that they are set to
values at least as high as those listed above.
AUTOEXEC.BAT- a Clipper environmental variable must be established to identify &
number of file handles to allocate. Add/Edit the following line in this file:
SET CLIPPER=F:55
** NOTE: For these settings to take effect after editing the above named files, the PC
must be re-booted (either via a Cntl-Alt-Del or "shutting off/then back on" the PC).
To execute GeneTox Manager, change directories to the sub-directory containing
GeneTox Manager executable files, type GTM and press the < ENTER> key.
You. must set at least one special option before entering data into the system the first
time. That is, you must register the initials of a Principal Investigator. See the "Special
Options-Principal Investigator" section of the Users Guide for further information on this.
*** Note: To execute any Special Option, you must enter a valid password. The initial
password' is GENETOX. Note that the password field is case-sensitive.
On-line help is available for the system by pressing the Fl function key. Specific
suggestion values are also provided for most data input fields.
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APPENDIX B
j GENETOX MANAGER TROUBLESHOOTING
This appendix explains what to do if problems occur that cause the system to crash or
lock up. These procedures should be followed after a system crash to insure as little data loss
as possible and mat further system problems are avoided.
If a system error occurs you will be presented with a system error message: A red box
with a line of text describing the error and a list of choices below. Choices may include Quit,
Retry, and Ignore. The Quit option will be highlighted. Choosing the Quit option will halt
system execution at the point of the error and return you to the DOS prompt. It should be
selected if choosing Retry does not work. The Ignore option may produce unpredictable results
and is not usually available.
If the error occurs during printing, the error message will come from DOS. It will say:
Write fault error writing device LPT1
Abort, Retry, Ignore, Fail?
Your printer may be turned off, off-line, or out of paper. In this case, fix the problem with the
printer and press R. Provided the problem has been fixed, the program should proceed
normally. Choosing Abort will return to GeneTox -without halting execution of the program.
Similar problems may occur when accessing a floppy disk drive.
If the error is an "Open error: PATHNAME FILENAME.EXT (DOS Error 2)",
GeneTox could not find a particular file it was looking for. It will tell you the name of the file
that is missing (FILENAME.EXT) and where the file should be (PATHNAME). Check that
directory for the specified file. It may not have been copied from the installation diskettes, or
it may have been inadvertently deleted from the hard disk. You may try copying the file
manually from the installation diskettes.
If the error is an "Open error: PATHNAME FILENAME.EXT (DOS Error 4)",
GeneTox tried to open too many files at once for DOS to handle at its current setting. Check
to make sure that the AUTOEXEC.BAT and CONFIG.SYS files were altered as described in
Appendix A. Remember to reboot your machine after modifying these files.
Other errors are most likely caused by interaction between GeneTox Manager and other
software running simultaneously or by bugs hi the system itself. Chances are the error is not
recoverable, and the only option will be to choose Quit (or reboot the machine hi the case of the
system locking up). Choosing the Quit option will cause GeneTox to abort execution and return
to the DOS prompt. The following procedure should be followed before restarting GeneTox
Manager.
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Any time the system has a non-recoverable error, check for the existence of any left-over
temporary files. Temp files have filenames of random letters and numbers, usually starting with
0 or 1, and having no extensions (e.g. Ola23e42). GeneTox creates and deletes these files to
do work while sorting and indexing databases. If the system crashes, GeneTox may not be able
to properly delete these files. Left-over temporary files may interfere with GeneTox and cause
further problems. These files should be deleted before restarting GeneTox. These temporary
files will reside either hi the same directory as the GeneTox executable files (i.e., the directory
you start GeneTox from by typing GTM) or in the root directory of that drive. NOTE: Be
careful when deleting these temporary files. Other programs may create files in this manner and
may use them for other purposes. Check the date/time stamp on these files to see if they were
created while GeneTox was running before deleting them.
When restarting GeneTox after a crash, it is always a good idea to first reindex the
databases using the Reindex option under the Utilities/PC Functions menu. If you were entering
or modifying data when the system crashed and had not saved that data, it will be lost. Check
your Experiment's raw data report to find out what previously entered data has been saved.
Unsaved data will have to be re-entered.
If the system "locks up" frequently, attempt to determine if other programs running
concurrently with GeneTox Manager are the cause. Remove the statements that load unneeded
memory resident programs and device drivers from your AUTOEXEC.BAT and CONFIG.SYS
files and reboot your machine. If this solves your problems, you can begin adding the programs
one at a tune until the problem reappears. You will then know which program or device driver
conflicts with GeneTox Manager, and you can arrange to remove it from memory when running
the GeneTox Manager application.
One conflict that system managers need to be aware of involves running GeneTox from
a network drive or with the DOS SHARE utility installed. The SHARE utility provides file
locking and sharing from DOS and is used hi some DOS network or multitasking situations.
Because GeneTox Manager was not designed as a multiuser application, this will cause conflicts
when opening database files. Typical messages that might occur would say "ALIAS DOES NOT
EXIST: " and give the name of a database file that could not be successfully opened (i.e.,
Experiment or General). The only available option will be to Quit to DOS. This problem will
only occur when attempting to Modify, Export, or Archive data. Data Entry and Reporting will
be unaffected by the problem. The only solution available is to not load the SHARE.EXE
program when starting your system or to move GeneTox Manager to a non-network drive (the
program and database files should not be run from a network file service).
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APPENDIX C
SYSTEM UPGRADE TO VERSION 2.2
Version 2.2 Changes:
The GeneTox Manager version 2.2 has had changes made to the underlying database
structures and for that reason a special set of Upgrade diskettes are provided for updating your
current databases to the new format. The upgrade will also make any necessary changes to
convert from GeneTox version 2.1 to 2.2. Upgrading from version l.X or 2.0 to 2.2 will
require a separate set of Installation diskettes to "reinstall" the new version.
The database changes involved moving several data fields from Sample information to
Experiment Specific Sample information. The fields Solvent Description, Solvent Amount,
Solvent Units, and Incubation Hours were the fields changed. This change means that this
information may now be entered distinctly for each sample analyzed under each experiment
strain. Previously, changing this information when re-using a sample in a second experiment
would also change the solvent and incubation hours information under the first experiment as
well.
The only observable changes to the system involve the data entry and modification
screens. In particular the solvent amd incubation hours fields have been moved from the Sample
Specific; screen (the screen where you enter Sample ID and Description information) to the
Quality Assurance Checks screen (where you enter the phenocopy and sample sterility
information). This is to allow entry of the information for each sample strain combination.
The Upgrade program provided will convert your databases to the new format. The
program will simply copy the information from the samples it is currently stored with to the
experiment specific sample data. Therefore the solvent and incubation hours information will
still be the same for each experiment the sample was used in, but you may now alter the data
under each experiment individually without affecting other experiments hi which the sample was
used.
The Upgrade program will not alter your current data in any respect. However to
provide maximum safeguards against data loss, the Upgrade program retains backup copies of
the current databases and executables to enable you to recover to the current version of the
system should there be any problems encountered during upgrading. You are advised to obtain
several "sample" raw data reports and then rerun these reports under version 2.2 to verify your
actual data has not been changed. Should you need to restore to the old version use the
GTMRest program provided.
The GeneTox Manager User's Guide has been updated to reflect these changes, and a
new copy is included with your upgrade diskettes.
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Upgrade Procedure:
The number of Upgrade diskettes is dependent on the type of floppy drive available on
your system. If you have high-density drives (either 5-1/4 or 3-1/2) you will have only one
diskette. If you have a low density 3-1/2 inch drive you will have 2 diskettes. If you have a
low density 5-1/4 inch drive you will have 3 diskettes.
To upgrade from version 2.1 to version 2.2, simply insert the disk marked Disk #1 of
the Upgrade diskette set and type UPGRADE. This will start the automated Upgrade program
provided to update both system executables and databases. The Upgrade program will prompt
you for the location of the GeneTox Manager executables and databases (defaulting to
C:\GENETOX and C:\GENETOX\DBASE respectively). You must have enough space on the
disk drive for the backup of current databases and executables for the upgrade to proceed (about
1.2 Megabytes of free space).
(JJ
The upgrade will take approximately 15-30 minutes.
Restoration Procedure:
To restore to the old version after an upgrade, simply type GTMRest .while hi the
directory you normally run the GeneTox Manager from by typing GTM. Provide the program
with the location for the GeneTox Manager program and Databases as you did hi the Upgrade
program.
WARNING: GTMRest restores from backups saved from before the upgrade was 01
If you have entered or modified any data since the upgrade was run this data will be lost!
Cleanup Procedure:
Two DOS batch files are provided to "clean up" your GeneTox disk after a successful
upgrade. They are called CLEANUP1.BAT and CLEANUP2.BAT and are located hi the
system executables and database directories respectively.
Together they DELETE the backups that allow you to restore to the old version of
GeneTox Manager. This will free up the 1.2 Megabytes of disk space the Upgrade program
used to backup the old system.
To run these cleanup programs change to the system executables directory (e.g.,
C:\GENETOX) and type CLEANUP1. After this finishes change to the database directory
(e.g., C:\GENETOX\DBASE) and type CLEANUP2.
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WARNING: This permanently DELETES the backups saved from before the upgrade
was run. You will NOT be able to restore to the old version after running either of these files.
Upgrading From Version l.X or 2.0:
This section covers upgrading from GeneTox Manager versions prior to version 2.1 to
2.0. This is somewhat more complicated. In this case a separate set of Installation diskettes
will be provided hi addition to the Upgrade diskettes. The procedure is basically to backup to
current databases, "install" a new version complete with empty databases, restore the databases
from the backups, and then run the Upgrade program to convert to the 2.2 database formats.
Very carefully observe the following instructions.
First we must backup the current databases to retain your data (this is because the
installation program "installs" the databases as well, and will overwrite the current ones with
empty databases). Two procedures are recommended for this: you may use the DOS backup and
restore utility (this is especially helpful if you wish to backup to floppy diskettes); or you may
simply create a new directory to hold your backup databases (e.g., MD (make directory)
C:\GENETOX\OLDDBS) and copy all the files in database directory to the backup directory
(e.g. COPY C:\GENETOX\DBASE\*.* C:\GENETOX\OLDDBS).
Once the data are saved, simply run the installation program provided on Disk #1 of the
Installation diskette set. After the installation is complete, you can restore your data from the
backups (e.g. COPY C:\GENETOX\OLDDBS\*.* C:\GENETOX\DBASE). Then execute the
new version of GeneTox Manager (by typing GTM) and choose "Reindex GeneTox Manager
Databases" from the Utilities-PC Functions menu. Finally you must run the Upgrade program
to convert to the new database format.
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APPENDIX D
COLONY COUNTER INTERFACE
A serial interface is required between the Artek Colony Counter and IBM AT-class PCs running
the GeneTox Manger system.
The interface will require the following hardware:
ARTEK COUNTER - Model 880
Omni-Interface Unit from ARTEK Systems Corporation
Dip Switch settings: 12345678
Bank 1 00100000
(nearer shell) Bank 2 11100110
Serial port interface from PC to Omni-Interface box
Parallel interface from Omni-Interface to ARTEK Counter
User Interface will operate as follows:
1) User will press key < F5 > to toggle communications (enable/disable) to the colony counter.
This key may be depressed to toggle the setting on the Negative/Positive control screen ard
on the Dose data entry screen.
2) Default reading iterations per plate will be set to 3. A password-protected function under
Special Options of the Defaults menu will allow the user to override the reading iterations
at either 1 or 5 per plate. The current setting for iterations per plate will be displayed on
screens with plate data entry (i.e., the Negative/Positive control screen and the Dose data
entry screen).
3) Collecting plate count data from the colony counter will only occur when the cursor is
positioned on plate count fields hi the Negative/Positive control screen and the Dose data
entry screen.
4) For each colony count reading, the user must first press the < COUNT > button on the
ARTEK counter, which will register a plate count in the red LED display area on the
counter. The user must then press the < PRINT > key on the Omni-Interface box to send
the plate count reading down to the PC. NOTE: This plate reading will only be
acknowledged by GeneTox Manager if the cursor is currently in a plate count field of either
the Negative/Positive control screen or the Dose data entry screen.
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Each of the individual readings for a plate count will be displayed hi a window on the
GeneTox Manager data entry screen when the required number of iterative readings have
been sent to GeneTox Manager from the colony counter (i.e., 1, 3 or 5), the system will
select the median value and place it hi the plate count data entry field. The cursor will tax
be forwarded to the next plate entry field, or the next dose line (if previously on the 5th
plate count)-just as is the case when a user manually enters a plate count.
5) The user can control data collection when hi the Instrument Enable mode with the following
keys:
pressing this key when hi instrument read mode will toggle the system out of
instrument read mode and retain the previous value for the plate count data
entry field (i.e., any iterative readings for this plate count will be ignored).
the system will ignore any iterative readings for this plate count and assign a
-1 for the plate count.
< E S C
the system will ignore any iterative readings for this plate count and proceed to the
data entry field.
>
next
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APPENDIX E
KNOWN PROBLEMS AND LIMITATIONS
1. GeneTox Manager will not save Strain information to the databases unless at least one
Sample has been entered for that Strain. GeneTox Manager will warn the user if Samples have
not been analyzed under all Strains when choosing "Save Data and Exit" from the Continue
Screen.
2. No replication of Samples is specifically provided for hi GeneTox Manager (i.e., you can
not run multiple instances of the same Sample in the same Experiment under the same Sample
ID). You must enter the information as either two different Sample ID's, or as two entirely
different Experiments.
3. You. cannot delete Positive or Negative Control information once it has been entered. You
can, however, delete a Test Dose by entering 0.0 as the Dose Amount and saving the Dose
Response.
4. The Defaults menu option "Communications Setup" was never fully implemented and its
setting has no effect on system behavior, even on VAX versions of GeneTox Manager.
5. Version 2.2 of GeneTox Manager is NOT network compatible. No code exists to manage
multiple user accesses to network copies of the databases. It can run on networked PCs
provided it resides on the hard drive of the workstation it will be used on, and it is accessed by
only one user at a time. Attempting to install and run the GeneTox Manager System hi a
networked environment (i.e., making one copy of the system/databases available to multiple
users) will most certainly cause severe problems.
6. There is currently no way (within the system) to get printouts of the screen output displayed
by the statistical models. Users can, however, use memory resident screen grabber programs
loaded before running GeneTox Manager, to capture these screens for later use hi documents.
[NOTE! Using the DOS PrintScreen key will not produce a printout of the graphic image.]
To do this using WordPerfect, first load the screen grab utility (GRAB.COM). [NOTE!
Loading this utility reduces the amount of memory available for GeneTox Manager. If you have
a limited amount of memory available on your system, GeneTox many not execute properly with
this utility loaded.] Once the utility is loaded, run GeneTox Manager as normal. When the
statistical model has displayed the screen you wish to capture, press < ALT > < SHIFT > < F9 >
and them < ENTER > to activate the grab program. A box will appear on the screen. Use the
< SHIFT >-arrow keys to size the box, and the key to toggle between fine/coarse
increments. Press < ENTER> to capture the screen area inclosed by the box. The image will
be saved to the file GRAB.WPG. Subsequently captured images will be saved to files named
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GRAB!.WPG. .GRAB999.WPG. These captured images are saved as WordPerfect graphic files
and may be printed using WordPerfect 5.0 or above. [NOTE! The captured image will be in
color.]
7. The behavior of the GeneTox Manager program can be dependant on the other software
(TSRs and device drivers) which are running on the system. One example current users have
noticed is that GeneTox Manager will not operate properly while the DOS SHARE utility is
resident hi memory (see Appendix B: GeneTox Manager Troubleshooting). Some portions of
the GeneTox Manager program may operate correctly under certain circumstances, while other
portions produce apparently unrelated errors. For example, attempting to use GeneTox Manager
with the SHARE TSR produces file opening errors when attempting to open certain database
files.
8. GeneTox Manager will probably not be executable or perform correctly when run from
certain shell or menuing software due to the reduced memory available to GeneTox Manager.
For performance concerns and to prevent errors and data loss that could result when GeneTox
Manager runs out of memory under these circumstances, it is recommended that GeneTox be
run from the DOS prompt or from a menuing system such as AutoMaxx, which does not stay
resident while called programs are executing. Attempting to use GeneTox Manager from
Windows (as a DOS application) or from DOSShell is at the user's risk. GeneTox Manager has
not been tested under those environments, and performance is certain to be degraded.
NOTE: See also Chapter 8 of the GeneTox Manager Programmer's Guide,
"Possible Enhancements" for details on correcting these and other
problems with GeneTox Manager.
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