United States
Environmental Protection
Agency
Office of Research and
Development
Washington DC 20460
EPA/600/R-94/032
March 1994
GeneTox Manager
System
User's Guide- VAX
Component
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EPA/600/R-94/032
March 1994
GeneTox Manager System
(GENETOX)
USER'S GUIDE
VAX Component
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
Ms. Debbie Pendretti and Mr. Joe Nader
Computer Sciences Corporation
4401 Alexander Drive
Research Triangle Park
North Carolina 27711
Prepared Under
Contract # 68-01-7365
June 1993
Version 2.0
Printed on Recycled Paper
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PREFACE
This User's Guide is the reference manual describing use of the GeneTox application
under! the VAX/VMS operating 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
whilel a]lso 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 infonnation and provides
unifojm 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.
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.]
Secordly, 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 FOCUS® could provide additional help and programming options for you.]
scienl
We sincerely hope that this software will be useful to you and will aid you in your
tjfic 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 Houk, 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, arid Dr. A.
Stead. If you use information from these statistical programs, we hope that you will give
proper acknowledgement 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 ifpr 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 documenthas 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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TABLE OF CONTENTS
I
j
PREFACE i
!
ACKNOWLEDGEMENT . ii
NOTICE : ii
LIST OF FIGURES v
I
t
1.0 INTRODUCTION 1
1.1 Intended Audience 1
1.2 Document Organization , 1
1.3 Documentation Conventions 2
1.3.1 Command Syntax Conventions 2
1.3.2 Keyboard Notations 3
1.3.3 Representation of Terminal Displays . 3
1.4 Associated Documents 3
2.0 OPERATIONAL OVERVIEW 5
i 2.1 Accessing the GeneTox Application 5
i 2.1.1 Logging on the VAX 5
I 2.1.2 Defining the GeneTox Environment
j for a Specific VAX ID .'...; 5
i 2.1.3 Invoking the GeneTox Application 6
I 2.2 User Interface 7
i 2.2.1 Menu-Driven Operation 7
| 2.2.2 Termination 7
j 2.3 Function Options 7
3.0 FUNCTION DESCRIPTIONS 9
! 3.1 LOAD Option 9
j 3.2 DOWNLOAD Option 10
| 3.2.1 User Input 10
j 3.2.2 Processing 10
| 3.2.3 Outputs 11
; 3.2.4 Quality Control 11
! 3.3 UPDATE Option 11
I 3.4 REPORT Option :' 11
j 3.4.1 User Input 12
| 3.4.2 Processing 13
I 3.4.2.1 Statistics Report Format 14
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3.4.2.1.1 Model Input Data to a File 14
3.4.2.1.2 Model Input Data to a Screen 15
3.4.2.1.3 Model Input Data to a Printer 15
3.4.2.1.4 Statistical Models Executed 15
3.4.2.1.4.1 User Input 15
3.4.2.1.4.2 Processing 16
3.4.2.1.4.3 Outputs 16
3.4.2.1.4.4 Quality Control 17
3.4.2.2 Inventory Report 17
3.4.2.2.1 User Input 17
3.4.2.2.2 Processing 18
3.4.2.2.3 Outputs 18
3.4.2.3 Raw Data Report • • • 19
3.4.2.3.1 User Input 19
3.4.2.3.2 Processing 19
3.4.2.3.3 Outputs 19
3.4.2.4 Summary Data Report 19
3.4.2.4.1 User Input 19
3.4.2.4.2 Processing 19
3.4.2.4.3 Outputs 20
3.4.3 Outputs 20
3.4.4 Quality Control 20
3.5 HELP Option 2JJ
3.5.1 User Input 20
3.5.2 Processing • 2^
3.5.3 Outputs 20
3.5.4 Quality Control • 21
3.6 EXIT Option 21
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LIST OF FIGURES
Figtire
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
2-1. Main Menu Screen 6
3-1. Download Selection Screen 10
3-2. Report Screen #1 12
3-3. Report Screen #2 13
3-4. Report Screen #3 14
3-5. Statistics Screen #1 14
3-6. Statistics Screen #2 15
3-7. Statistical Model Selection Menu 16
3-8. Stead Model Output Media Prompt 17
3-9. Bernstein Model Output Media Prompt 17
3-10. Report Screen #4 18
3-11. Report Screen #5 18
APPENDICES
Appendix A - Extract File via the Statistics Report
Appendix B - Sample Output from Stead Model
Appendix C - Sample Output from Bernstein Model
Appendix D - Inventory Report Example
Appendix E - Raw Data Report Example
Appendix F - Summary Report Example
Appendix G - GENETOX MANAGER Transfer File Format Specifications
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1.0 INTRODUCTION
The GeneTox Manager System has been developed for the Health Effects Research Laboratory
(HERL) of EPA in Research Triangle Park, North Carolina for the purpose of systematizing
the| collection of experimental results of In-Vitro tests run by the EPA Genetic Bioassay Branch
and their contractors.
A pries of computer programs has been written to allow for verification of experimental
results, statistical analysis of data, and reports of raw data collected. The GeneTox Manager
system is comprised of several different programs on two different computer systems The data
acquisition program uses dedicated PCs connected to laboratory equipment to collect the
In-Vitro data. The FOCUS data base and report generation programs iare located on the VAX
Cluster. Programs for statistical analysis and graphic output of the In-Vitro data are also
located on the Cluster and can be accessed from the FOCUS program.
Thi|s User's Guide covers the use of the FOCUS GeneTox system and the statistical programs
that; reside on the VAX Cluster system called VAXTM1. The PC programs for GeneTox
Manager are discussed in a User's Guide for GeneTox Manager on flic PC; Appendix G of
this, document provides a description of file formats used in transferring data between the PC
and the VAX.
1.1 [Intended Audience
I
I i
This manual is intended for all users of the application. The user community consists of
laboratory technicians responsible for the collection of experimental results of In-Vitro tests run
by the EPA Genetic Bioassay Branch and their contractors.
Accpss to the application is restricted. The GeneTox Application Manager is responsible for
the [operation and maintenance of the GeneTox application. System identifiers and Access
Control Lists (ACLs) have been established to grant the GeneTox Application Manager
administrative authority.
1.2 Document Organization
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Sectjion 1 provides an overall introduction to facilities offered by the application.
I
Section 2 describes how to access the application and how the user interacts with the
application.
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Section 3 is arranged in sections organized by the commands available to the user- LOAD
UPDATE, REPORT, STATISTICS, HELP, and EXIT. '
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Appendix A provides an example of a data base extract file generated for input to statistical
model runs.
Appendix B provides an example of the report generated by the Stead Statistical Model.
Appendix C provides an example of the report generated by the Bernstein Statistical Model. ,
Appendix D provides an example of an Inventory Report.
Appendix E provides an example of a Raw Data Report.
Appendix F provides an example of a Summary Data Report.
Appendix G provides the detailed file specification for transfer files used to migrate experiment
data between the VAX and PCs.
1.3 Documentation Conventions
The following conventions are used hi this manual.
1.3.1 Command Syntax Conventions
Typically the user will enter a value on the command line to indicate the action to be
performed. This manual uses special conventions and symbols to describe correct usage of the
command components.
UPPER CASE letters indicate characters that must be entered as they are shown. Where
abbreviation of command components is allowed, the shortest form will be indicated in
uppercase with the remainder in lowercase.
Lower case letters indicate general terms to be replaced by specific names or values.
Braces ( { } ) denote one or more required components. If more than one component is
enclosed in braces, one (but no more than one) must be chosen.
Brackets ( [ ]) enclose one or more components that are optional. If more than one component
is shown, one or none of the components may be selected.
Angle brackets ( < > ) enclosing a word indicate the component is common to several
commands.
Ellipsis (...) indicate that the preceding component may be repeated.
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1.3.2 Keyboard Notations ;
i • ;
The following special terminal keys are referenced:
< keyname > refers to special keys indicated by inclusion within angle brackets. Examples:
, .
refers to the carriage return, or RETURN, key. concludes all operator
responses.
is the control, or CTRL, key. This key is often used in conjunction with other
ke^s. The symbol < CTRL/key > indicates that CONTROL and another key should be entered
simultaneously.
indicates the TAB key, or < CTRL/I > on terminals without a TAB key.
1.3.3 Representation of Terminal Displays
In |this manual, the terminal displays produced are indicated hi exactly the form as seen by the
operator and are indented from the surrounding text. The underscore ( " _ " ) indicates a
position at which the operator is expected to enter information.
i
1.4 Associated Documents
I [
GelneTox software on the VAX is a component of the total GeneTox Manager application.
This manual deals only with the components that reside on the Cluster VAX computer system.
Thjese components consist of the data base storage of test results data and the reporting and
processing of this data. The data input portion, which resides on the PC, is referenced hi
Appendix G and hi other documents as detailed therein.
The system that supports GeneTox is Digital Equipment Corporation's (DEC) VAX computer.
'introduction to VAX/VMS' is a DEC manual that describes the VAX/VMS operating system
and the use of the command language. This manual is recommended for users who lack
experience with interactive computer systems or users new to the VAX/VMS environment.
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2.6 OPERATIONAL OVERVIEW
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Trie GeneTox application is installed in a production directory on the VAX Cluster. This
section provides detailed information on the procedures for accessing the GeneTox application.
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2.1 Accessing the GeneTox Application
This section describes the procedures for logging on to the VAX, establishing a set of
commands that define the GeneTox environment (a one-time effort), and invoking GeneTox on
an; ongoing basis.
2.1.1 Logging on the VAX
i
The user may log on to the host computer in one of two ways. One method is for the user to
log on independent of the GeneTox Manager system (standard logon process from a DEC
terminal or a PC to the VAX). For detailed information on this method of access to the
computer, refer to the VAX User's Guide. The second method is for the user to log on to the
VAX via a menu option from the GeneTox PC application. Details for this method can be
found in the GeneTox Manager User's Guide for the PC.
2.1.2 Defining the GeneTox Environment for a Specific VAX ID
i
Injorder to access GeneTox, there are two items related to the user's VAX ID that must be
completed. The first of these is the allocation of an appropriate GeneTox Access Control List
(ApL) entry for" the user's ID. See the GeneTox Application Manager for issuance of a
GejneTox ACL for your VAX ID.
i ;
Thje second item is the definition of VAX 'Symbols' and 'Logicals' on the user's ID that are
specific to GeneTox. (An understanding of 'Symbols' and 'Logicals' is not required, but the
user may reference VAX documentation for further information on these constructs if desired.)
Upon logon to the VAX, the system will check a file called LOGIN.COM for initialization of
the user environment. The following two commands must be added to the user's LOGIN.COM
file (or a .COM file called by LOGIN.COM) in order to initialize the; GeneTox environment
for the user.
| (1) The following command invokes a .COM file that will establish required
GeneTox logicals:
@$2$DUA90: [IN VITRO] GTMSET
(2) The following command establishes a symbol for invocation of GeneTox:
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GENETOX: = = "@GTM$SYS:GENETOX"
To define a printer to accept GeneTox output, include the following command as well:
DEFINE GTM$SYS$PRINTER pppppp
where:
pppppp is the name of a printer defined on the VAX network
From this point forward, this manual assumes that the user has logged on to the VAX.
2.1.3 Invoking the GeneTox Application
After logging on to the VAX computer, enter "GeneTox" at the DCL prompt ($). to start«the
application. (Moving into a separate subdirectory (SET DEFAULT) before initiating this
application will isolate print listings and various work files that the application will produce
from outputs from other programs or tasks.)
$ GeneTox < RET >
The GeneTox Main Menu is then displayed on the screen. The main menu presents a list of
options and corresponding functions; a function is selected by entering the appropriate letter
at the command prompt.
f* e
'F>C
Figure 2-1. Main Menu Screen
The user invokes the desired option by entering the first initial of the particular function. Each
function has an associated menu (see Section 3).
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i
2.2 User Interface
! ;
Input screens allow the user to enter GeneTox options and data. The screens have been
implemented with the following design:
i
• | The key allows the user to move from one input field to another.
i
• I The key submits an entire input screen, at which time validation procedures
; are performed.
• ; The key cancels a transaction and returns the user to the next highest level
! menu screen.
!
1.2.1
Menu-Driven Operation
i
GesneTox provides menus that guide the user in operation of the application. Menu items are
identified by the first letter of the particular function. Each function provides its own menu,
with options to perform subsequent functions.
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2.2.2 Termination
i
There are several ways to terminate a GeneTox session. The recommended method is to select
the! main menu EXIT option. After pressing , the user is returned to the VMS
prompt.
A built-in feature of FOCUS enables the user to enter a to cancel an operation and
return to the FOCUS single prompt " >". The user then enters "FINI!1 at the FOCUS prompt
to terminate the session.
2.3, Function Options ;
i
Download - Module that extracts data for an experiment specified by the user from the VAX
GeneTox data bases and stores the data in a flat ASCII file on the user's VAX directory.
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Report - Module that produces output reports of current GeneTox data.. Four different report
formats exist: Statistical output, Inventory output, Raw Data output, and Summary Data output.
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Help - Module that displays further information on all functions and commands described in
this User's Guide.
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Exit - Exit GeneTox system and return to command line prompt ($).
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3.0 FUNCTION DESCRIPTIONS
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This section provides a description of each function offered by GeneTox. The following
conventions are common to all functions.
. i
1. 1 User input must be in upper case.
i
2. or null entry in response to any command line prompt will cause the prompt
| to be issued again with no action taken.
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3. For screens where the cursor has been left on a line below tabular displayed
| information, the user is required to enter selection values in one or more of the tabular
I fields.
• When all data for the screen has been entered, must be pressed to
process the entire screen. A < TAB > may be entered in any given field to
indicate no data or no action for that item (field); however, at least one value
must be entered per line of valid data entry.
• A < CR> on a line by itself will skip the command action for the current line
of data and either continue to the next item (or line of items) within the current
group or return to the command line prompt (if there are no more items for this
command).
• The word "END" entered on a line by itself will terminate the command action
for the current group or level within the current group.
Terminal display output may be temporarily suspended at any particular point by
touching the "Hold Screen" or "Scroll" key. Resume terminal display by touching the
key again. On older terminals, typing and provides this
XON/XOFF screen control.
3.1 LOAD Potion
Note:
This option is not currently available for use. Currently, the LOAD function
is initiated from the PC containing the required experiment data and control is
returned to the PC-based GeneTox application once the Load has been
completed.
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3.2 DOWNLOAD Option
This function allows the user to define a set of experiment data to be extracted from the VAX
data bases in a format in which it can be transferred to the PC. Upon selection of the
Download option, the following screen is displayed to the user:
Experiment
GENEIOX
•set'ecS".'pn?SCEeen:'::Hena?:
ssfi ifflRftfS
Figure 3-1. Download Selection Screen
3.2.1 User Input
The following field is input for the Download option:
Experiment Name - The 10-character name of the experiment which the user wishes to
download to the PC. An Experiment name does not have to be 10 characters in length;
however, the entire Experiment name must be provided.
The PF4 key may be pressed to abort execution of the Download option before leaving this
screen.
3.2.2 Processing
The system will search the GeneTox master data base for the requested experiment. If it is not
found, a message is displayed and the user is returned to the input screen to specify another
experiment name or exit the Download option.
If the requested experiment name is found, the system will proceed to extract all data pertaining
to that experiment and generate an ASCII file.
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3.2.3 Outputs
s
The extract ASCII file generated by this option has a default name of PCDOWN.VAX. The
sta'tus field in applicable records of this file has a value of 'V to indicate that this type of
extract file was a download from the VAX and will provide 'read-only' access to users who
loi
.d the file in their PC-based, GeneTox data bases.
When returning to the $ prompt in VMS, the user may make use of communication software
on the VAX and on the PC to transfer the file to the PC. If the user wishes to save the extract
file, PCDOWN.VAX, that was generated, it is recommended that the file be renamed since it
wiil be over-written the next time the user executes the Download option. It should be noted
that a VAX Download option may be initiated from the PC component of GeneTox, which will
automatically access the VAX, extract experiment data and retrieve the extract file to the PC.
f '
3.2.4 Quality Control
The system checks for the existence of the requested Experiment name hi the VAX data bases
before performing an extraction, and notifies the user with an error message if it cannot be
found.
3.3 UPDATE Option
Note: This option is not currently available for use. Currently, the Update function
I is initiated from the PC containing the required experiment data and control is
: returned to the PC-based GeneTox application once the update has been
; completed.
3.4 REPORT Option
i
Tliis function allows the user to report the In-Vitro experiment data in several different formats.
Trie formats are: Statistical Report, Inventory Report, Raw Data Report, and Summary Data
Report. Each of the formats is discussed in detail in the following sections.
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The Report option is selected from the main menu by entering an 'R' at the command prompt
an|d pressing . The following screen will be displayed.
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•; o.xv:::;;V:'x^x:x?S;;':':;;'SeleotJbn:xSpr;fien;:
Sampl e •..': IdentTf leati on
Researeh/xLalixib'^
Bacteria ::St rain
. Entervxvalue'aw: offy.
optional;
Between
Wm
te'Ssea'fcB:
pressv
&ta}ft;xhe.tpx
•,equi;re
ete:";
t) :an(c;
ranges
are'
Figure 3-2. Report Screen #1
3.4.1 User Input
The following fields are input for the REPORT Selection screen:
Experiment Name - The 10-character name of the experiment performed to obtain the data.
All 10 characters do not need to be filled in to select data to be reported. Any samples
containing the input characters will be retrieved for the report.
Sample Identification - The 10-character sample identification number that identifies the agent
being tested. A range of samples may be selected by entering both a beginning and ending
sample ID.
Experiment Date - The date the experiment was started. Use the standard Year-Month-Day
format to enter this date, for example: 890215. A range of dates may be used to select
samples for reporting by entering a beginning and ending sample date.
Research Lab ID - The 4-letter code from the table of valid research lab IDs that identifies the
organization to report. This identifies the group that conducted the experiment.
Test Type Code - The 2-digit code from the table of valid test types available. Up to five
different test type codes can be entered to select sample data for reporting.
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Babteria Strain - The 6-character strain abbreviation from the table of valid bacteria strains.
A total of seven different bacteria strains can be entered to select the sample data for reporting.
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Atj least one of the selection fields must be selected or the following error message will be
displayed:
******* PLEASE ENTER AT LEAST ONE VALUE TO TEST *******
Any number of selection fields may be entered; experiment data that meets all selection criteria
are reported.
i '
Hejlp may be obtained while completing this screen by pressing the NEXTJSCREEN keypad
key (PAGE DOWN on PC keypad.) The following screen will be displayed.
•^vXYlvlYXYXvX-lvX-:^^^
vX-XvX~vXX-X-X-X-XvX~-vX~^^
v:YXv:YXv>~£XYXYXvXy>XyXv^
v/Xvx:xv:^~x-x-x-x-x~vXv>/>>x-x^
vXvX-Xvx:x-x:x-XvX-XvX-Xv:v:-x^^^
vx:xo:v>Xv>:;x-x-xcv:v>x~x~vXoxBTOteE^^
X>X"X"X'X'X'X'X'X'X'X'X'X'X'X*X*X'X
-------
iiiS^
';ff^^^S^^^^j^jja^^Qfmi^^K^^:
Figure 3-4. Report Screen #3
The user may select one of the four report formats, return to the data selection screen, or
return to the mam GeneTox menu.
3.4.2.1 Statistics Report Format
This option allows the user to produce an extract of experiment data from the VAX data bases
in an output form that the statistical analysis programs can use as input for processing. The
user may direct output to any one of three output media (ASCII file, the terminal screen, or
a printer), or request the extract of experiment data and associated execution of the statistical
models. The following screen, which lists these statistical reporting alternatives, will be
displayed.
^^^^^f^mjmjMiiMM
WM^I^^f^^^K^M/^^^X<^M^M
'^MMoMl^rvi^j^a^^p^y^^^K^a^r^y.
''''^^'^^^^^^^•^^i^^^i^^'S^MSM.
y1VA\svAYT-GP^t"na'CG^RSppf*;tY |K&^
^
Figure 3-5. Statistics Screen #1
3.4.2.1.1 Model Input Data to a File
Upon selection of this option, the user will be prompted for a file name which will contain
extracted data. The following screen is displayed to the user:
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; Figure 3-6. Statistics Screen #2
Thje file name (and an optional file extension) must be specified to produce the file.
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3.4.2.1.2 Model Input Data to the Screen
Upon selection of this option, extracted data is displayed to the screen in model input form.
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3.4.2.1.3 Model Input Data to a Printer
Upon selection of this option, extracted data is routed to the system printer defined by the VAX
logical GTM$SYS$PRINTER. This logical definition is discussed above in Section 2.1.2.
3.4.2.1,4 Statistical Models Executed
I
Thjis function allows the user to execute statistical models that analyze experiment data
extracted from the VAX-based master data bases for GeneTox. The: two statistical analysis
programs currently supported on the VAX are the STEAD Model and the BERNSTEIN Model.
When selecting this option, both programs are executed - the STEAD Model first, followed by
the BERNSTEIN Model. Statistical and graphical analysis of experiment data are performed
by
the statistical models; output for this option is described below in the Outputs section.
3.4.2.1.4.1 User Input
Up|on selection of this option, the user will be prompted with the following screen to select one
or both of the available statistical models to run.
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^iMMMiMei^im^eMii^
^^^MM^^M^i^^^^^
Figure 3-7. Statistical Model Selection Menu
No user input is required to initiate processing of the statistical models. Data will be extracted
from the GeneTox data bases on the VAX according to selection criteria specified in the screen
described in Section 3.4 above.
3.4.2.1.4.2 Processing
In the first execution step for this option, data is extracted from the GeneTox data bases and
output to an intermediate ASCII file, MODEL.DAT. The second execution step invokes one
or both of the statistical models (according to the user selection), using the MODEL.DAT file
as input. Invalid data found hi MODEL.DAT may result in abnormal termination of the
statistical models.
3.4.2.1.4.3 Outputs
Under the first execution step of this option, a data extract file named MODEL.DAT, which
contains requested experiment data, is generated. An example of this extract file may be found
in Appendix A. This file serves as an input file to both statistical models, under the second
execution step of this option.
Output reports for the Stead and Bernstein Models are stored in default files
STEADMODEL.RPT and BERNSTEIN.RPT, respectively. After successful execution of each
statistical model, the user is prompted for an output destination for the report file to either the
screen or a printer, as shown below.
GeneTox Manager VAX User's Guide
Version 2.0
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:r:esui:ts
Figure 3-8. Stead Model Output Media Prompt
result's;:
Figure 3-9. Bernstein Model Output Media Prompt
I
i
Appendix B provides an example of a Stead Model report. Appendix C provides an example
of a Bernstein Model report.
3.42.1.4.4 Quality Control
Dalja is extracted from GeneTox master data bases on the VAX according to the selection
criteria specified on the screen listed in Section 3.4.
3.412.2 Inventory Report
i
The| Inventory Report produces a report of high-level information for each experiment,
including: specific test types, identification of analyzed samples, relevant experiment strains^
andi associated batch dates.
3.4:2.2.1 User Input
Before the report is generated, the user is prompted for the desired output device, as listed on
the [screen below:
GeneTox Manager VAX User's Guide
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::::£:gnt£K!SM:Tosf^
Figure 3-10. Report Screen #4
Output reports may be displayed on the terminal screen, sent to a named file, or sent directly
to the default laser printer. If the screen or printer options are selected, no further input is
necessary to process the report (the output will also be saved in a default file name of
REPORT.LIS). If the user explicitly selects the option of sending the output to a file, the
following screen is displayed.
Figure 3-11. Report Screen #5
The file name (and an optional file extension) must be specified to produce the file.
3.4.2.2.2 Processing
Data is extracted according to the selection criteria entered on the selection screen, as described
in Section 3.4 above.
3.4.2.2.3 Outputs
An example of the Inventory Report is found hi Appendix D.
GeneTox Manager VAX User's Guide
Version 2.0
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3.4.2.3 Raw Data Report
ThJ2 Raw Data Report produces a report with Ml descriptive information for each selected
experiment.
3.4.2.3.1 User Input
The only user input for this report is the same as that for the Inventory Report above, i.e., the
user need only specify the intended output device as described in Section 3.4 above.
3.4.2.3.2 Processing
Data is extracted according to the selection criteria entered on the selection screen, as described
in jSection 3.4 above. One important note is that the text for sample description is only
provided with the first set of sample analysis information for the experiment. Any additional
references to the same sample for a given experiment do not include the sample description,
as it would be redundant.
3.412.3.3 Outputs
i '
Anjexample of the Raw Data Report is found in Appendix E.
i
3.412.4 Summary Data Report
i
The; Summary Data Report provides high-level information on Experiment Strains and
Experiment Controls, ordered by Test Type.
3.4,2.4.1 User Input
I
The! user input for this report is the same as that for the Inventory Report above, i.e., the user
need only specify the intended output device as described in Section 3.4.2.2.1 above.
i
i
3.4.;2.4.2 Processing
i
Data is extracted according to the selection criteria entered on the selection screen, as described
in Section 3.4 above.
GeneTox Manager VAX User's Guide
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3.4.2.4.3 Outputs
An example of the Summary Report is found in Appendix F.
3.4.3 Outputs
Sample output for each of the available reports is provided in Appendices D through F of this
User's Guide.
3.4.4 Quality Control
Only experiment data that meets all of the input selection criteria is reported to the user.
3.5 HELP Option
This function displays Help text on the GeneTox system to the terminal screen. The Help text
is the same information contained hi this User's Guide.
3.5.1 User Input
The Help screen is invoked by selecting 'H' on the main menu.
- The return key is the only response to the Help screens displayed.
3.5.2 Processing
The selected Help text is retrieved and displayed to the user. No other processing takes place
for this option.
3.5.3 Outputs
No output files are produced for this option. The Help text is displayed to the user on the
terminal screen only.
GeneTox Manager VAX User's Guide
Version 2.0
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3.5.4 Quality Control
No quality control constraints are relevant for this option.
3.6 EXIT Option
This function allows the user to exit from the GeneTox system and return to the command line
prompt ($). This option is selected from the main menu by entering an 'E' at the command
prompt and pressing < RET >.
GeneTox Manager VAX User's Guide
Version 2.0
Page 21
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-------
APPENDIX A
Extract File via the Statistics Report
GeneTox Manager VAX User's Guide
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SAMPLE ID: PARC-91-0010 LAB: EHRT DATE: 91/09/06
SAMPLE~DESCRIPTION: 6-MTRO-3,4-BENZOCOUMARIN
SESSION ED: PARC9I0041 TECHNICIAN: MST
STRAIN: YG1024 BATCH: 91/08/07 ACTIVATION: - RLAOS8
TEST TYPE: 17 - Reduced Kado Assay, 100 ul ran vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
.000 UL 24 29 31
150.000'ng 1358 1146 1231
.500 ng 130 113
1.000 ng 253
5.000 ng 691 978
10.000 ng 1616 1598
50.000 ng 2296 2916
100.000 ng 3113 2376
©EOF
SAMPLE ID: PARC-91-0010 LAB: EHRT DATE: 91/09/06
SAMPLE~DESCRIPnON: 6-NITRO-3,4-BENZOCOUMARIN
SESSION ID: PARC910041 TECHNICIAN: MST
STRAIN: YG1024 BATCH: 91/08/07 ACTIVATION: + RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul ran vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
.000 UL 24 39 29
12S.OOO*NG 2178 2168 2117
.500 ng 31 25
1.000 ng 33 41
5.000 ng 39 36
10.000 ng 41 56
50.000 ng 177 210
100.000 ng 474 612
©EOF
SAMPLE ID: PARC-91-0010 LAB: EHRT DATE: 91/09/06
SAMPLE~DESCRIPTION: 6-NITRO-3,4-BENZOCOUMARIN
SESSION ED: PARC910041 TECHNICIAN: MST
STRAIN: YG1029 BATCH: 91/08/07 ACTIVATION: - RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul rxn vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
.000 UL 225 207 198
500.000'ng 419 397 409
1.000 ng 243 280
5.000 ng 237 261
10.000 ng 487 291
50.000 ng 1526 312
100.000 ng 2310 2283
500.000 ng 1969 2376
©EOF
SAMPLE ID: PARC-91-0010 LAB: EHRT DATE: 91/09/06
SAMFLE~DESCRIPTION: 6-NITRO-3,4-BENZOCOUMARIN
SESSION ID: PARC910041 TECHNICIAN: MST
STRAIN: YG1029 BATCH: 91/08/07 ACTIVATION: + RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul ran vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
.000 UL 135 147 175
125.000'NG 1214 1098 1302
1.000 ng 188 174
5.000 ng 179 191
10.000 ng 225 211
50.000 ng 738 654
100.000 ng 1113 1186
500.000 ng 1952 1930
©EOF
SAMPLEJD: PARC-91-0011 LAB: EHRT DATE: 91/09/06
SAMPLE DESCRIPTION: 7-NITRO-3,4-BENZOCOUMARIN
SESSION ID: PARC910041 TECHNICIAN: MST
STRAIN: YG1024 BATCH: 91/08/07 ACTIVATION: - RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul rxn vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
.000 UL 24 29 31
150.000*ng 1358 1146 1231
.500 ng 68 29
1.000 ng 98 38
5.000 ng 115 98
10.000 ng 416 486
50.000 ng 1155 638
100.000 ng 1101 2825
©EOF
SAMPLEJD: PARC-91-0011 LAB: EHRT DATE: 91/09/06
SAMPLE DESCRIPTION: 7-NITRO-3,4-BENZOCOUMARIN
SESSION ID: PARC910041 TECHNICIAN: MST
STRAIN: YG1024 BATCH: 91/08/07 ACTIVATION: + RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul ran vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
.000 UL 24 39 29
125.000*NG 2178 2168 2117
.500 ng 18 29
1.000 ng 27 25
5.000 ng 56 55
10.000 ng 76 43
50.000 ng 146 179
100.000 ng 745 845
©EOF
SAMPLE_ED: PARC-91-0011 LAB: EHRT DATE: 91/09/06
SAMPLE DESCRIPTION: 7-NITROr3,4-BENZOCOUMARIN
SESSION n>: PARC910041 TECHNICIAN: MST
STRAIN: YG1029 BATCH: 91/08/07 ACTIVATION: - RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul ran vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
.000 UL 225 207 198
500.000*ng 419 397 409
5.000 ng 179 181
10.000 ng 187 207
50.000 ng 280 260
100.000 ng 519 212
500.000 ng 1500 1485
1000.000 ng 1543 1686
©EOF
SAMPLEJD: PARC-91-0011 LAB: EHRT DATE: 91/09/06
SAMPLE DESCRIPTION: 7-NITRO-3,4-BENZOCOUMARIN
SESSION ID: PARC910041 TECHNICIAN: MST
STRAIN: YG1029 BATCH: 91/08/07 ACTIVATION: + RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul ran vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
.000 UL 135 147 175
125.000*NG 1214 1098 1302
5.000 ng 198 200
10.000 ng 144 183
50.000 ng 200 163
100.000 ng 187 177
500.000 ng 596 450
1000.000 ng 771 788
©EOF
GeneTox Manager VAX User's Guide
Version 2.0
Page 24
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APPENDIX B
Sample Output from Stead Model
-------
-------
* S'TEAD MODEL ANALYSIS
SAMPLE_ID: PARC-91-0010 LAB: EHRT E'ATE: 91/09/06
SAMPLE DESCRIPTION: 6-NITRO-3,4-BENZOCOUMARIN
SESSION ID: PARC910041 TECHNICIAN: MST
STRAIN: YG1024 BATCH: 91/08/07 ACTIVATION: - RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul rxn vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
MEAN S.D.
DOSE DNITS PLATE COUNTS
28100 3.61
j
1245.00 106.69
I
121150 12.02
i
253 LOO 0.00
I
834150 202.94
leoy.oo 12.73
2606.00 438.41
2744.50 521.14
0.00 UL 24 29 31
150.00* ng 1358 1146 1231
0.50 ng 130 113
1.00 ng 253
5.00 ng 691 978
10.00 ng 1616 1598
50.00 ng 2296 2916
100.00 ng 3113 2376
ESTS.
TEST
B(0)
24.0623
5.5421
POISSON
ADEQUACY
TOXICITY '
MUTAGENICITY
CHI-SQUARE DF
224.28 7
176.47 3
785.05 1
28104.82 2
AVERAGE SLOPE (NONLIN. MODEL)
; B(2)
0.7776
B(3)
0.01250
'DLOGL
0.0000 -167.8005
0.0000 -256.0340
0.0000 -648.5595
0.0000 -14308.4430
" 10S.896
WARNING: 4 PARAMETER MODEL DID NOT CONVERGE
WARNING: 3 PARAMETER MODEL DID NOT CONVERGE
AVERAGE SLOPE (LINEAR REGR.) = 4B.437
95% CONF. LIMITS - ( 32.033, , 64.840)
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Version 2.0
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SAMPLE_ID: PARC-91-0010 LAB:EHRT DATE: 91/09/OS
SAMPLE DESCRIPTION: 6-NITRO-3 ,4-BENZOCOUMARIN
SESSION ID: PARC910041 TECHNICIAN: MST
STRAIN: YG1024 BATCH: 91/08/07 ACTIVATION: - RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul rxn vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
SOOO+-
0
B
S
B
R
V
B
D
C
0
U
N
T
s
A
N
D
P
R
E
D
I
C
T
B
D
C
U
R
V
E
3
j
I
4000 +
•
•
-
:
,*
•
-
;
3000+ X
*
.
: ....
: ...
: ... X
1 . . "
; . .
• t t
2000+
•
: * .
i • .
:
:
1
: X.'
J m
1000+
: . X
•X
!*
o.oo 20.00 40.00 eo.oo
X
80.00 100.00
DOSE (ng )
GeneTox Manager VAX User's Guide
Version 2.0
Page 28
-------
APPENDIX C
Sample Output from Bernstein Model
-------
******************************************************
*BERNSTEIN MODEL ANALYSIS*
******************************************************
SAMPLEJD: PARC-91-0010 LAB: EHRT DATE: 91/09/06
SAMPLE DESCRIPTION: 6-NITRO-3,4-BENZOCOUMARIN
SESSION ID: PARC910041 TECHNICIAN: MST
STRAIN: YG1024 BATCH: 91/08/07 ACTIVATION: - RLA058
TEST TYPE: 17 - Reduced Kado Assay, 100 ul IOT vol.
TIME: 1.5 (In Hours) TEMP: 37.0 (Centigrade)
DOSE UNITS PLATE COUNTS
0.00 UL
150.00* UL
0.50 ng
1.00 ng
5.00 ng
10.00 ng
50.00 ng
100.00 ng
24. 29. 31.
1358. 1146. 1231.
130. 113.
253.
691. 978.
1616. 1598.
2296. 2916.
3113. 2376.
5 Dose Levels Used.
NOTE: B(0) is the estimated Intercept
B(l) is the estimated Slope
C is the estimated Variance/Mean Ratio
S. D.
B(0)
ESTS. 29.0300007 161.6000061 7.6160002
7.6236472 6.4799695 3.4842503
TEST
CHI-SQUARE DF
Adequacy
Regr
Cntrls
Mutagenicity
3.7800 3
1.8650 2
1.9150 1
790.8000 1
0.2863
0.3936
0.1664
0.0000
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SAMPLEJD: PARC-91-0010 LAB: EHRT DATE:91/09/06
SAMPLE DESCRIPTION: 6-NrTRO-3,4-BENZOCOUMARIN
SESSION ID: PARC910041 TECHNICIAN: MST
STRAIN: YQ1024 BATCH: 91/08/07 ACTIVATION: -RLA058
TIME: 1.5 (In Hours) TEMP: 37.0 (CenOgnde)
o
B
S
E
R
V
E
D
C
O
U
N
T
S
A
N
D
P
R
E
D
I
C
T
E
D
C
U
R
V
E
5,000
4,000
3,000
*
..*.
*
2,000
1,000
*/
20
40 60
DOSE (ng)
80
100
GeneTox Manager VAX User's Guide
Version 2.0
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APPENDIX D
Inventory Report Example
GeneTox Manager VAX User's Guide
Version 2.0
Page 32
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1 1
ON ON
O O
^H ~H
ON ON
h EI
C^ W
I 1
ON O\
rt O -<
Sp
3333
8888
W3
-------
APPENDIX E
Raw Data Report Example
-------
! **************************
i * Raw Data Output Report *
i **************************
1 Report Date: 10/20/92
j Page Num.: 1
Sample ID: PARC-91-0010 ResLab..: EHRT Exp Date.: 09/06/91
Samp Desc: 6-NITRO-3.4-BENZOCOUMARIN
Exp Name.: PARC910041 Lab Tech: MST P Invest.: JL
Strain.!..: YG1024 Str Date: 08/07/91 Act Type.:
Test Type: 17 - Reduced Kado Assay, 100 ul rxn vol. Act Level: 0
Time(Hr): 1.5 TempC..: 37.0 Input By.: MST
Dose1 Dose
Amount Units
0.000 UL
.500 ng
l.oi)0 ng
5.060 ng
10.000 ng
50.(}00 ng
100.000 ng
Plate Plate Plate
Plate Plate
Count Count Count Count Count Mean SD
24 29 31
130 113
253
691 978
1616 1598
2296 2916
3113 2376
28.0000 3.6056
121.5000 12.0208
253.0000 .0000
834.5000 202.9396
1607.0000 12.7279
2606.0000 438.4062
2744.5000 521.1377
I POSITIVE CONTROL NAME..: Nitrofluorene,2-
150.000 *ng 1358 1146 1231 1245.0000 106.6911
Negative Control Name: DMSO
Laboratory Book Num..: MT-6
Computer Entry Date..: 09/25/91
Pheno [Copy Check : 1
Samp Sterility Before: 1
S9 Sterility Before..: 1
Solvent : DMSO
Culture Density...: 5X
Incubation Hours....: 72.00
Samp Sterility After: 1
S9 Sterility After..: 1
Solv Amt: 2 Solv Unt: UL
Assay Modification...: 5X cells, 2 ul sample, 50ul culture
GeneTox Manager VAX User's Guide
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-------
**************************
* Raw Data Output Report *
* Sample Description *
**************************
Sample ID: PARC-91-0010 P Invest: JL
Source Batch and Lot No.:
Page Num.: 2
Cas Number:
Sample Description: 6-NITRO-3.4-BENZOCOUMARIN
GeneTox Manager VAX User's (Guide
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Page 36
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* Raw Data Output Report *
* S9 Description *
**************************
Page Num.: 3
Activation Type: RLA058
S9 Level 1 : 50 S9 Units 1 : UL
S9 Level 2 : S9 Units 2 :
GeneTox Manager VAX User's Guide
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-------
**************************
* Raw Data Output Report *
**************************
Report Date: 10/20/92
Page Num.: 4
Snmple ID: PARC-91-0011 ResLab..: EHRT Exp Date.: 09/06/91
Samp Dcsc: 7-NITRO-3.4-BENZOCOUMARIN
Exp Name.: PARC910041 Lab Tech: MST P Invest.: JL
Strain...: YG1024 Str Date: 08/07/91 Act Type.:
Test Type: 17 - Reduced Kado Assay, 100 ul rxn vol. Act Level: 0
Time(Hr): 1.5 TempC..: 37.0 Input By.: MST
Dose Dose Plate Plate Plate Plate Plate
Amount Units Count Count Count Count Count Mean
SD
0.000 UL
24 29 31
28.0000 3.6056
48.5000 27.5772
68.0000 42.4264
106.5000 12.0208
451.0000 49.4975
896.5000 365.5742
1963.0000 1219.0521
POSITIVE CONTROL NAME..: Nitrofluorene,2-
150.000 *ng 1358 1146 1231 1245.0000 106.6911
.500 ng
1.000 ng
5.000 ng
10.000 ng
50.000 ng
100.000 ng
68 29
98 38
115 98
416 486
1155 638
1101 2825
Negative Control Name: DMSO
Laboratory Book Num..: MT-6
Computer Entry Date..: 09/25/91
Phcno Copy Check : 1
Samp Sterility Before: 1
S9 Sterility Before..: 1
Solvent : DMSO
Culture Density...: 5X
Incubation Hours....: 72.00
Samp Sterility After: 1
S9 Sterility After..: 1
Solv Aflit: 2 Solv Unt: UL
Assay Modification...: 5X cells, 2 ul sample, SOul culture
-------
**************************
* Raw Data Output Report *
* Sample Description *
**************************
| , Page Num.: 5
Sample ID: PARC-91-0011 P Invest: JL Cas Number:
Source Batch and Lot No.:
Samplk Description: 7-NITRO-3,4-BENZOCOUMARIN
GeneTox Manager VAX User's Guide
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**************************
* Raw Data Output Report *
**************************
Report Date: 10/20/92
Page Num.: 6
Sample ID: PARC-9I-0010 ResLab..: EHRT Exp Date.: 09/06/91
Samp Dcsc: 6-NITRO-3,4-BENZOCOUMARIN
Exp Name.: PARC910041 Lab Tech: MST P Invest.: JL
Strain...: YO1024 Str Date: 08/07/91 Act Type.: RLA058
Test Type: 17 - Reduced Kado Assay, 100 ul rxn vol. Act Level: 1
Time(Hr): 1.5 TempC..: 37.0 Input By.: MST
Dose Dose Plate Plate Plate Plate Plate
Amount Units Count Count Count Count Count
Mean
SD
0.000 UL
.500 ng
1.000 ng
5.000 ng
10.000 ng
50.000 ng
100.000 ng
24 39
31 25
33 41
39 36
41 56
177 210
474 612
29
30.6667
28.0000
37.0000
37.5000
48.5000
193.5000
543.0000
7.6376
4.3426
5.6569
2.1213
10.6066
23.3345
97.5807
POSITIVE CONTROL NAME..: Aminpanthracene,2-
125.000 *NG 2178 2168 2117 2154.3333 32.7159
Negative Control Name: DMSO
Laboratory Book Num..: MT-6
Computer Entry Date..: 09/25/91
Phcno Copy Check : 1
Samp Sterility Before: 1
S9 Sterility Before..: 1
Solvent : DMSO
Culture Density...: 5X
Incubation Hours....: 72.00
Samp Sterility After: 1
S9 Sterility After..: 1
Solv Amt: 2 Solv Unt: UL
Assay Modification...: 5X cells, 2 ul sample, 50ul culture
-------
**************************
* Raw Data Output Report *
* Sample Description *
[ Page Num.: 7
Sample|ID: PARC-91-0010 P Invest: JL Cas Number:
Source Batch and Lot No.:
SamplejDescription:6-NITRO-3,4-BENZOCOUMARIN
GeneTox Manager VAX User's Guide
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-------
**************************
* Raw Data Output Report *
Report Date: 10/20/92
Page Num.: 8
Sample ID: PARC-91-001 1 ResLab. . : EHRT Exp Date. : 09/06/91
Samp Dcsc: 7-NITRO-3.4-BENZOCOUMARIN
Exp Name.: PARC910041 Lab Tech: MST P Invest. : JL
Strain...: YG1024 Str Date: 08/07/91 Act Type.: RLA058
Test Type: 17 - Reduced Kado Assay, 100 ul rxn vol. Act Level: 1
Time(Hr): 1.5 TempC..: 37.0 Input By.: MST
Dose Dose Plate Plate Plate Plate Plate
Amount Units Count Count Count Count Count
Mean
SD
0.000 UL
24 39 29
.500 ng
1.000 ng
5.000 ng
10.000 ng
50.000 ng
100.000 ng
18 29
27 25
56 55
76 43
146 179
745 845
30.6667
23.5000
26.0000
55.5000
59.5000
162.5000
795.0000
7,6376
7.7782
1.4142
.7071
23.3345
23.3345
70.7107
POSITIVE CONTROL NAME..: Aminoanthracene,2-
125.000 *NG 2178 2168 2117 2154.3333 32.7159
Negative Control Name: DMSO
Laboratory Book Num..: MT-6
Computer Entry Date..: 09/25/91
Phono Copy Check : 1
Samp Sterility Before: 1
S9 Sterility Before..: 1
Solvent : DMSO
Culture Density...: 5X
Incubation Hours....: 72.00
Samp Sterility After: 1
S9 Sterility After..: 1
Solv Amt: 2 Solv Unt: UL
Assay Modification...: 5X cells, 2 ul sample, 50ul culture
-------
! **************************
| * Raw Data Output Report '*
! * Sample Description *
i **************************
I Page Num.: 9
Sample ID: PARC-91-0011 P Invest: JL Cas Number:
Source Batch and Lot No.:
Sample Description: 7-NITRO-3.4-BENZOCOUMARIN
GeneTox Manager VAX User's Guide
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**************************
* Raw Data Output Report *
Report Date: 10/20/92
Page Num.: 10
Sample ID: PARC-91-0010 ResLab..: EHRT Exp Date.: 09/06/91
Samp Desc: 6-NITRO-3.4-BENZOCOUMARIN
Exp Name.: PARC910041 Lab Tech: MST P Invest.: JL
Strain...: YG1029 Str Date: 08/07/91 Act Type.:
Test Type: 17 - Reduced Kado Assay, 100 ul rxn vol. Act Level: 0
Time(Hr): 1.5 TempC..: 37.0 Input By.: MST
Dose Dose
Amount Units
0.000 UL
1.000 ng
5.000 ng
10.000 ng
50.000 ng
100.000 ng
500.000 ng
Plate Plate Plate Plate Plate
Count Count Count Count Count Mean St»
225 207 198
243 280
237 261
487 291
1526 312
2310 2283
1969 2376
210.0000 13.7477
261.5000 26.1630
249.0000 16.9706
389.0000 138.5929
919.0000 858.4276
2296.5000 19.0919
2172.5000 287.7925
POSITIVE CONTROL NAME..: Sodium Azide
500.000 *ng 419 397 409
Negative Control Name: DMSO
Laboratoiy Book Num..: MT-6
Computer Entry Date..: 09/25/91
Pheno Copy Check : 1
Samp Sterility Before: 1
S9 Sterility Before..: 1
Solvent : DMSO
408.3333 11.0151
Culture Density...: 5X
Incubation Hours....: 72.00
Samp Sterility After: 1
S9 Sterility After..: 1
Solv Amt: 2 Solv Unt: UL
Assay Modification...: 5X cells, 2 ul sample, 50ul culture
-------
: **************************
1 * Raw Data Output Report *
l * Sample Description *
I **************************
! Page Num.: 11
Sample ID: PARC-91-0010 P Invest: JL Cas Number:
Source Batch and Lot No.:
Sample Description: 6-NITRO-3.4-BENZOCOUMARIN
-------
**************************
* Raw Data Output Report *
Report Date: 10/20/92
Page Num.: 12
SampIeID:PARC-91-001I ResLab..: EHRT Exp Date.: 09/06/91
Samp Dcso: 7-NITRO-3.4-BENZOCOUMARIN
Exp Name.: PARC910041 Lab Tech: MST P Invest.: JL
Strain...: YG1029 Str Date: 08/07/91 Act Type.:
Test Type: 17 - Reduced Kado Assay, 100 ul rxn vol. Act Level: 0
Time(Hr): 1.5 TempC..: 37.0 Input By.: MST
Dose Dose Plate Plate Plate Plate Plate
Amount Units Count Count Count Count Count Mean
SD
0.000 UL
225 207 198
5.000 ng
10.000 ng
50.000 ng
100.000 ng
500.000 ng
1000.000 ng
179 181
187 207
280 260
519 212
1500 1485
1543 1686
210.0000 13.7477
180.0000 1.4142
197.0000 14.1421
270.0000 14.1421
365.5000 217.0818
1492.5000 10.6066
1614.5000 101.1163
POSITIVE CONTROL NAME..: Sodium Azide
500.000 *ng 419 397 409
Negative Control Name: DMSO
Laboratory Book Num..: MT-6
Computer Entry Date..: 09/25/91
Phcno Copy Check : 1
Samp Sterility Before: 1
S9 Sterility Before..: 1
Solvent : DMSO
408.3333 11.0151
Culture Density...: 5X
Incubation Hours..,.: 72.00
Samp Sterility After: 1
S9 Sterility After..: 1
Solv Amt: 2 Solv Unt: UL
Assay Modification...: 5X cells, 2 ul sample, 50ul culture
GeneTox Manager VAX User's Guide
Version 2.0
Page 46
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**************************
* Raw Data Output Report *
* Sample Description *
**************************
I Page Num.: 13
Sampll; ID: PARC-91-0011 P Invest: JL Cas Number-
Source Batch and Lot No.:
Sample Description: 7-NITRO-3.4-BENZOCOUMARIN
GeneTox Manager VAX User's Guide
Version 2.0
Page 47
-------
**************************
* Raw Data Output Report *
Report Date: 10/20/92
Page Num.: 14
Sample ID: PARC-91-0010 ResLab..: EHRT Exp Date.: 09/06/91
Samp Dcsc: 6-NITRO-3.4-BENZOCOUMARIN
Exp Name.: PARC910041 Lab Tech: MST P Invest. : JL
Strain...: YG1029 . Str Date: 08/07/91 Act Type.: RLA058
Test Type: 17 - Reduced Kado Assay, 100 ul rxn vol. Act Level: 1
Time(Hr): 1.5 TempC..: 37.0 InputBy.:MST
Dose Dose Plate Plate Plate Plate Plate
Amount Units Count Count Count Count Count Mean
SD
0.000 UL
135 147 175
1.000 ng
5.000 ng
10.000 ng
50.000 ng
100.000 ng
500.000 ng
188 174
179 191
225 211
738 654
1113 1186
1952 1930
152.3333
181.0000
185.0000
218.0000
696.0000
1149.5000
1941.0000
20.5264
9.8995
8.4853
9.8995
59.3970
51.6188
15.5563
POSITIVE CONTROL NAME..: Aminoanthracene,2-
125.000 *NG 1214 1098 1302 1204.6667 102.3198
Negative Control Name: DMSO
Laboratory Book Num..: MT-6
Computer Entry Date..: 09/25/91
Phono Copy Check : 1
Samp Sterility Before: 1
59 Sterility Before..: 1
Solvent : DMSO
Culture Density...: 5X
Incubation Hours....: 72.00
Samp Sterility After: 1
S9 Sterility After..: 1
Solv Amt: 2 Solv Unt: UL
Assay Modification...: 5X cells, 2 ul sample, 50ul culture
-------
**************************
I * Raw Date Output Report *
: * Sample Description *
: **************************
{ Page Num.: 15
Sample ID: PARC-91-0010 P Invest: JL Cas Number:
Source Batch and Lot No.:
Sample Description: 6-NITRO-3.4-BENZOCOUMARIN
GeneTox Manager VAX User's Guide
Version 2.0
Page 49
-------
* Raw Data Output Report *
**************************
Report Date: 10/20/92
Page Num.: 16
Sample ID: PARC-91-0011 ResLab..: EHRT Exp Date.: 09/06/91
Samp Dcsc: 7-NITRO-3.4-BENZOCOUMARIN
Exp Name.: PARC910041 Lab Tech: MST P Invest.: JL
Strain...: YG1029 Str Date: 08/07/91 Act Type.: RLA058
Test Type: 17 - Reduced Kado Assay, 100 ul rxn vol. Act Level: 1
Time(Hr): 1.5 Temp C..: 37.0 Input By.: MST
Dose Dose Plate Plate Plate Plate Plate
Amount Units Count Count Count Count Count
Mean
SD
0.000 UL
135 147 175
5.000 ng
10.000 ng
50.000 ng
100.000 ng
500.000 ng
1000.000 ng
198 200
144 183
200 163
187 177
596 450
771 788
152.3333
199.0000
163.5000
181.5000
182.0000
523.0000
779.5000
20.5264
1.4142
27.5772
26.1630
7.0711
103.2376
12.0208
POSITIVE CONTROL NAME..
125.000 *NG 1214 1098 1302
Aminoanthracene,2-
1204.6667 102.3198
Negative Control Name: DMSO
Laboratory Book Num..: MT-6
Computer Entry Date..: 09/25/91
Phcno Copy Check : 1
Samp Sterility Before: 1
S9 Sterility Before..: 1
Solvent : DMSO
Culture Density...: 5X
Incubation Hours....: 72.00
Samp Sterility After: 1
S9 Sterility After..: 1
Solv Amt: 2 Solv Unt: UL
Assay Modification...: 5X cells, 2 ul sample, 50ul culture
-------
* Raw Data Output Report *
* Sample Description *
**************************
Page Num.: 17
Sample ID: PARC-91-0011 P Invest: JL Cas Number:
Source Batch and Lot No.:
source Batch ai
Sample Description: 7-NITRO-3.4-BENZOCOUMARIN
GeneTox Manager VAX User's Guide
Version 2.0
Page 51
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APPENDIX F
Summary Report Example
-------
33
00
cs
oo in
T-H ON ON f-
cn oA T-H r-i
!! S S S S
o '-•
13
oo oo oo oo
SS SS
o -< o -*
ON ON ON ON
s
« II O O O O
-------
APPENDIX G
GENETOX MANAGER SYSTEM
TRANSFER FILE RECORD DESCRIPTIONS
-------
Record Type ST01 - Required with all associated records below for EACH
experiment/strain combination.
Description
ST01 - Master record for an experiment strain
Experiment strain key
Data record status in PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)ead Only,(V)ax Download, (X)Arehived
Experiment Name
Strain Abbreviation
Strain Date (YYMMDD)
Activation Level
General Experiment Info included (Y/N)
Number of Samples included! for this experiment
strain analysis
Number of negative controls for this
experiment strain analysis
Number of positive controls for this
experiment strain analysis
Culture Density
Transfer file format (N = new)
Col
1-4
5-13
14
15-14
25-30
31-36
37
38
39-41
42-43
44-45
Field
RecType
ExpKeys
RecStal
ExpNam
StrnAbr
StrnDate
ActLevel
GenRec
NumSmp
NumNeg
NumPos
Data Type
Character
Integer
Character
Character
Character
Date
Character
Character
Integer
Integer
Integer
Len
4
9
1
10
6
6
1
1
2
2
2
46-5,5 CultDnsy Character
56 TFFormat Character
i
**End-of-record**
10
1
Record Type GE01 - Required if GenRec field in STO1 record = Y.
Col Field
1-4 RecType
5-13 ExpKeys
14 ! RecStat
15-20
21-22
23-28
29-32
33-67
**End-of-record**
ExpDate
TesTypCod
S9TypLot
LabTech
TesTypDes
Data Type Len
Character 4
Integer 9
Character 1
Date
Integer
Character
Character
Character
6
2
6
4
35
Description
GE01 - General experiment information
Experiment strain key
Data record status in PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)ead Only, (V)ax Download, (X)Archived
Experiment Date (YYMMDD)
Test type code
S9 Type and Lot
Lab Technician initials
Test type description
GeneTox Manager VAX User's Guide
Version 2.0
Page 55
-------
Record Type GE02 - Required if GenRec field in STO1 record = Y.
Col Field
1-4 RecType
5-13 ExpKeys
14-16 TimeMi
17-22 TimeHr
23-28 TempF
29-34 TempC
35-59 LabBook
60-63 ResLabID
**End-of-record**
Record Type GE03
goj Field
1-4 RecType
5-13 ExpKeys
14-48 AsyModf
49-54 EnDate
55-58 PJnvest
59-62 EntryTech
Data Type
Character
Integer
Integer
Floating
Floating
Floating
Character
Character
- Required
Data Type
Character
Integer
Character
Date
Character
Character
Len
4
9
3
6.1
6.1
6.1
25
4
Description
GE02 - General experiment information
Experiment strain key
Experiment tune in minutes
Experiment tune in hours
Temperature in Farenheit
Temperature in Centigrade
LabBook Number
Research Lab ID
••
if GenRec field in STO1 record = Y.
Len
4
9
35
6
4
4
Description
GE03 - General experiment information
Experiment strain key
Assay Modification
Data entry date (YYMMDD)
Principal investigator initials
Data entry technician initials
**End-of-record**
Record Type GE04 - Required if GenRec field in STO1 record = Y.
Col Field
1-4 RecType
5-13 ExpKeys.
14 S9StrB
15 S9StrA
16-21 S9Levell
22-27 S9Level2
28-31 S9Unitsl
32-35 S9Units2
36 S9Used
37-40 NmS9Desc
Data Type
Character
Integer •
Integer
Integer
Character
Character
Character
Character
Character
Integer
Len
4
9
1
1
1
1
4
4
1
4
Description
GE04 - General experiment information
Experiment strain key
S9 sterility before
S9 sterility after
S9 level 1
S9 level 2
S9 units 1
S9 units 2
S9 used (+/-)
Number of S9 description records to follow
(i.e., number of GEOSs)
GeneTox Manager VAX User's Guide
Version 2.0
Page 56
-------
* *End-of-record* *
Record Type GE05 - Number of GE05 records must correspond to value in NmS9Desc
field in GE04 record.
Col Field Data Type Len
1-4 RecType Character 4
5-13 ExpKeys Integer 9
14-78 S9Desc Character 65
Description
GE05 - General experiment information
Experiment strain key ,
S9 description line
**Ehd-of-record**
Record Type NP01 - Number of NP01/NP02 record sets must correspond to value in
Col
1-4
5-13
14
NumNeg field in ST01 record.
Field Data Type Len
RecType Character 4
NegKey Integer 9
RecStat Character 1
15-16 NegCode
17-36 NegName
37-45 NegAmt
46-4|8 NegUnit
49-5;8 NegMean
59-68 NegStDev
69 NmNegCnt
|
i
**End-of-record**
Integer
Character
Floating
Character
Floating
Floating
Integer
2
20
9.3
3
10.4
10.4
1
Description
NP01 - Negative control general information
Negative control key
Data record status in PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)ead Only, (V)ax Download, (X)Archived
Negative control code
Negative control name
Negative control amount
Negative control units
Negative control mean
Negative control standard deviation
Number of negative control plate counts to
follow in NP02 record
Record Type NP02 - Number of NP01/NP02 record sets must correspond to value in
NumNeg field in ST01 record.
Col
1-4
5-13
14-18
19
20-24
25
26-30
31
32-36
37
38-<
VI
43
Field
RecType
NegKey
NegPlCntl
NegBkgndl
NegPlCnt2
NegBkgnd2
NegPlCntS
NegBkgndS
NegPlCnt4
NegBkgnd4
NegPlCnt5
NegBkgndS
Data Type
Character
Integer
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Len
4
9
5
1
5
1
5
1
5
1
5
1
Description
NP02 - Negative control plate counts
Negative control key
Plate count 1
Background code 1
Plate count 2 \
Background code 2
Plate count 3
Background code 3
Plate count 4
Background code 4
Plate count 5
Background code 5
GeneTox Manager VAX User's Guide
Version 2.0
Page 57
-------
**End-of-record**
Record Type PP01 - Number of PP01/PP02 record sets must correspond to value in
NumPos field in ST01 record.
Description
PP01 - Positive control general information
Positive control key
Data record status in PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)ead Only, (V)ax Download, (X)Archived
Positive control code
Positive control name
Positive control amount
Positive control units
Positive control mean
Positive control standard deviation
Number of positive control plate counts to
follow in PP02 record
Col Field
1-4 RecType
5-13 PosKey
14 RecStat
15-16 PosCode
17-36 PosName
37-45 PosAmt
46-48 PosUnit
49-58 PosMean
59-68 PosStDev
69 NmPosCnt
Data Type
Character
Integer
Character
Integer
Character
Floating
Character
Floating
Floating
Integer
Len
4
9
1
2
20
9.3
3
10.4
10.4
1
**End-of-record**
Record Type PP02 - Number of PP01/PP02 record sets must correspond to value in
NumPos field in ST01 record.
Col
1-4
5-13
14-18
19
20-24
25
26-30
31
32-36
37
38-42
43
Field
RecType
PosKey
PosPlCntl
PosBkgndl
PosPlCnt2
PosBkgnd2
PosPlCntS
PosBkgndS
PosPlCnt4
PosBkgnd4
PosPlCntS
PosBkgndS
Data Type Len
Character 4
Integer 9
Integer 5
Character 1
Integer 5
Character 1
Integer 5
Character 1
Integer 5
Character 1
Integer 5
Character 1
Description
PP02 - Positive control plate counts
Positive control key
Plate count 1
Background code 1
Plate count 2
Background code 2
Plate count 3
Background code 3
Plate count 4
Background code 4
Plate count 5
Background code 5
**End-of-record**
GeneTox Manager VAX User's Guide
Version 2.0
Page 58
-------
i
Record Type SM01 - Number of SM01 record sets must correspond to value in NumSmp
! field in ST01 record.
Description
SM01 - Sample analysis header information
Sample key
Data record status in PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)ead Only, (V)ax Download, (X)Archived
Not currently used
Sample lab ID
Sample year
Sample number
Phenocopy code check
Sample sterility before
Sample sterility after
Dose units
Number of doses
General sample information included (Y/N)
(i.e., do SM02-SM04 records follow?)
Number of remarks records Ihat follow (SM05s)
Number of sample description records that
follow (SM02s)
Old sample key if the SampKey field is a
replacement
Col
1-4
5-13
14
Field
RecType
SampKey
RecStat
15-18 Filler
19-22 SmpLabID
23-24 SmpYr
25-28 SmpNo
29
30
31
32-5
56-5
58
PhenoCod
SmplStrB
SmplStrA
5 DosUnits
7 NumDose
GenSm
59-6^t RemCt
63-66 NumSDc
Data Type
Character
Integer
Character
Character
Integer
Integer
Integer
Integer
Integer
Character
Integer
Character
Integer
Integer
Len
4
9
1
4
2
4
1
1
1
24
2
1
4
4
67-7J5 OldKey Integer 9
**B
;nd-of-
record**
Record Type SM02 - Required for each SM01 record.
Col
1-4
5-13
14-38
39-4
43-4
2
5
46-5i
Field
RecType
SampKey
SolvDesc
SolvAmtPt
SolvUnits
IncubatHr
Data Type
Character
Integer
Character
Integer
Character
Floating
Len
4
9
25
4
3
6.2
Description
SM02 - Sample description records
Sample key
Solvent description
Solvent amount per
Solvent units
Incubation hours
plate
* *End-of-record* *
GeneTox Manager VAX User's Guide
Version 2.0
Page 59
-------
Record Type SM03 - Number of SM03 records must correspond to value in NumSpc
field in SM01 record.
Col Field
1-4 RecType
5-13 SampKey
14-64 SampDesc
**End-of-record**
Data Type Len
Character 4
Integer 9
Character 51
Description
SM03 - General sample information
Sample key
Sample description line
Record Type SM04 - Required if GenSm field = Y in SM01 record.
Col
1-4
5-13
14-64
46-60
RecType
SampKey
ScJBatJLot
CasNum
Data Type Len Description
Character 4 SM04 - General sample information
Integer 9 Sample key
Character 51 Source/Batch/Lot
Character 15 CAS number
**End-of-record**
Record Type SM05 - Number of SM05 records must correspond to value in RemCt field
in SM01 record.
Description
SM05 - Sample remarks records
Sample key
Sample remark line
Col Field
1-4 RecType
5-13 SampKey
14-73 SampDesc
Data Type Len
Character 4
Integer 9
Character 60
**End-of-record**
GeneTox Manager VAX User's Guide
Version 2.0
Page 60
-------
Recprd Type TD01 - Number of TD01/TD02 record sets must correspond to value in
NumDose field in SM01 record.
Description
TD01 - Dose analysis information
Experiment strain key
Sample key
Data record status in PC databases:
(A)ctive, (I)nactive, (M)odified,
(R)ead Only, (V)ax Download, (X)Archived
Dose amount
Test dose mean
Test dose standard deviation
Number of test plate counts to follow in
TD02 record
Col Field
1-4 RecType
5-13
ExpKeys
14-2|2 SampKey
23
RecStat
24-3J2 Dose
33-42 TestMean
43-5J2 TestDev
53
**Ei
TestCnt
id-of-record**
Data Type
Character
Integer
Integer
Character
Floating
Floating
Floating
Integer
Len
4
9
9
1
9.3
10.4
10.4
1
Record Type TD02 - Number of TD01/TD02 record sets must correspond to value in
NumDose field hi ST01 record.
Description
TD02 - Test plate counts
Sample key
Plate count 1
Background code 1
Plate count 2
Background code 2
Plate count 3
Background code 3
Plate count 4
Background code 4
Plate count 5
Background code 5
Col Field
1-4 RecType
5-13
SampKey
14-1|8 TstPlCntl
19
20-2
25
TstBkgndl
4 TstPlCnt2
TstBkgnd2
26-30 TstPlCntS
31 TstBkgndS
32-36 TstPlCnt4
37 TstBkgnd4
38-42 TstPlCntS
43
*L. «i.Tr~i
TstBkgndS
1 r* •» •!**!•
Data Type
Character
Integer
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Integer
Character
Len
4
9
5
1
5
1
5
1
5
1
5
1
**End-of-record**
GeneTox Manager VAX User's Guide
Version 2.0
Page 61
•&U.S. GOVERNMENT PRINTING OFFICE: 1994 - 550-001/80386
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