EPA/600/R-94/033
March 1994
GeneTox Manager System
(GENETOX)
PROGRAMMER'S GUIDE
VAX Component
Prepared For:
Health Effects Research Laboratory
U.S. Environmental Protection Agency
Research Triangle Park
North Carolina 27711
Prepared By:
Joe Nader
Computer Sciences Corporation
4401 Alexander Drive
Research Triangle Park
North Carolina 27711
Prepared Under
Contract # 68-WO-0043
Delivery Order # 507
June 1993
Version 2.0
Printed on Recycled Paper
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PREFACE
This programmer's guide is the reference manual explaining how the EPA GeneTox
Manager System operates on the VAX. It is intended for use by anyone who has to perform
program maintenance of the application.
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 microcomputer (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. The PC
system is designed to function with the 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.
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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. Berstein, Dr. D. Krewski, and Mr. 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. Thanks are also extended to Mr. Ken Mullins and Dr.
David Svendsgaard for review of this document.
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/oruser documentau'onand 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 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
PREFACE ; i
ACKNOWLEDGEMENT ii
NOTICE ii
CHAPTER 1: INTRODUCTION 1
CHAPTER 2: ORGANIZATION OF GENETOX MANAGER ON THE VAX 2
2.1 GeneTox Manager Logicals and Symbols 2
2.2 Invoking the GeneTox Application 3
2.2.1 End User Access .3
2.2.2 Execution Entry Points for Developers . 4
2.3 Developer Access to GeneTox Manager 4
2.4 GeneTox Manager File Organization 4
2.5 GeneTox Manager Application Code Notes 5
2.6 GeneTox Manager Data Bases 5
2.6.1 Data Base Definitions 5
2.6.2 GeneTox Manager Server to Support
Multi-User Access 5
2.7 Note on GeneTox Manager Source Code 6
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CHAFFER 1
INTRODUCTION
The GeneTox Manager System is an 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
in 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 in 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 in nature, and they can be seen on the computer screen,
sent to a printer, or written to a PC file.
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.
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CHAPTER 2
ORGANIZATION OF GENETOX MANAGER ON THE VAX
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The VAX component of the GeneTox Manager System is implemented on the VAX Cluster of
EPA's National Computer Center (NCC). The specific VAX machine on which GeneTox
Manager is installed is VAXTM1.
2.1 GeneTox Manager Logicals and Symbols
In order 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
(ACL) entry for the user's ID. See the GeneTox Application Manager for issuance of a
GeneTox ACL for your VAX ID.
The 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 in the user's root
directory 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: PNVITRO]GTMSET
(2) The following command establishes a symbol for invocation of GeneTox:
GENETOX : = = "@GTM$SYS:GENETOX"
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To define a printer to accept GeneTox output, include the following command as well:
DEFINE GTM$SYS$PRINTER ppppppp
where:
pppppp is the name of a printer defined on the VAX network
2.2 Invoking the GeneTox Application
2.2.1 End User Access
After logging on to the VAX computer, enter "GeneTox" at the DCL prompt ($) 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 mam menu presents a list of
options and corresponding functions; a function is selected by entering the appropriate letter at
the command prompt.
*h|li*Il
xr.etUFBxio:
5:ii:ex:::fbr
ecirariiarid
Figure 2-1. Main Menu Screen
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2.2.2 Execution Entry Points for Developers ;
GeneTox Manager actually has four discrete entry points. GENETOX.COM initiates the main
menu of the application and is the typical entry point for the end user. However, in support of
automatic upload and download to/from the VAX of GeneTox Manager data collected on the PC,
there are three additional .COM files that are supported.
PCLOAD.COM is invoked from a SetHost script file on the PC to load new experimental data
to the VAX. :
PCEDIT.COM is invoked from a SetHost script file on the PC to load 'modified' experimental
data to the VAX.
PCDOWN.COM is invoked from a SetHost script file on the PC to download data from the VAX
to a PC.
2.3 Developer Access to GeneTox Manager
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The GeneTox Manager application is installed on a separate application directory, called
INVITRO, on the VAX Cluster machine. Application developers are assigned their own specific,
development directory along with their VAX ID. In order to access the code on the INVITRO
directory, the developer must be assigned an ACL desigpation and disk quota for INVITRO.
GeneTox ACLs are available as follows: '
I
GENESTAT_CONTROL developer access to modify GeneTox |
GENESTAT USER user access to execute GeneTox
2.4 GeneTox Manager File Organization
The INVITRO directory is divided into a number of sub-directories to store various Components
of the GeneTox Manager application as follows:
INVITRO
root directory stores production data bases
DEVL development environment for changing application code
TEST test environment for reviewing application changes |
PROD production location for application code
(except statistical models) i
STATS location of statistical models
DOC location of application documentation
BAK back-up directory storing previous versions of the application |
SERVER
contains pointer
application
information for the FOCUS server for this
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2.5 GeneTox Manager Application Code Notes
GeneTox Manager code on the VAX consists primarily of FOCUS EXEC files (typically known
as FEX files). These files are 'fourth generation language' code files which are interpreted at
execution time rather than compiled. Most FOCUS code cannot be compiled. All elements of
the GeneTox Manager system on the VAX (except for the statistical models) have been developed
and are supported by Computer Sciences Corporation. The statistical models, Stead and
Bernstein, were developed and are supported by Dr. John Creason, of HERL.
2.6 GeneTox Manager Data Bases
2.6.1 Data Base Definitions
There are currently two data bases on the VAX which serve as a master repository for GeneTox
Manager experimental data. The EXPRMNT data base contains all information for an
experiment, including sample information related to its analysis under an experiment. The
SAMPLES data base contains information specific to a sample independent of an experiment
(e.g., sample name). The actual data is stored hi Focus data bases with a file extension of .FOC.
The master file descriptions which define the fields, data type and relationships for these data
bases are hi Focus files with a file extension of .MAS. The EXPRMNT and SAMPLES data
bases are cross referenced to allow storage and retreival of all GeneTox Manager data by the
user.
2.6.2 GeneTox Manager Server to Support Multi-User Access
GeneTox Manager on the VAX supports multi-user access for retrieval of data from the system.
It also supports multi-user update of information (as long as two users are not attempting to
update the same experiment at the same tune - the system will lock out the second user hi such
a situation). In order to provide multi-user access for GeneTox Manager, a FOCUS server is
allocated on the VAX cluster specifically for this application. The server process name is
SUSERVJNVITRO, and should be listed as such when it is 'up' by issuing a SHOW SYSTEM
commandT This server name should also be listed when it is 'up' by issuing a '? SU' command
from within interactive Focus.
While an individual developer can disable this server, NCC support personnel are the only staff
authorized to re-start the server. Start-up of the INVITRO server is included hi VAXTM1
initialization, should the VAX Cluster ever crash or be brought down for maintenance.
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2.7 Note on GeneTox Manager Source Code ;
Because of the rapid changes that occur within computer hardware and software development and
because implementation of this portion of the GeneTox Manager System is likely to be very
different from location to location, the source code listings have not been included.
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•fcu.S. GOVERNMENT PRINTING OFFICE: 1994 - 550-001/80380
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