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AUTOMATING LABORATORY OPERATIONS BY INTEGRATING
LABORATORY INFORMATION MANAGEMENT SYSTEMS (LIMS) WITH
ANALYTICAL INSTRUMENTS AND SCIENTIFIC DATA MANAGEMENT
SYSTEM (SDMS)

Jianyong Zhu

Submitted to the faculty of the University Graduate School
in partial fulfillment of the requirements
for the degree
Master of Science
in the School of Informatics,
Indiana University
June 2005 Master’s Committee

__________________________________________
Mahesh Merchant, Ph.D

__________________________________________
Douglas Perry, Ph.D

__________________________________________
Michael Evans, Ph.D

Accepted by the Graduate Faculty, Indiana University,
in partial fulfillment of the requirements for the degree of Master’s of Science in
Laboratory Informatics GraduateProgram

ii

ACKNOWLEDGEMENTS

During my two-year academic career I am grateful to many people who helped me in my
research and studies. Firstly most important of all I would like to thank Dr. Mahesh
Merchant and Dr. Douglas Perry for their guidance, encouragement, support and
unconditional faith in my abilities. I would also like to thank Dr. Michael Evans for
giving me the opportunity tointern in his laboratory and for his generosity of letting me
use his analytical instruments, software and hardware. In the end I want to thank my
friends and family, particularly my wife, Ping, without their endurance and relentless
support it would have been impossible for me to coordinate my studying and working
schedules and fulfill my responsibilities.

iii

ABSTRACT

The largevolume of data generated by commercial and research laboratories, along
with requirements mandated by regulatory agencies, have forced companies to use
laboratory information management systems (LIMS) to improve efficiencies in tracking,
managing samples, and precisely reporting test results. However, most general purpose
LIMS do not provide an interface to automatically collect data fromanalytical
instruments to store in a database. A scientific data management system (SDMS)
provides a “Print-to-Database” technology, which facilitates the entry of reports
generated by instruments directly into the SDMS database as Windows enhanced
metafiles thus to minimize data entry errors. Unfortunately, SDMS does not allow
performing further analysis. Many LIMS vendors provide plug-ins for singleinstrument
but none of them provides a general purpose interface to extract the data from SDMS and
store in LIMS.

In this project, a general purpose middle layer named LabTechie is designed, built
and tested for seamless integration between instruments, SDMS and LIMS. This project
was conducted at American Institute of Technology (AIT) Laboratories, an analytical
laboratory thatspecializes in trace chemical measurement of biological fluids. Data is
generated from 20 analytical instruments, including gas chromatography/mass
spectrometer (GC/MS), high performance liquid chromatography (HPLC), and liquid
chromatography/mass spectrometer (LC/MS), and currently stored in NuGenesis SDMS

iv

(Waters, Milford, MA). This approach can be easily expanded to include additionalinstruments.

v

TABLE OF CONTENTS

ABSTRACT ..................................................................................................................... IV
LIST OF FIGURES ..................................................................................................... VIII
LIST OF TABLES............................................................................................................X
LIST OF ABBREVIATIONS ........................................................................................ XI
1.

INTRODUCTION .................................................................................................... 1
1.1.
1.2.

Analytical instruments ........................................................................................ 5

1.3....
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