Designing a Laboratory Information Management System by Using Open-Source Tools OSIRIS: Open Source Integrated Research Information System Open Access

Abstract

Storing all scientific data in a small-scale drug discovery lab requires comprehensive approach. In order to tackle this problem, a centralized resource for cross-disciplinary interaction called Open Source Integrated Research Information System (OSIRIS) has been developed to create a compound registration and project management environment. OSIRIS has been implemented as a group-wide accessible webpage to avoid individual user-side installation and platform compatibility problems.

This system includes modules for creation of projects with custom user privileges, a document management system based on projects, registration of new chemical compounds, text and structure based search, addition of experimental results to individual
compounds, structure and data export, administrator controlled ticket management, and is PC/Mac browser platform independent.

OSIRIS has been created by using open-source tools to keep the cost to minimum
and to give maximum customization of the capabilities of the system. It can be modified to work with different public health informatics related projects; such as, creation of hazardous chemicals database for environmental health research, or a collaboration platform for teams working in different parts of the world.

This work has been done at the Emory Institute for Drug Discovery (EIDD) in Atlanta, GA over a 2 year period, and is based on user feedback. The source code will be available free of charge to academic and non-profit institutions in the spirit of opensource collaboration.

Table of Contents

TABLE OF CONTENTS

1 Chapter 1: Introduction 1
1.1 Background 1
1.2 Problem Statement 1
1.3 Purpose Statement 2
1.4 Significance Statement 3

2 Chapter 2: Review of Laboratory Information Management Systems 4
2.1 Commercial Laboratory Information Management Systems 4
2.2 Open-Source Laboratory Information Management Systems 4
2.3 Existing Software vs. Core Requirements 4

3 Chapter 3: Methodology 6
3.1 System Requirements 6
3.2 Logical Design 7
3.3 Database Design 9
3.4 Data Types 10
3.5 Features 12
3.5.1 User Privileges 12
3.5.2 File Upload 13
3.5.3 Compound Registration 13
3.5.4 Data Management 14
3.5.5 Ticket Management 15
3.5.6 Search Function 16
3.5.7 Data Export 16
3.5.8 User Statistics 17
3.6 Limitations 18

4 Chapter 4: Results 19
4.1 Registered Compounds 19
4.2 Uploaded Files 20
4.3 Compounds vs. Files 21

5 Chapter 5: Conclusions, Implications, and Recommendations 22
5.1 Summary 22
5.2 Conclusion 22
5.3 Implications for Practice 23
5.4 Recommendations 23

6 References 24

About this Master's Thesis

Rights statement

• Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.

School	Rollins School of Public Health
Department	Biostatistics and Bioinformatics
Subfield / Discipline	Public Health Informatics - MSPH
Degree	MSPH
Submission	Master's Thesis
Language	English
Research Field	Biology, Bioinformatics Health Sciences, Public Health Information Science
Keyword	database informatics software open-source
Committee Chair / Thesis Advisor	Hertzberg, Vicki S, Emory University
Partnering Agencies	Emory University schools, faculty or affiliated programs

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