Laboratory Information Management System LIMS

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Laboratory Information Management System (LIMS)

• Joseph Cruz
• 29 April 2005

2
Overview

• Introduction
• Human component
• Mouse component
• Implementation details
• Future development / modifications

3
Overview

• Introduction
• Human component
• Mouse component
• Implementation details
• Future development / modifications

4
LIMS or SDMS

• LIMS Laboratory Information Management System
• SDMS Scientific Data Management System
• Academics use the term LIMS
• IBM (and industry?) use the term SDMS
• Does anyone really care?

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LIMS
Mouse
Human
ELabBook / Scheduler
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Overview

• Introduction
• Human component
• Mouse component
• Implementation details
• Future development / modifications

7
Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
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Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
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Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
11
Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
12
(No Transcript)
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Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
14
Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
15
(No Transcript)
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Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
19
Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
20
(No Transcript)
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Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
22
Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
23
(No Transcript)
24
Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
25
Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
26
(No Transcript)
27
Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
28
Patient
Donor
Transplant
Biopsy
Histology
Clinical Information
Pathology Report
RNA Extraction
Microarray
PCR
Agilent
29
Overview

• Introduction
• Human component
• Mouse component
• Implementation details
• Future development / modifications

30
Experiment
Group 1
Group 2
Group 3
Mouse 1
Mouse 2
Mouse 3
RNA Extraction
Histology
Pathology
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Experiment
Group 1
Group 2
Group 3
Mouse 1
Mouse 2
Mouse 3
RNA Extraction
Histology
Pathology
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(No Transcript)
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Experiment
Group 1
Group 2
Group 3
Mouse 1
Mouse 2
Mouse 3
RNA Extraction
Histology
Pathology
34
Experiment
Group 1
Group 2
Group 3
Mouse 1
Mouse 2
Mouse 3
RNA Extraction
Histology
Pathology
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(No Transcript)
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Experiment
Group 1
Group 2
Group 3
Mouse 1
Mouse 2
Mouse 3
RNA Extraction
Histology
Pathology
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Experiment
Group 1
Group 2
Group 3
Transplant 1
Transplant 2
Transplant 3
Recipient
Donor
RNA Extraction
Pathology
Histology
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(No Transcript)
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Experiment
Group 1
Group 2
Group 3
Mouse 1
Mouse 2
Mouse 3
RNA Extraction
Histology
Pathology
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(No Transcript)
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Experiment
Group 1
Group 2
Group 3
Mouse 1
Mouse 2
Mouse 3
RNA Extraction
Histology
Pathology
42
Experiment
Group 1
Group 2
Group 3
Transplant 1
Transplant 2
Transplant 3
Recipient
Donor
RNA Extraction
Pathology
Histology
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(No Transcript)
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Experiment
Group 1
Group 2
Group 3
Mouse 1
Mouse 2
Mouse 3
RNA Extraction
Histology
Pathology
45
(No Transcript)
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(No Transcript)
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Overview

• Introduction
• Human component
• Mouse component
• Implementation details
• Future development / modifications

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Implementation

• Linux O/S (Fedora Core 3)
• IBM DB2 8.2 database
• Apache / Tomcat web server
• WebSphere Application Developer 5.1
• Eclipse
• Local test server
• J2EE
• JSP, HTML, JavaScript

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Application Development
Joseph
Xiaoli
Chunyan
CVS / Test Server
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Model-View-Controller (MVC) Framework

• Command Pattern
• Servlet handles all requests and responses
• No JSP page to JSP page communication

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LIMS object

• empty constructor
• accessors modifiers (i.e. getters setters)
• methods
• copy(LIMS object)
• setLIMSobject(id)
• addLIMSobject(Connection)
• addLIMSobject()
• updateLIMSobject(Connection)
• updateLIMSobject()

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AddEditLIMSObjectCommand

• implements Command interface
• execute(HttpServletRequest)
• add(HttpServletRequest)
• update(HttpServletRequest)
• setLIMSObject(HttpServletRequest)

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Javadoc
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Overview

• Introduction
• Human component
• Mouse component
• Implementation details
• Future development / modifications

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Future Development / Modifications

• Query capabilities
• Output results as Excel file?
• Analysis module(s)
• Modify the primary keys within the human
  component to be similar to mouse component
• Do not need sample tracking within key

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Acknowledgements

• Dr. Wishart
• Xiaoli and Chunyan
• Dr. Halloran
• The members of Dr. Wisharts and Dr. Hallorans
  respective labs