Laboratory Information Management Systems Douglas Perry, Ph.D. IU School of Informatics

Laboratory Information Laboratory Information Management SystemsManagement Systems

Douglas Perry, Ph.D.Douglas Perry, Ph.D.

IU School of InformaticsIU School of Informatics

22

Laboratory InformationLaboratory Information

The sole product of The sole product of anyany laboratory, laboratory, serving serving anyany purpose, in purpose, in anyany industry, is industry, is iinformationnformation

33

Laboratory Informatics DefinedLaboratory Informatics Defined

The specialized application of The specialized application of information technology to optimize and information technology to optimize and extend laboratory operationsextend laboratory operations

44

Data Flow in the LaboratoryData Flow in the Laboratory

Lab Automation& Robotics

EquipmentInterfacing

LaboratoryInstruments

ChromatographyData Systems

Laboratory InformationManagement

Systems (LIMS)

DataAnalysis

DataMining

DataWarehousing

ElectronicLaboratoryNotebooks

Data Acquisition Information Processing Knowledge Management

55

Data Data AcquisitionAcquisitionArchitectureArchitecture

Local Laboratory Network

Instrument Network

InstrumentData Manager

Specialized Data System

PC

ABFSPManual

Data EntryLC GCSC GC

66

Information Information ProcessingProcessingArchitectureArchitecture

DBMS LIMS

Instrument Network

Local Laboratory Network

ABFSP

InstrumentData Manager

ManualData EntryGC LC

Specialized Data System

GCSC

PC

Specialized Data System

77

Scientific DataScientific DataManagement ArchitectureManagement Architecture

DBMS LIMS

Instrument Network

Local Laboratory Network

ABFSP

InstrumentData Manager

ManualData EntryGC LC

Chromatography Data System

GCSC

PC

DataWarehousing

ElectronicLaboratoryNotebook

Data Mining/Data Analysis

Specialized Data System

88

DBMS LIMS

Wide Area Network

DataWarehousing

ElectronicLaboratoryNotebook

Data Mining/Data Analysis

Enterprise ArchitectureEnterprise Architecture

99

Functional HierarchyFunctional Hierarchyin Laboratory Informaticsin Laboratory Informatics

rules

rules

context

people

SDMS, ELN

DAQ, LAB AUTO

CDS, LIMS

1010

Basic Concept of LIMSBasic Concept of LIMS

LLaboratory aboratory IInformation nformation MManagement anagement SSystemystem Definition: A collection of computerized methods to acquire, Definition: A collection of computerized methods to acquire,

analyze, store, and report laboratory dataanalyze, store, and report laboratory data No “standard” LIMSNo “standard” LIMS

DevelopedDeveloped CustomizedCustomized ConfiguredConfigured

LIMS are disparate because client labs are highly diverseLIMS are disparate because client labs are highly diverse AnalyticalAnalytical ClinicalClinical EnvironmentalEnvironmental ForensicForensic ProductionProduction

1111

Genesis of LIMSGenesis of LIMS

SampleLabeling Job

Assignment ProgressTracking

ResultsEntryResults

VerificationReporting

IN

OUT

Facilitation of Routine Laboratory Operations

SampleLabeling Job

Assignment ProgressTracking

ResultsEntryResults

VerificationReporting

1212

Modern Lab WorkflowModern Lab WorkflowNew Project

PageNew Study

Page

Project/Study Maintenance

Basis of study may be multspecies:

PatientBloodTissue

Cellular BasedCell type

Sample BasedSample Type

AddSamples

Add tests

AssignTests/work

Project Manager/Owner

AssignWorkMgmt

AssignWorkMgmt

Sample Handling Manager/Owner

Activate/AssignTests/Work

Test DataEntry

Test ResultsPreview

Gel Makeand Load Pass

Sample Management

Samples may be:

SubmissionsCustomerInternal

Librariestypically internal

Requestsspecific samp type

AddSamples

ReceiveSamples

FindSamples

RequestSamples

UpdateStatus

SampleType

Tissue

Blood

Synth

Serum

OtherSoluble

ProteinProduction

Gel ImagePreview

Pass

Protein Sample Manager/Owner

ReadySamples

SamplePrep/Dilute

SelectTreatment

Fractionate

PerformTreatment

Make andLoad 1D

Gel

Select 2DGels type

and transfer

Run 1D andTreatmentSelection

Run 2D gelsand set

notification

Image Analysis Manager/Owner

Acquire GelImages inProgeneraGel Staining

AcquireGlobal Spot

List

SapphireSync

AcquireDifferentialSpot List

MS Prep Manager/Owner

Spot List toPAA

New SpotPlate

Created

SpotDigestion

Maldi SpotLoad

Run Maldi

MS and PID Search Manager/Owner

Get MS filefor each

SpotSearch MS

Ident peptidesand protein(s)

Store SpotPlate

View MS

IN

OU

T

1313

Challenge and OpportunityChallenge and Opportunity

1988 2003

1 experiment

1 gene

10 data

1 experiment

10,000 genes

10,000,000 data

1414

# S

am

ple

s (

M/y

r)

1998 2002

3.5

1998 2002

One Real-Life ExampleOne Real-Life Example

3.5

150

1515

Preparation and AnalysisPreparation and Analysis

1988

1 experiment

1 gene

10 data

2003

1 experiment

10,000 genes

10,000,000 data

DAYS, WEEKS,OR MONTHS

ONEAFTERNOON

1616

Universal Need for LIMSUniversal Need for LIMS

Regardless of focus, all labs need:Regardless of focus, all labs need: Quality assurance and controlQuality assurance and control Error reductionError reduction Fast sample turnaroundFast sample turnaround Management of informationManagement of information

1717

Increasing Need for LIMS:Increasing Need for LIMS:Information ManagementInformation Management

Advances in instrument automationAdvances in instrument automation Robotics for sample processingRobotics for sample processing Microarray technologyMicroarray technology

Increased government regulationsIncreased government regulations GxP: GLP, GMP, GCPGxP: GLP, GMP, GCP

Demands of enterprise resource planningDemands of enterprise resource planning CRM, MRP, MESCRM, MRP, MES

1818

Increasing Need for LIMS:Increasing Need for LIMS:Quality Assurance & ControlQuality Assurance & Control

Quality assurance (QA)Quality assurance (QA) Quality control (QC)Quality control (QC) Statistical process control (SPC)Statistical process control (SPC) ISO 9000ISO 9000

1919

Increasing Need for LIMS:Increasing Need for LIMS:Error ReductionError Reduction

Data entry restrictionData entry restriction Acceptable parametersAcceptable parameters Drop-down listsDrop-down lists

Range checkingRange checking Customer specificationsCustomer specifications Internal controlsInternal controls

Sample log-inSample log-in Bar code readerBar code reader

Automatic calculationsAutomatic calculations

2020

Increasing Need for LIMS:Increasing Need for LIMS:Sample TurnaroundSample Turnaround

Automated data entryAutomated data entry Automatic calculationsAutomatic calculations Rapid data retrievalRapid data retrieval Automatic reportingAutomatic reporting

2121

Types of DataTypes of DataUsed in LIMSUsed in LIMS

AlphanumericAlphanumeric DescriptiveDescriptive LimitsLimits NumericNumeric TDU StampTDU Stamp

2222

Types of LaboratoriesTypes of LaboratoriesUsing LIMSUsing LIMS

Research & Development labsResearch & Development labs Analytical labsAnalytical labs Manufacturing labsManufacturing labs

2323

Research & Development Research & Development LaboratoriesLaboratories

ObjectiveObjective Support pure or applied researchSupport pure or applied research

CharacteristicsCharacteristics Small, autonomousSmall, autonomous Diverse, non-routine testsDiverse, non-routine tests Low sample volumeLow sample volume Flexible operationsFlexible operations High internal securityHigh internal security Low, circumscribed data flowLow, circumscribed data flow

2424

LIMS requirements forLIMS requirements forR&D LabsR&D Labs FlexibilityFlexibility

Sample types, tests, methods, reportsSample types, tests, methods, reports

TraceabilityTraceability Audit trails, on-the-fly notationAudit trails, on-the-fly notation

SecuritySecurity Very limited access, but with lateral Very limited access, but with lateral

authorizationauthorization

TimeTime Usually not an issueUsually not an issue

2525

Analytical LaboratoriesAnalytical Laboratories

ObjectiveObjective Provide a service (information)Provide a service (information)

CharacteristicsCharacteristics Large, organization-dependentLarge, organization-dependent Routine testsRoutine tests High sample volumeHigh sample volume Client-driven operationsClient-driven operations High, narrow data flowHigh, narrow data flow

2626

LIMS Requirements for LIMS Requirements for Analytical LabsAnalytical Labs

TrackingTracking Samples, orders, reportsSamples, orders, reports

SchedulingScheduling Tests, equipment maintenanceTests, equipment maintenance

Quality assuranceQuality assurance Validation, QA/QCValidation, QA/QC

Data access and sharingData access and sharing Instrument interfacingInstrument interfacing Client-centered reporting, CoAClient-centered reporting, CoA

2727

Manufacturing Manufacturing LaboratoriesLaboratories

ObjectiveObjective Assure product specificationsAssure product specifications Statistical process controlStatistical process control

CharacteristicsCharacteristics Ongoing testing: raw materials, process, final Ongoing testing: raw materials, process, final

product, stabilityproduct, stability Dynamic, demanding environmentDynamic, demanding environment High, wide data flowHigh, wide data flow Fast turnaroundFast turnaround

2828

LIMS Requirements for LIMS Requirements for Manufacturing LabsManufacturing Labs

Rapid sample turnaroundRapid sample turnaround Automation, bar-code entryAutomation, bar-code entry

ConnectivityConnectivity MRP, ERP, CRMMRP, ERP, CRM

Statistical analysisStatistical analysis Statistical process controlStatistical process control

Flexible reportingFlexible reporting Diverse information demandsDiverse information demands

2929

Functional Model of Functional Model of LIMSLIMS

CB

data capturesyste

ms mgt

A

data

ana

lysi

slab m

gtreporting

DBMS

3030

Data CaptureData Capture

Sample identificationSample identification Log-In, reading, labelingLog-In, reading, labeling

Work schedulingWork scheduling Test initiation, test assignmentTest initiation, test assignment

Data acquisitionData acquisition Interfacing, instrument controlInterfacing, instrument control

3131

Data AnalysisData Analysis

Data transferData transfer Buffer tapping, file transferBuffer tapping, file transfer

Data processingData processing Conversion, reduction, specification Conversion, reduction, specification

review, statistical analysisreview, statistical analysis

3232

ReportingReporting

Client-centered reportsClient-centered reports User-defined reportsUser-defined reports Automated batch reportsAutomated batch reports Tabular and graphical formatsTabular and graphical formats Ad hoc queriesAd hoc queries Event triggersEvent triggers Exportation to external ISExportation to external IS

3333

Lab ManagementLab Management

Work schedulingWork scheduling Sample trackingSample tracking Job trackingJob tracking Standard Operating Protocols Standard Operating Protocols

(SOP)(SOP) Pricing and invoicingPricing and invoicing Cost analysisCost analysis

3434

Systems ManagementSystems Management

SecuritySecurity External: unauthorized accessExternal: unauthorized access Internal: data sabotageInternal: data sabotage

Data archivingData archiving MirroringMirroring Off-loadingOff-loading

Data warehousingData warehousing Long-term storageLong-term storage Far-off retrievalFar-off retrieval

3535

Enterprise-ScaleEnterprise-ScaleInformation ManagementInformation Management

Research &Development

Manufacturing

QualityControl

ProductSupport

RegulatoryAffairs

RawMaterials

CustomerService

QualityAssurance

Laboratory

3636

LIMS ImplementationLIMS Implementationlaboratoryobjectives

laboratoryoperations

functional requirement specifications

productselection

installation

lab personnel

vendors

customers

administration

IT department

validation

TIME (months)4

+6

+8

+9

+3 = 2.5 years

LIMS FunctionalityLIMS Functionality

Examples using LabwareExamples using Labware™™ LIMS LIMS

3838

Configuring for Each Configuring for Each UserUser

3939

Configuring LIMS for GxPConfiguring LIMS for GxP

4040

Providing SOPsProviding SOPs

4141

Labeling SamplesLabeling Samples

4242

Maintaining InstrumentsMaintaining Instruments

4343

Configuring Test ComponentsConfiguring Test Components

4444

Assigning Tests for SamplesAssigning Tests for Samples

4545

Scheduling TestsScheduling Tests

4646

Acquiring DataAcquiring Data

4747

Capturing DataCapturing Data

4848

Setting Result ResponsesSetting Result Responses

4949

Retesting with Audit TrailRetesting with Audit Trail

5050

Reviewing Sample StatusReviewing Sample Status

5151

Determining Chain of Determining Chain of CustodyCustody

5252

Reviewing ResultsReviewing Results

5353

Performing Quality ControlPerforming Quality Control

5454

Using Statistical Process ControlUsing Statistical Process Control

5555

Analyzing Laboratory OperationsAnalyzing Laboratory Operations

5656

Submitting ReportsSubmitting Reports

LIMS FunctionalityLIMS Functionality

Examples using LabVantage SapphireExamples using LabVantage Sapphire™™

5858

Web-Based Client PortalWeb-Based Client Portal

Source: Terry Smallmon, LabVantage

5959

Process-Oriented Process-Oriented NavigationNavigation

Source: Terry Smallmon, LabVantage

6060

Automated 2D Gel Automated 2D Gel LoadingLoading

Source: Terry Smallmon, LabVantage

6161

System IntegrationSystem Integration

Source: Terry Smallmon, LabVantage

6262

Access Image Data via Access Image Data via LIMSLIMS

Source: Terry Smallmon, LabVantage

6363

Connect DisparateConnect DisparateData Sources via LIMSData Sources via LIMS

Source: Terry Smallmon, LabVantage

6464

Link Results toLink Results toDatabase via Database via LIMSLIMS

Source: Terry Smallmon, LabVantage

6565

Link Multiple Search Link Multiple Search EnginesEnginesto Database via LIMSto Database via LIMS

Source: Terry Smallmon, LabVantage

6666

Link Visualization ToolsLink Visualization Toolsvia LIMSvia LIMS

Source: Terry Smallmon, LabVantage

6767

Automate Workflow via Automate Workflow via LIMSLIMS

Source: Terry Smallmon, LabVantage

Questions & Questions & CommentsComments