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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