Laboratory Information Management Systems Revised & Expanded PDF
Preview Laboratory Information Management Systems Revised & Expanded
Laboratory Information Management Systems Second Edition, Revised and Expanded Christine Paszko Accelerated Technology Laboratories West End, North Carolina Elizabeth Turner USACE Washington Aqueduct Washington, D.C. Marcel Dekker, Inc. New York Basel • TM ThefirsteditionwaspublishedasLaboratoryInformationManagementSystems:De- velopmentandImplementationforaQualityAssuranceLaboratory,byMaryD.Hinton (1994). ISBN:0-8247-0521-1 This bookisprintedonacid-freepaper. Headquarters MarcelDekker,Inc. 270 MadisonAvenue,NewYork,NY10016 tel:212-696-9000;fax:212-685-4540 Eastern HemisphereDistribution MarcelDekkerAG Hutgasse4,Postfach 812,CH-4001 Basel,Switzerland tel:41-61-261-8482;fax:41-61-261-8896 WorldWideWeb http://www.dekker.com Thepublisheroffersdiscountsonthisbookwhenorderedinbulkquantities.Formore information,writetoSpecialSales/ProfessionalMarketingattheheadquartersaddress above. Copyright 2002byMarcelDekker,Inc.AllRightsReserved. Neither this book nor any part may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, microfilming, and re- cording, or by any information storage and retrieval system, without permission in writingfromthepublisher. Current printing(lastdigit): 10987654321 PRINTED INTHEUNITEDSTATESOFAMERICA Preface Theconceptoflaboratorydatamanagementisnotanewone.Theevolutionin LaboratoryInformationManagementSystems(LIMS)overthepast20yearsis astounding. There have been many changes in technology, including but not limitedtohardwareadvances,improvedsoftwaredevelopmenttools,commu- nications, and networking, that have accelerated the development of LIMS. ItisalsoimportantthatthereaderbeawarethataLIMSismorethansoftware; itisaprocessofintegrationthatencompasseslaboratoryworkflowcombined with user input, data collection (instrument integration), data analysis, user notification anddelivery ofinformation and reporting.This book attemptsto provide the reader with an easy-to-understand explanation of each aspect of aLIMSandabetterunderstandingofwhatisimportantinselectingandimple- menting a successful LIMS project. LIMS have evolved from notebooks to spreadsheetstosimplelaboratorydataacquisitionandstoragesystemstocom- plex relational database systems that integrate laboratory information with enterprise-widecomputingenvironmentstofacilitaterapidaccessofinforma- tion throughout an entire organization. The goal of this book is to introduce theconceptofaLIMS,LIMSfeatures,anexaminationoftheunderlyingtech- nology, and a look at the human factors involved. To assess the future direction of LIMS, it is necessary to understand how the current systems have evolved. Chapter 1 provides a brief historical perspectiveontheevolutionofLIMSandthetechnologythathasenabledthe data management revolution, and introduces future technological trends that willfuelthedevelopmentofLIMS.CommercialLIMShavebeenaroundsince the 1980s. In addition, many organizations have designed and implemented an in-house or ‘‘home brew’’ LIMS. The organizations that utilize a LIMS varygreatly,fromresearchlaboratoriestomanufacturinglaboratoriestocom- mercial testing laboratories; however, they are all basically organizing their iv Preface informationtomakequicker,moreinformeddecisionsandtosharethatinfor- mation. Thenextportionofthebookdealswiththehumanelement,thelabora- tory processes, and the people. Far too often this critical piece of a LIMS implementationisoverlooked.TheLIMSplanningcommitteecanspendcon- siderable time and resources in selecting a LIMS. However, if those in the laboratory are not allowed to participate in the process and are simply led to the LIMS, the results may be less than favorable. The input from laboratory personnelinLIMSselectionisvitaltoselectingtherightLIMSforthelabora- tory.Oneveryrealissuethathasn’tbeenaddressedinthepastisthepsychol- ogy of implementing a LIMS. Obtaining group acceptance of change in the laboratory infrastructure and incorporation of the needs of specific groups is critical for successful implementation. Additionally, many fear that automa- tion(LIMS)willeliminateorseriouslythreatentheirpositioninthecompany. These fears are real and need to be addressed. The next section examines LIMS in more detail and provides an over- view of how they are used across industries. Although the functions and re- quirementsofaLIMSmayvarybyindustry,therearesharedconceptsfunda- mental to all LIMS. We review a LIMS framework and discuss what the fundamentalelementsofaLIMSshouldinclude,regardlessoflaboratorytype. The features available in a LIMS are numerous and growing rapidly. Some features are basic to all LIMS while others are industry-specific. The role of the Internet as it relates to LIMS is also explored. Specific LIMS features integral to many LIMS, such as audit trails, automatic reporting capabilities (via e-mail, fax, or printed copy), import/export capabilities and data ware- housing will also be discussed. Theremainingchaptersdealwithmoretechnicalissues,includingestab- lishing laboratory requirements, outlining/ranking desirable features in a LIMS,databasedesignconsiderations,hardwareandoperatingsystemrequire- ments,andotherfundamentalconsiderationsinselectingaLIMS.Sincemany readersmayhavetheresponsibilityforpreparingarequestforproposal(RFP), achapterhasbeenincludedthatoutlinescriticalelementsinpreparingasolid RFPandprovidesanexample.FollowingtheRFPprocess,evaluationcriteria must be established so that when the proposals are received there is already amechanisminplacetoevaluatetheresponses.Theprocessofselectingand implementing a LIMS can be relatively painless if realistic selection criteria and a practical implementation plan are developed and followed. In addition tosatisfyingbasiclaboratoryfunctionssuchassampletrackinganddataentry, a LIMS must also comply with regulatory requirements and electronic data security in a laboratory. Regulations are often industry-specific. An entire Preface v chapter is dedicated to reviewing the regulatory requirements with which a LIMS must comply for various industries. Hardware and operating system requirementsofaLIMSmustalsobecarefullyconsidered.Softwareandhard- warecompatibility,networkdesign,andresourceutilizationarecriticaltothe optimization of a LIMS. A LIMS implementation plan should be developed once a LIMS has beenselected.Chapter11discusseskeyconsiderations,comparesphasedver- sus‘‘shotgun’’implementationapproaches,andprovidesasampleimplemen- tationplan. Validationisthelast stepoftheLIMS implementationand often a continual step as new functionality is incorporated. The validation process ensuresthattheLIMSwillmeetspecificationsandconformtopredefinedqual- ity assurance criteria. Requirements of a successful LIMS validation are dis- cussed. Thefinalchapterscoverthedevelopmentofimplementationandvalida- tion plans of the LIMS. It is important to realize that purchasing a LIMS is notastaticprocess;rather,itisconstantlychanginginresponsetothelabora- torydatamanagementrequirements.Advancesintechnologyoccur,thesead- vances are transferred to the laboratory environment. One example is, Web access to laboratory results. We have provided several pages of additional LIMS resources, including a list of LIMS vendors, a listing of Web sites, a comprehensive glossary of terms, and a suggested reading list. The authors wish to thank Don Kolva and Lisa Gorenflo of ATL, Inc. for their critical review and encouragement; Tom Jacobus and Lloyd Stowe of the USACE WashingtonAqueduct;andKevinDixonoftheNJ-AmericanWaterCompany for their support. We also wish to thank Annie Cok of Marcel Dekker, Inc. forher support andassistance;and DavidTurner,who put upwithElizabeth usurpingtheircomputerfornumerousmonths,forhissupportandencourage- ment. It is our hope that after having read this book the reader will have a solid LIMS knowledge base on which to build. Christine Paszko Elizabeth Turner Contents Preface 1. Historical Perspective 2. LIMS Fundamentals: Overview of Laboratory Information System Development and Project Planning 3. Data Management and Basic LIMS: Functional Requirements and Features 4. Data Management and Advanced LIMS: Functional Requirements and Features 5. Life Cycle of LIMS Software Development 6. Regulatory Requirements 7. Hardware and Operating System Requirements 8. Obtaining Laboratory Personnel Input 9. Critical Elements in Preparing a Request for Proposal 10. LIMS Evaluations 11. Enhancing Data Quality with LIMS viii Contents 12. LIMS Validation Appendix A: Sample Request for Proposal Appendix B: Sample Scripted Demonstration 1 Historical Perspective BeforewecandiscussLaboratoryInformationManagementSystems(LIMS), wemustfirstunderstandthetechnologyandtoolsthatenabledthecreationof thesesophisticatedsoftwarepackagesthatarereplacingscientists’notebooks. Table1outlinesabriefdescriptionofthetechnologicaleventsrelevanttothis through today. With the pace that technology is moving, there will undoubt- edlybemanymoreadvancementsafterthepublicationofthisbook.Theevolu- tionofLIMSisaninterestingone.Inthebeginning,therewerescientistswith laboratory notebooks and everything was hand-written: dates, experimental designs, results, comments, observations, and more. In the early days of computer-basedLIMS,therewerehost-basedsystemsconnectedtoterminals byseriallines:alloftheprocessingwasperformedonthehost.Uponcomple- tion oftheprocessing,thehost wouldpostresults totheterminalswithin the laboratory. These systems lacked flexibility. Only very wealthy companies had access to these early systems and advancedtechnology.TheymadeacommitmenttotheLIMSconceptdespite the high cost because they realized that those who could deliver the correct information, ahead of their competition and at a competitive price, would emergeasthemarketleader.Theseindustriesunderstoodthatknowledgetruly ispower.Thesameistruetoday.Onlytoday,inadditiontofasterandbetter, themarketalsodemandsevenmoreaffordableinformationmanagementsolu- tions.Todayclient/serverLIMSarchitectureasshowninFigure1isincreas- ingly popular. 2 Chapter1 Table1 ABriefChronologyofComputers 5000yearsago,itwastheabacus;thatwaseventuallyreplaced bypaper andpen- cils. 1623 GermanscientistWilhelmSchikardinventsamachinethatuses11com- pleteand6incompletesprocketedwheelsthat couldaddand,withthe aidof logarithmtables,multiplyanddivide. 1642 Frenchphilosopher,mathematician,andphysicistBlaisePascalinventsa machine(thePascaline) thataddedandsubtracted,automaticallycar- ryingandborrowingdigitsfromcolumntocolumn. 1694 GottfriedWilhemvonLeibniz(1646–1716)improvesthePascalinebycre- atingamachinethatcouldalsomultiply.Likeitspredecessor,Leibniz’s mechanicalmultiplierworkedbyasystemofgearsanddials. 1822 TheDifference EngineisdesignedbyBritishmathematicianandscientist Charles Babbage.Babbage’sassistant,AugustaAdaKing,theCountess ofLovelace (1815–1842)anddaughterofEnglishpoetLordByron,is instrumentalinthemachine’sdesign.Inthe 1980s,theUSDepartment ofDefense namedaprogramminglanguageADAafterher. 1930 AmericanelectricalengineerVannBushproducesthefirstpartially elec- troniccomputercalledadifferentialanalyzer,capableofsolvingdiffer- entialequations. 1942 AmericantheoreticalphysicistJohnV.AtanasoffandhisassistantClifford Barrybuildthe firstcomputerthatsuccessfully usesvacuumtubesto performcalculations.ThemachineiscalledtheAtanasoffBerryCom- puter,orABC. 1944 AtHarvardUniversity,theHarvard–IBM AutomaticSequenceControlled Calculatorisdevelopedunderthedirectionof HowardHathawayAiken. Itcontainedmorethan750,000partsandtakesafewsecondstocom- pletesimplearithmeticcalculations. 1945 AttheInstituteforAdvancedStudyinPrinceton,Hungarian–American mathematicianJohnVonNeumanndevelopsoneofthe firstcomputers usedtosolveproblemsinmathematics,meteorology,economics,andhy- drodynamics.VonNeumann’sElectronicDiscreteVariableComputer (EDVAC)isthefirstelectroniccomputertouseaprogramstoreden- tirelywithinitsmemory. 1946 Thefirstautomaticelectronicdigitalcomputer,ENIAC,constructedatHar- vardUniversitybyelectricalengineersJohnPresperEckertandJohn WilliamManchlyinconsultationwithJohnAtanasoff.Theelectronicnu- mericalintegratorandcomputercontainsradiotubesandrunsbyelectri- calpowertoperformhundredsofcomputationspersecond. 1946 Theword‘‘automation’’isusedforthefirsttime,byFord MotorCom- panyengineerDelmarHardertodescribethe14minprocessbywhich Ford enginesareproduced. HistoricalPerspective 3 Table1 Continued 1948 AtBellTelephone Laboratories,AmericanphysicistsWalterHouserBrat- tain,JohnBardeen,andWilliamBradfordShockleydevelopthetransis- tor:adevicethat canactasanelectricalswitch. 1949 BritishbiochemistDorothyCrowfootHodgkinisthefirsttoenlisttheaid ofanelectroniccomputerindiscoveringthestructureofanorganiccom- pound:penicillin. 1951 TheUnivaccomputerisintroducedforbusinessusebyRemingtonRand. 1953 IBMintroducestheIBM701,thefirstcomputerforscientificandbusiness use. 1955 TheIBM752,thecompany’sfirstcomputerdesignedexclusivelyforbusi- nessuse,isproduced. 1959 Themicrochip,an integratedcircuitmadeof asinglesiliconwafer,isin- ventedbyAmericanengineersJackKilbyofTexasInstrumentsandRob- ertNoyceofFairchildSemiconductors. 1960s RaymondGoertzatArgonneNationalLaboratoryinArgonne,Illinois,and IvanSutherlandatthe MassachusettsInstituteofTechnologyinCam- bridge,Massachusetts,demonstratedearlyversionsofhead-mounteddis- plays(HMDs)usedinvirtualreality. 1960s Computerscomeintocommonusageingovernment andindustry,butfor manyyearstheyarenotavailabletomostconsumers. 1970 U.S.scientistTedHoff,workingforIntel,inventsthemicroprocessor,a siliconchipcontainingthe centralprocessorofacomputer. Theversa- tilechipwillleadtothe proliferationofsmallinexpensive computers forhomeandbusinessuse.Intelmicroprocessorswillbemarketedcom- merciallyin1971forthefirsttime. 1973 TheInternetiscreatedinlargepartbyAmericancomputerscientistVin- tonCerf,aspartoftheUnitedStatesDepartmentofDefenseAdvanced ResearchProjectsAgency(DARPA). 1974 Atext-editingcomputerwithacathode-raytubevideoscreenanditsown printerisputonthe AmericanmarketbyVydek. 1975 Thefirstpersonalcomputer,theAltair,isputonthemarketbyAmerican inventorEdRoberts.TheAltair8800usesan8-bitIntel8080micropro- cessor,has256bytesofRAM,receivesinputthroughswitchesonthe frontpanel,anddisplaysoutput onrowsoflight-emitting diodes (LEDs). 1975 AmericansWilliamHenryGatesIIIandPaulGardnerAllenfoundMicro- soft,whichwillbecometheworld’s mostsuccessfulmanufacturerof computersoftware. 1976 Ironicallyjustayearlater,Tagamet,adrugforthetreatmentofulcers,be- comesavailable.By1990,itwillbe themostfrequentlyprescribeddrug intheUnitedStates.
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