The methodology used to design a useful and workable laboratory electronic notebook is described along with some of the technology needed to implement the smart lab systems

Frey, Jeremy

Hughes, Gareth V.

Mills, Hugo R.

Payne, Terry R.

schraefel, mc

Smith, Graham M.

English

Southampton (e-Prints Soton)

1Making TeaJeremy FreySchool of ChemistryUniversity of Southampton, UKA human centred approachto designing a pervasivesmart lab “notebook”TalkThe UK e-Science ProgrammeThe Comb-e-Chem ProjectSmart Tea or How to introduce ComputerScientists to the LabSmart Labs - data streams & inferenceRelational databases in science?The Ontological ImperativeThe future’s bright the future’s….2e-Science‘e-Science is about global collaboration in key areasof science, and the next generation ofinfrastructure that will enable it.’‘e-Science will change the dynamic of the wayscience is undertaken.’John Taylor, DG of UK OST ‘[The Grid] intends to make access to computingpower, scientific data repositories and experimentalfacilities as easy as the Web makes access toinformation’    Tony Blair, 2002The Comb-e-Chem ProjectThe exponential world of CombinatorialSynthesis and High throughput analysismeets the exponentially growing power ofcomputingFundingEPSRC, JISC, IBM, GSK, AZ, Southampton3•Comb-e-Chem Partners•Bristol •Chemistry •ECS•Stats•Chemistry•Combi •Centre•Southampton •IUPAC•RSC•IBM•CCDC•Pfizer•OMII•GSK•AZ•NCS •IT •InnovationSmart Tea PeopleElectronics and Computer ScienceGareth Hughes, Hugo Mills, Graham Smith, monicaSchraefel, Luck Moreau, Terry Payne, Dave DeRoureChemistryMartin Grossel & research groupJamie Robinson, Hongchen Fu, Sam Peppe4Laboratory ContextCOSHH Plan RecordAnnotationGuideExperimentersDigital ContextA chemistry lab is a hostile environmentwithout much room to maneuver                                          what can be captured capturedautomatically with sensors?what must rely on manual annotation?The fume cupboardThe chemist5Fume cupboardbad chemist: no gloves- with gloves - how id a process?Potential bar code location for process idvery precise scales - but not connected to any recording device Competition for space6multiple chemists concurrentlyworking in the labShared benchDirty glasswarestuffLog book of another chemistcritical data entryIndustrial supportBig block to publication@source: if it’s notdigital, it’s difﬁcult to share7no dedicated locationvulnerability of datacapturedaccess to data byothers is limitedprivilege (IP) • rightsuniquenesshistoryThe Lab book IIMany Lab book Replacements have been tried.Currently Southampton Chemists don’t use oneSo…..How would we succeed?8Getting not just the what and how, but the whyBy Making Tea!Problem: why make tea?We wanted to build a digitallab book replacement and theservices to support thatsystem.Even after the observationsand interviews, they knewabout the environment (good)But they didn’t know beyond ageneral sensewhat chemists did,how they did it orthe role the lab bookplayed in their doings.9Background: available approaches                      and problems in ucdObservation of an ExperimentExpert and artefact walk throughsApprenticeship and PrototypingCultural ProbesTask AnalysisDeconstruction/ReconstructionWhat we neededA way to compress timeA faithful, not overly simplified processA way to engage the processA language we (chemists and designers)could all understand to interogate theprocess (the experiment)Enter Analogy10Making Tea: designelicitation through analogyDeveloped and validatedthe analogy with chemistsGave us a way to askquestions that would nototherwise have beenpossibleLet us maximizeobservationGave us repeatabilityDerived rudiments of aprocess model, tooProvided lingua francawith chemistsReview over TeaWe ran through our lo-fi prototypes withchemists by running the tea experimentThey knew what was going on and couldcomment on veracity, features, processme11Cup of tea demoDigital Tea IIWe join our heroesafter havingcompleted Exp 1,Making Tea, and arenow into Exp 2Making a cup of Teawith Milk and SugarDesign based onwhat chemistsalready doRecording takes place throughout an experiment.In this clip- a reagent is measured out- the weight is entered by fast keypad input- a step is selected and ticked off when completed- the compound is  tested- that action is annotatedThe recording of steps is part of the COSSH requirementWe leverage this in our systemGetting realFunctional prototype for in-lab, real usetesting12ResultsIn real use,chemists wereable to record theirexperimentsAfter about tenminutes of use,they forgot about itas a new thing,and just used it“I can go anywhere and its, like,this is me and my data. It’s allthere! Bang!”Extensions: 3rd Yr UGProjectsRay CookeScrollingthrough labbooksWill DaviesAutomatingTLC platecapture forrecord andannotation13ModelsMaking Tea gave us:A new design elicitation method for looselystructured, high expertise domain processesFrom this, a way to model the interactionA functional interaction prototype toevaluate approachNo clearly defined architecture or modelNo plan entry or data retrieval interfaces(hope you don’t need your notes, guys)But…More ModelsBut TeaNot only valuable for understandinginteraction but also for developing a processmodelMaking Tea as an experiment formed  thebasis of our initial discussions for describingexperimental process for provenancemodelling14Data modelProcess recordProvenance recordMeasurementsProcessesAnnotationsService invocationsSecure time-stampsetc…Increasing detailPlanIntended actions:guide to chemist,or [later] workﬂowProcess record notationAnalyse a real experimentWhat information do chemists record?What should they record?What do they want to record?How does this differ from their experimentplan?Evolved our own graph of plan and recordInitially, this was to be modelled on tea, butwe tested it on one of the actualexperiments a chemist ran with the tea tablet151 1 2 2 1 3Sample of 4-flourinatedbiphenylAdd RefluxButanone Sample ofK2CO3PowderWeighgrammes 0.9031Measure40 mlAddWeigh2.0719 gtextButanone dried via silica column andmeasured into 100ml RB flask.Used 1ml extra solvent to wash outcontainer.Started reflux at 13.30. (Had tochange heater stirrer) Only refluxfor 45min, next step 14:15.Add Reflux AddDissolve 4-flourinatedbiphenyl inbutanoneAdd K2CO3powderHeat at refluxfor 1.5 hourstextAnnotateAnnotateIngredient ListFluorinated biphenyl 0.9 gBr11OCB 1.59 gPotassium Carbonate 2.07 gButanone 40 ml1 1 2 2 1 3Sample of 4-flourinatedbiphenylAdd RefluxButanone Sample ofK2CO3PowderWeighgrammes 0.9031Measure40 mlAddWeigh2.0719 gtextButanone dried via silica column andmeasured into 100ml RB flask.Used 1ml extra solvent to wash outcontainer.Started reflux at 13.30. (Had tochange heater stirrer) Only refluxfor 45min, next step 14:15.Add Reflux AddDissolve 4-flourinatedbiphenyl inbutanoneAdd K2CO3powderHeat at refluxfor 1.5 hourstextAnnotateAnnotateIngredient ListFluorinated biphenyl 0.9 gBr11OCB 1.59 gPotassium Carbonate 2.07 gButanone 40 ml16LessonsThat we need two related ontologiesPlan – that are going to be doneRecord – what was doneNot necessarily the same thingSteps are added/repeated during theexperimentDifferent annotations required for each17GridSemantic Grid?The Ontological ImperativeIs this categorical?Process Record Ontology18Example Record InstancesServicesResultsDataSemantic WebLinksUserData access viaSemantic WebSemanticDataProvenanceDataMiddleware(SOAP)Data storage via Jena Services ServicesResultsDataSemantic WebLinksUserData access viaSemantic WebSemanticDataProvenanceDataMiddleware(SOAP)Data storage via Jena19Questions – Plan ViewerA personal tablet ordistributedterminals?A pervasive issueGridPervasive Semantic Grid?20Web sites?www.combechem.orgwww.smarttea.orgThe Semiotic WebAre semantics sufficient?Chemists use signs and symbols as muchas, if not more than wordsIcons have a great significance – ThePeriodic TablePeople & Computers need to communicatewith each other as well as themselvesNeed a more powerful (general) conceptthan the semantic web & grid.

Making tea: a human centred approach to designing a pervasive smart lab notebook

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