myExperiment A Web 2.0 Virtual Research Environment
David De Roure Carole Goble
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *Overviewe-Science is about
scientists doing scienceA Tale of Two ProjectsmyExperimentDesign
Patterns for a VRE
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *X-Ray
e-LabAnalysisPropertiesProperties
e-LabSimulationVideoDiffractometerGrid MiddlewareStructures
DatabaseCombeChem pilot projectwww.combechem.org
NeSC VRE Workshop
E-ScientistsEntire e-Science Cycle Encompassing experimentation,
analysis, publication, research, learningDigital
LibraryE-ScientistsGraduate StudentsUndergraduate
StudentsE-ExperimentationE-Scientistshttp://www.ukoln.ac.uk/projects/ebank-uk/Reducing
time-to-experiment
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *The key observation!
Publication at Source describes the need to capture data and its
context from the outset and maintain a complete end-to-end
connection between the laboratory bench and the intellectual
chemical knowledge that is published as a result of the
investigation
ProvenanceThe details of the origins of data are just as
important to understanding as their actual values
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *My Chemistry ExperimentBox of
Chemists
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *The RDF Graph
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
e-Research workflowsAggregator servicesInstitutional data
repositoriesData curation & preservation: databases &
databanksValidationHarvestData creation & capture in Smart
labDeposit Publishers: peer-review journals, conference proceedings
PublicationValidationData analysis, transformation, mining,
modellingSearch, harvestPresentation services: portalsData
discovery, linking, citationLinking, citationLaboratory
repositoryDeposit (Chemistry Central)e-Crystals Federation
modelThis work is licensed under a Creative Commons Licence
Attribution-ShareAlike 2.0
NeSC VRE Workshop
* | | Slide * Key collective activities in
e-scienceinterpretation of data/eventsfollowing through decisions/
coordinating activitiesproducing documents & other
artifactsarchiving/recovering information informal and formal
communicationmeetingshttp://www.aktors.org/coakting/
NeSC VRE Workshop
What we learnt about VREsReducing time-to-experimentDatasets as
publicationProvenance mattersPublish the pieces, dont
warehouseSemantic Lab notebooks in the VREBlogging the labFederated
back endSemantic DataGrid, built sociallyDeep integration with
collaborative tools26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *Bioinformatics is not
Chemistry There are many pieces, from many boxes, but no box, and
no lid with a complete picture of what the puzzle is supposed to
be.
Planning? No.Metadata an afterthought
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *myGridOpen Source middleware
for Life Scientists that enables them to undertake in silico
experiments and share those experiments and their results.Machinery
for linking together datasets and toolsIndividual scientists, in
under-resourced labs, who use other peoples datasets and
applications.Ad hoc & exploratory workflows (data flows) To
support sharing and collaboration between scientists to disseminate
best practice and improve the quality of science33,000 downloads;
200+ user sites; 400+ workflows;3500 third party external services
accessible.Moved from prototype to production quality.Open
Middleware Infrastructure Institute UKhttp://www.mygrid.org.uk
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *Users in US, Asia, UK, Europe,
AustraliaSystems biologyProteomicsGene/protein annotationMicroarray
data analysisMedical image analysisHeart simulation
orchestrationHigh throughput screening of chemical
compoundsPhenotypical studiesPublic Health studiesClinical trial
analysisPlants, Mouse, HumanAstronomyCultural HeritageWidespread
Adoption
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *Identified a pathway for which
its correlating gene (Daxx) is believed to play a role in
trypanosomiasis resistance. Manual analysis on the microarray and
QTL data failed to identify this gene as a candidate. Repetitive,
unbiased analysis. Paul Fisher et al A Systematic Strategy for
Large-Scale Unbiased Analysis of Genotype-Phenotype Correlations
Bioinformatics in reviewTrypanosomiasis cattle workflow reused
without change to identify the biological pathways involved in sex
dependence in the mouse model, previously believed to be involved
in the ability of mice to expel the parasite. Previously a manual
two year study of candidate genes had failed to do this. Recycling,
Reuse, Repurposing
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *Service and workflow
annotationOntology 710 classesFull time curatorTagging by the
masses3500 service. 350 curatedProvenanceOntology 35
classesEnriched with domain ontologies and service ontologies.
Possibly.Export with data. Desirably.
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *New Scientific Digital
ArtefactsDesignWorkflow design historyExperiment
purposeScientistLogBookWorkflow run logData lineageResults
interpretation log
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *New digital artefacts
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *myExperiment.org Portal
Party28th & 29th Sept 2006Hand picked Taverna users + Taverna
development teamFacilitated by NCeSS. AJAX based
developmentCombeChem xfer
A social networking environment for sharing any workflowA
Taverna workflow run environmentA multi-workflow launch
environment
NeSC VRE Workshop
* | | Slide *Virtual Research EnvironmentsVRE
1Technology-focusedExperimental Diverse design & development
approachesStand-alone solutions
VRE 2User- & research practice-focusedDevelopmental Unified
design & development approachesIntegrated solutions
CollaborationSupporting small & large-scale researchSupport
for single-disciplinary and multi-disciplinary research
NeSC VRE Workshop
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *openwetware.org
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *What are we trying to
do?Enabling scientists to be (more) creative.Enabling scientists to
be scientists. And not programmers.Enabling mediocre scientists to
become better and thus have better science.Enabling smart
scientists to be smarter and propagate their smartness.Accelerate
dissemination, pooling, insight.Encouraging sanctioned
plagiarism.
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *PrinciplesFocus on making it
easy to publish informationDiscovering and sharing experimental
artefactsPublishing results to standard community
repositoriesPublishing scholarly outputFamiliar social networking /
web paradigmsKeeping it free and fluid and creative.
Me-Science.Crossing system boundariesTrans-workflowCrossing
discipline boundariesMulti-disciplinary, Inter-disciplinary,
Trans-disciplinaryClustering expertiseIntellectual fusion outside
discipline. We-Science. Life Science, Social Science, Astronomy,
Chemistry
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *Scoping exerciseWorkflow
warehouse / federation of repositories Open Archives Initiative.
Federated myExperiments. Sharepoint.Social space + organised rich
site Social discourse + organised service / workflow space using
curated semantics.Granularity and identifiers Rolling-up
provenance. Id resolutionOpen vs protected content Quality,
Reliability, Validation, Safety, Intellectual Property, Ownership,
Secrecy, A duty of guardianship. Curation? Policing? Local data
mixed with shared resourcesDesktop integration Google gadgets for
workflows. Interacting with workflows through Office
products.Workflow execution (WHIP) Workflows Hosted in Portals
projectEvolving the myExperiment software Community development
Enabling Scientists added value through applications and
collaborative tagging
NeSC VRE Workshop
Hack Fest26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
NeSC VRE Workshop
NeSC VRE Workshop
Q1. Workflow Warehouse orFederation of Repositories?
Everything on the myExperiment.org web sitevsDistributed
stores
Multiple myExperiments26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
Q2. Social Space or Shoe Shop?26/2/2007 | myExperiment | Slide
*26/2/2007 | myExperiment | Slide *Shopping for Workflows and
Services and Data should be as easy as shopping for shoes.Organic
growth is good and bad.Social tagging might help discover workflows
but we need good metadata for automated use.
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Q3. How open is the content?OpenWetware is openOur users dont
want thisProvenance helps26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
Q4. IntegrationBring user to Web SitevsBringing myExperimentness
to existing interfaces26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
Web 2.0 Design
Patternshttp://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html26/2/2007
| myExperiment | Slide *The Long TailData is the Next Intel
InsideUsers Add ValueNetwork Effects by DefaultSome Rights
ReservedThe Perpetual BetaCooperate, Don't ControlSoftware Above
the Level of a Single Device
NeSC VRE Workshop
1. The Long TailOur target users are not just the specialist
e-Scientists using computing resources to tackle major scientific
breakthroughs, but also the large number of scientists conducting
the routine processes of science on a daily basis. Through sharing
we have the potential to enable smart scientists to be smarter and
propagate their smartness, in turn enabling other scientists to
become better and conduct better science.
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
2. Data is the Next Intel InsidemyExperiment understands that
scientists are focused on data, not software or one particular
workflow engine. Workflows are components of customised
applications, many of which are data-oriented rather than
process-oriented. Users manipulate, through their own applications,
the product (data, model) yielded by the workflow. Furthermore,
workflows themselves are the data of myExperiment and provide its
unique value.
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
3. Users Add ValuemyExperiment makes it easy to find workflows
and is designed to make it useful and straightforward to share
workflows and add workflows to the pool. To succeed we draw on the
insights into the incentive models of scientists gained through
experience with Taverna.
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
4. Network Effects by DefaultmyExperiment aggregates user data
as a side-effect of using the VRE. The ability to execute workflows
from myExperiment, and the integration of tools such as Taverna
with myExperiment, further enable us to achieve increased value
through usage.
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
5. Some Rights ReservedmyExperiment users require protection as
well as sharing, but the environment is designed for maximum ease
of sharing to achieve collective benefits workflows are "hackable"
and "remixable". Initiatives such as Science Commons provide a
useful context for this.26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
6. The Perpetual BetamyExperiment is an online service (a
collection of online services) and is continually evolving in
response to its users. To support this, the project commenced with
developers being embedded in the user community. Through day-to-day
contact between designers and researchers, design is both inspired
and validated.
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
7. Cooperate, Don't ControlmyExperiment is a network of
cooperating data services with simple interfaces which make it easy
to work with content. It both provides services and reuses the
service of others. It aims to support lightweight programming
models so that it can easily be part of loosely coupled
systems.
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
8. Software Above the Level of a Single DeviceThe current model
of Taverna running on the scientists desktop PC or laptop is
evolving into myExperiment being available through a variety of
interfaces and supporting workflow execution.
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
Closinge-Science is difficult workflows and Web 2.0 make it
easier.Our design workshops and the review against Web 2.0 design
patterns have revealed the relationship between myExperiment and
Web 2.0. The collective benefits of participation arise not only
from the users but also from the developers ease of use and ease of
development. It might be useful to review other VREs against the
design patterns.
26/2/2007 | myExperiment | Slide *
NeSC VRE Workshop
26/2/2007 | myExperiment | Slide *Take homesmyExperiment is a
Web 2.0 Environment for Scientists to share experiments
Join us!
David De Roure [email protected]
Carole Goble [email protected]
NeSC VRE Workshop
CreditsmyGrid and CombeChemMatt LeeDavid WithersDon
CruickshankRob ProcterAlex VossJune FinchEd ZaluskaAll the users
inc. embedders
26/2/2007 | myExperiment | Slide *
********Experiment API: Requests for information return
subgraphs not just triples containing requested resourcee.g.
getRecord() returns all processes and materials in the record
**ComplexOpen and trad publishersThis is the scope jisc
worldJsic work with all these stakeholders* We have constructed
some more pieces.
And some meta-pieces*SBML model building, sequence analysis,
microarray analysis, proteomics, QTL analysis, chemoinformatics,
high throughput screening, image processing, rendering Dilbert
cartoons
Taverna workflow workbench. Soaplab Web Service + Java +
Beanshell +++++
**Commercial use by Apple Corp + BioTeamUsers across USA and
EuropeEU EMBRACE NoESoaplab services supported by European
Bioinformatics Institute
Service providersBioMOBY, BluePrint, EMBOSS, BioMART Middleware
developersSemantic Grid technologies, workflowSIMDAT,EGEE,
GridSphere, SCECLife Science users and tool developersVirginia
Bioinformatics Institute, SDSC, UC Davis, USC, VL-e, Purdue, caBIG,
EMBRACECommercialLexicon Genetics, Apple, BioTeamHigh profile three
citations in Science May 2004 Distributed Computing
issueInternational invitations
*Confirmed by the biologistsWorm Lady's name is Joanne Pennock
and as far as I know she works for Prof. Richard K.Grencis.
DescriptionTrichuris muris - the mouse whipworm is a useful
parasite model of the human parasite - Trichuris trichuria.
Whipworms derive their name from their characteristic morphology.
Adults occupy the large intestine with their anterior ends embedded
in the cells lining the intestine. Transmission occurs by ingestion
of contaminated material.
Jo didnt know about the tools; she didnt know how to do it
properly. REUSE
Identified sex-dependant biological pathways involved in mouse
model. The correlation of sex depandance and the ability of mice to
expel the parasite had previously been hypothesised, however, had
not been verified using conventional manual analysis
techniques.
***Combine different formalisms in one system?E.g. a dataflow
Kahn network and a central- clock based calculus
Kepler logo**********
