evolution of e-research
DESCRIPTION
Three generations of e-Research - a 20min presentation at the launch of e-XPO 2010 at Monash in August 2010TRANSCRIPT
The Evolution of e-Research
David De Roure
Overview
• e-Science: The Destination and the Journey
• Generation 1 – Early adopters
• Generation 2 – Embedding
• Generation 3 – Radical sharing
• Reflections
e-Science
• e-Science was defined by John Taylor (Director General of the UK Research Councils) asglobal collaboration in key areas of science and the next generation of infrastructure that will enable it
• e-Science was the name of the destination• It became the name of the journey• When we arrive, the destination is just called
science
26/2/2007 | myExperiment | Slide 4
Jeremy Frey
• Workflows are the new rock and roll
• Machinery for coordinating the execution of (scientific) services and linking together (scientific) resources
• The era of Service Oriented Applications
• Repetitive and mundane boring stuff made easier
Carole Goble
E. Science laboris
Kepler
Triana
BPEL
Taverna
Trident
Meandre
Galaxy
Box of Chemists
My Chemistry Experiment
Current practices of early adoptors of tools.Characterised by researchers using tools within their particular problem area, with some re-use of tools, data and methods within the discipline. Traditional publishing is supplemented by publication of some digital artefacts like workflows and links to data. Science is accelerated and practice beginning to shift to emphasise in silico work.
1st Generation Summary
• Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis in cattle
• Paul meets Jo. Jo is investigating Whipworm in mouse.
• Jo reuses one of Paul’s workflow without change.• Jo identifies the biological pathways involved in
sex dependence in the mouse model, believed to be involved in the ability of mice to expel the parasite.
• Previously a manual two year study by Jo had failed to do this.
Reuse, Recycling, Repurposing
“A biologist would rather share their toothbrush than their gene name”
Mike Ashburner and othersProfessor in Dept of Genetics,
University of Cambridge, UK
“Data mining: my data’s mine and your data’s mine”
mySpace for scientists!Facebook for scientists!Not Facebook for scientists!
Web 2
Open Repositories
Researchers
Social Network
The experiment that is
Developers
Social Scientists
“Facebook for Scientists” ...but different to Facebook!
A repository of research methods
A community social network of people and things
A Social Virtual Research Environment
A probe into researcher behaviour
Open source (BSD) Ruby on Rails app
REST and SPARQL interfaces, Linked Data compliant
Inspiration for: BioCatalogue, MethodBox and SysmoDB
myExperiment currently has 4989 members, 234 groups, 1260 workflows, 345 files and 129 packs
data
method
Results
Logs
Results
Metadata PaperSlides
Feeds into
produces
Included in
produces Published in
produces
Included in
Included in Included in
Published in
Workflow 16
Workflow 13
Common pathways
QTLPaul’s PackPaul’s PackPaul’s Research
Object
Paul’s Research
Object
1. Define tissue-containing area on slide→ nucleated area
2. Define relative stromal area (ratio: stroma/nuclei)
3. Define number of blood vessels
Antibody-treateduntreated
Nuclei Blood vessels
stroma merged
Biomedical TaskEffect of antibody treatment on tumour blood vessels and stroma?
David Abramson
Projects delivering now.Some institutional embedding.Key characteristic is re-use - of the increasing pool of tools, data and methods across areas/disciplines. Contain some freestanding, recombinant, reproducible research objects. New scientific practices are established and opportunities arise for completely new scientific investigations.Some expert curation.
2nd Generation Summary
Francois Belleau
“…to discover proteins that interact with transmembrane proteins, particularly those that can be related to neuro-degenerative diseases in which amyloids play a significant role”1) Taverna provenance exposed as RDF2) myExperiment RDF document for a protein discovery workflow3) Mocked-up BioCatalogue document using myExperiment RDF
data as example4) Provisional RDF documents obtained from the ConceptWiki
(conceptwiki.org) development server5) An RDF document for an example protein, obtained from the RDF
interface of the UniProt web site
A Bioinformatics Experiment A Bioinformatics Experiment Scott Marshall Marco Roos
How country is my country?
Digital Music Collections Crowdsourced
ground truthCommunity
Software
Linked Data Repository
Supercomputer
Structural Analysis of Large Amounts of Music Information
Digital Social ResearchDigital Social Research
• Data. ‘Born-digital’ data sources including social transactional data. Ease of access to secure data
• Capability. Increased capability in tools, infrastructure and services
Harnessing advances in digital technology and practice to achieve world-class social research with maximum impact
• Methods. Taking advantage of new data and capability, new forms of interpretative research
• Studies. Study of e Science, ‑understanding innovation pathways, and assessment of impact
The solutions we'll be delivering in 5 yearsCharacterised by global reuse of tools, data and methods across any discipline, and surfacing the right levels of complexity for the researcher. Routine use.Key characteristic is radical sharing .Research is significantly data driven - plundering the backlog of data, results and methods. Increasing automation and decision-support for the researcher - the VRE becomes assistive. Curation is autonomic and social.
3rd Generation Summary
Reflections
• Co-Evolution, Co-Design, Co-Constitution• Intellectual Access Ramps
– Incremental engagement– Safe places to play
• Datascopes– From signal to understanding– Medical images, music, ancient manuscripts– New born-digital data
Thanks to: Jeremy Frey & CombeChem; Carole Goble & myGrid; Iain Buchan, Sean Bechhofer & e-Laboratories; myExperiment; David Abramson; Marco Roos; Stephen Downie & SALAMI; the e-Social Science Directorate; Malcolm Atkinson
[email protected] Visit wiki.myexperiment.org
This presentation is in myExperiment Pack 141 and http://www.slideshare.net/dder/evolution-of-eresearch