Science 2.0 and the Future of Publishing David De Roure
Position
The paper is an archaic human-readable form of a Research Object
The social process of Science 2.0 1.0
Digital Libraries
Virtual Learning Environment
Undergraduate Students
Next Generation Researchers
scientists
Graduate Students
Reprints PeerReviewed Journal & Conference Papers
Technical Preprints Reports & Metadata
experimentation
Repositories
Local Web
Certified Experimental Results & Analyses
Data, Metadata, Provenance, Scripts, Workflows, Services, Ontologies, Blogs, ...
“Facebook for Scientists” ...but different to Facebook! A repository of research methods A community social network of people and things A Virtual Research Environment
Open source (BSD) Ruby on Rails application with HTML, REST and SPARQL interfaces Project started March 2007 Closed beta July 2007 Open beta November 2007
myExperiment currently has 1800 registered users, 150 groups, 700 workflows and 50 packs. Go to www.myexperiment.org to access publicly available content or create an account.
myExperiment Features
User Profiles Groups Friends Sharing Tags Workflows Developer interface Credits and Attributions Fine control over privacy Packs Federation Enactment
Distinctives
Bringing myExperiment to the user
iGoogle
Taverna
Facebook
Windows 7
Sharing pieces of process
http://www.mygrid.org.uk/tools/taverna/
http://www.microsoft.com/mscorp/tc/trident.mspx
http://usefulchem.wikispaces.com/page/code/EXPLAN001
Reuse, Recycling, Repurposing
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.
Paul’s Pack
Included in
Workflow 16 Results
produces
QTL
Published in
Included in Feeds into
Logs
produces
Included in
Included in
Metadata
Slides
produces
Paper
Published in
Common pathways
Workflow 13
Results
Exporting packs
http://rdf.myexperiment.org/Aggregation/Pack/56
Scientific Discourse Relationships Ontology Specification
Open Provenance Model
Communications of the ACM 51, 4 (Apr. 2008), 52-58
The Seven Rs of Research Objects
Research Objects enable research to be: 1. 2. 3. 4. 5. 6. 7. Replayable – go back and see what happened Repeatable – run the experiment again Reproducible – new expt to reproduce results Reusable – use as part of new experiments Repurposeable – reuse the pieces in new expt Replicatable – run more of the same Robust – unbiased systematic science at speed
Curation
Self by Service Providers
refine validate seed refine validate
Experts
seed
Workflows and Services
refine validate seed
seed
refine validate
Social by User Community
Automated
e-Laboratory Evolution
1st Generation Current practice of early adoptors of e-Labs tools 2nd such as Taverna, ELNs, LIMS. Generation Designing and delivering tools within their Characterised by researchers using now, based on experience 3rd Generation with Taverna, myExperiment and tools, particular problem area, with some- re-use ofLablogs. delivering in 5 years The vision the e-Labs we'll be data and methods within the discipline. of science and open source science. Key characteristic is re-use - the increasing pool of illustrated by open Traditionaltools, data and methods, across areas & disciplines. publishing isCharacterised by global reuse of tools, data and supplemented by publication of some digital items like freestanding, recombinant, and surfacing the methods across links to data. Contain some workflows and any discipline, reproducible right not shared and Provenance is recordedResearch Objects. re-used. researcher. but levels of complexity for the analytics plays a role. Science is Provenance and practice beginning to accelerated Key characteristic is radical sharing Research shift to emphasise in silico supplemented by community Expert curation work. is significantly data driven - plundering the backlog of data, results and methods. curation. Research Objects supersede papers. New scientific practices are established and Increasing automation and decision-support for the opportunities arise for completely new scientific researcher - the e-Laboratory becomes assistive. investigations. Provenance assists design. Curation is autonomic and social. Entirely new research outcomes are obtained.
Summary
• Understand the Web 2 generation of researchers and the changing nature of research practice • Papers will be superseded by discoverable and shareable Research Objects that are:
replayable repeatable reproducible reusable repurposeable replicatable robust
• “Could I have a copy of your Research Object please?”
Contact David De Roure
dder@ecs.soton.ac.uk
Carole Goble
carole.goble@manchester.ac.uk
Visit wiki.myexperiment.org