Co-evolution of digital technologies and research methods David De Roure

e-Science e-Science was defined by John Taylor (Director General of the UK Research Councils) as global 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

Infrastructure Researchers

Infrastructure Researchers

Infrastructure Researchers

...the imminent flood of scientific data expected from the next generation of experiments, simulations, sensors and satellites Tony Hey and Anne Trefethen Source: CERN, CERN-EX ,

4 th Paradigm The Fourth Paradigm: Data-Intensive Scientific Discovery Presenting the first broad look at the rapidly emerging field of data- intensive science

BioEssays, 26(1):99–105, January 2004 Doug Kell

“e-research extends e-Science and cyberinfrastructure to other disciplines, including the humanities and social sciences.” e-Research

Digital Music Collections Student-sourced ground truth Community Software Linked Data Repositories Supercomputer 23,000 hours of recorded music Music Information Retrieval Community SALAMI

NRAO/AUI/NSF telescopes for the naked mind Datascopes Malcolm Atkinson From Signal to Understanding

Jeannette M. Wing COMMUNICATIONS OF THE ACM March 2006/Vol. 49, No. 3 Pages 33-35

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

co-shaping co-design co-creation co-constitution co-evolution co-construction co-  co-realisation

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 Carole Goble

“A biologist would rather share their toothbrush than their gene name” Mike Ashburner and others Professor in Dept of Genetics, University of Cambridge, UK

Data mining: my data’s mine and your data’s mine

 “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, supports Linked Data  Inspiration for: BioCatalogue, MethodBox and SysMO-SEEK myExperiment currently has 4767 members, 270 groups, 1848 workflows, 424 files and 174 packs

data method

Results Logs Results Metadata Paper Slides Feeds into produces Included in produces Published in produces Included in Published in Workflow 16 Workflow 13 Common pathways QTL Paul’s Pack Paul’s Research Object

Research Objects enable data-intensive research to be: 1.Replayable – go back and see what happened 2.Repeatable – run the experiment again 3.Reproducible – independent expt to reproduce 4.Reusable – use as part of new experiments 5.Repurposeable – reuse the pieces in new expt 6.Reliable – robust under automation 7.Referenceable – citable and traceable The Six Rs of Research Object Behaviours De Roure, D. (2010) “Replacing the Paper: The Twelve Rs of the e-Research Record”, Nature Network eResearch blog, article posted November 27, Available on

Semantically enhanced publication versus Shared digital Research Objects Challenging the mindset of immutable paper-sized chunks “Documents under glass”

Jeremy Frey

MethodBox Enable cross disciplinary research into Major Public Health problems Ease handling data and sharing results and insights

“…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 RDF 2)myExperiment RDF document for a protein discovery workflow 3)Mocked-up BioCatalogue document using myExperiment RDF data as example 4)Provisional RDF documents obtained from the ConceptWiki (conceptwiki.org) development server 5)An RDF document for an example protein, obtained from the RDF interface of the UniProt web site A Bioinformatics Experiment Scott Marshall Marco Roos

A scientific publishing perspective The “executable journal” is a platform for publishing experiments – the platform hosts the experiments – journal submissions both run on and add components to the platform To be discussed at the Future of Research Communication Executable Journals

Programmatic use, e.g. autonomic curation Research Objects contain process specifications Developing a “semantics” of Research Object execution and composition Combines REST, Linked Data and Programming Language semantics Computational Research Objects

1.Primacy of method in a data-centric world 2.Emergence of new sharable digital artefacts 3.Social Media elsewhere in the cycle 4.Executable papers and journals 5.Computational Research Objects Headlines

Thanks to: Carole Goble, myGrid and myExperiment; Iain Buchan; Sean Bechhofer; Doug Kell; Jeremy Frey; Marco Roos; Malcolm Atkinson.