1. my Experiment – A Web 2.0 Virtual Research Environment David De Roure Carole Goble

2. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 2 Overview e-Science is about scientists doing science –A Tale of Two Projects my Experiment Design Patterns for a VRE

3. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 3 X-Ray e-Lab Analysis Properties Properties e-Lab Simulation Video Diffractometer Grid Middleware Structures Database CombeChem pilot project www.combechem.org

4. E-Scientists Entire e-Science Cycle Encompassing experimentation, analysis, publication, research, learning Institutional Archive Local Web Publisher Holdings Digital Library E-Scientists Graduate Students Undergraduate Students Virtual Learning Environment E-Experimentation E-Scientists Technical Reports Reprints Peer- Reviewed Journal & Conference Papers Preprints & Metadata Certified Experimental Results & Analyses Data, Metadata & Ontologies http://www.ukoln.ac.uk/projects/ebank-uk/ Reducing time-to- experiment

5. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 5 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 Provenance The details of the origins of data are just as important to understanding as their actual values

6. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 6 My Chemistry Experiment Box of Chemists

7. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 7

8. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 8 The RDF Graph

9. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 9

10. e-Research workflows Aggregator services Institutional data repositories Data curation & preservation: databases & databanks Validation Harvest Data creation & capture in “Smart lab” Deposit Publishers: peer-review journals, conference proceedings Publication Validation Data analysis, transformation, mining, modelling Search, harvest Presentation services: portals Data discovery, linking, citation Linking, citation Laboratory repository Deposit (Chemistry Central) e-Crystals Federation model This work is licensed under a Creative Commons Licence Attribution-ShareAlike 2.0

11. NeSC VRE Workshop 9/15/2015 | | Slide 11 Key collective activities in e-science interpretation of data/events following through decisions/ coordinating activities producing documents & other artifacts archiving/recovering information informal and formal communication meetings http://www.aktors.org/coakting/

12. NeSC VRE Workshop What we learnt about VREs Reducing time-to-experiment Datasets as publication Provenance matters Publish the pieces, don’t warehouse Semantic Lab notebooks in the VRE Blogging the lab Federated back end Semantic DataGrid, built socially Deep integration with collaborative tools 26/2/2007 | myExperiment | Slide 12

13. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 13 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

14. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 14 my Grid Open 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 tools Individual scientists, in under-resourced labs, who use other people’s 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 science 33,000 downloads; 200+ user sites; 400+ workflows; 3500 third party external services accessible. Moved from prototype to production quality. Open Middleware Infrastructure Institute UK http://www.mygrid.org.uk

15. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 15 Taverna Workflow Workbench

16. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 16 Users in US, Asia, UK, Europe, Australia Systems biology Proteomics Gene/protein annotation Microarray data analysis Medical image analysis Heart simulation orchestration High throughput screening of chemical compounds Phenotypical studies Public Health studies Clinical trial analysis Plants, Mouse, Human Astronomy Cultural Heritage Widespread Adoption

17. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 17 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 review Trypanosomiasis 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

18. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 18 Service and workflow annotation Ontology 710 classes Full time curator Tagging by the masses 3500 service. 350 curated Provenance Ontology 35 classes Enriched with domain ontologies and service ontologies. Possibly. Export with data. Desirably.

19. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 19 New Scientific Digital Artefacts Design Workflow design history Experiment purpose Scientist LogBook Workflow run log Data lineage Results interpretation log

20. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 20 Kepler Triana New digital artefacts

21. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 21 myExperiment.org Portal Party 28th & 29th Sept 2006 Hand picked Taverna users + Taverna development team Facilitated by NCeSS. AJAX based development CombeChem xfer 1.A social networking environment for sharing any workflow 2.A Taverna workflow run environment 3.A multi-workflow launch environment

22. NeSC VRE Workshop 9/15/2015 | | Slide 22 Virtual Research Environments VRE 1 Technology-focused Experimental Diverse design & development approaches Stand-alone solutions VRE 2 User- & research practice- focused Developmental Unified design & development approaches Integrated solutions Collaboration Supporting small & large-scale research Support for single-disciplinary and multi-disciplinary research

23. NeSC VRE Workshop

24. 26/2/2007 | myExperiment | Slide 24 openwetware.org

25. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 25

26. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 26 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.

27. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 27 Principles Focus on making it easy to publish information –Discovering and sharing experimental artefacts –Publishing results to standard community repositories –Publishing scholarly output Familiar social networking / web paradigms –Keeping it free and fluid and creative. Me-Science. Crossing system boundaries –Trans-workflow Crossing discipline boundaries –Multi-disciplinary, Inter-disciplinary, Trans-disciplinary –Clustering expertise –Intellectual fusion outside discipline. We-Science. –Life Science, Social Science, Astronomy, Chemistry

28. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 28 Scoping exercise Workflow 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 resolution Open vs protected content Quality, Reliability, Validation, Safety, Intellectual Property, Ownership, Secrecy, A duty of guardianship. Curation? Policing? Local data mixed with shared resources Desktop integration Google gadgets for workflows. Interacting with workflows through Office products. Workflow execution (WHIP) Workflows Hosted in Portals project Evolving the myExperiment software Community development Enabling Scientists added value through applications and collaborative tagging

29. NeSC VRE Workshop Hack Fest 26/2/2007 | myExperiment | Slide 29

32. NeSC VRE Workshop Q1. Workflow Warehouse or Federation of Repositories? Everything on the myExperiment.org web site vs Distributed stores Multiple my Experiments 26/2/2007 | myExperiment | Slide 32

33. NeSC VRE Workshop Q2. Social Space or Shoe Shop? 26/2/2007 | myExperiment | Slide 33 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.

34. NeSC VRE Workshop Q3. How open is the content? OpenWetware is open Our users don’t want this Provenance helps 26/2/2007 | myExperiment | Slide 34

35. NeSC VRE Workshop Q4. Integration Bring user to Web Site vs Bringing my Experimentness to existing interfaces 26/2/2007 | myExperiment | Slide 35

36. NeSC VRE Workshop Web 2.0 Design Patterns http://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html 26/2/2007 | myExperiment | Slide 36 1.The Long Tail 2.Data is the Next Intel Inside 3.Users Add Value 4.Network Effects by Default 5.Some Rights Reserved 6.The Perpetual Beta 7.Cooperate, Don't Control 8.Software Above the Level of a Single Device

37. NeSC VRE Workshop 1. The Long Tail Our 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 37

38. NeSC VRE Workshop 2. Data is the Next “Intel Inside” my Experiment 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 my Experiment and provide its unique value. 26/2/2007 | myExperiment | Slide 38

39. NeSC VRE Workshop 3. Users Add Value my Experiment 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 39

40. NeSC VRE Workshop 4. Network Effects by Default my Experiment aggregates user data as a side-effect of using the VRE. The ability to execute workflows from my Experiment, and the integration of tools such as Taverna with my Experiment, further enable us to achieve increased value through usage. 26/2/2007 | myExperiment | Slide 40

41. NeSC VRE Workshop 5. Some Rights Reserved my Experiment 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 41

42. NeSC VRE Workshop 6. The Perpetual Beta my Experiment 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 42

43. NeSC VRE Workshop 7. Cooperate, Don't Control my Experiment 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 43

44. NeSC VRE Workshop 8. Software Above the Level of a Single Device The current model of Taverna running on the scientist’s desktop PC or laptop is evolving into my Experiment being available through a variety of interfaces and supporting workflow execution. 26/2/2007 | myExperiment | Slide 44

45. NeSC VRE Workshop Closing e-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 my Experiment 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 45

46. NeSC VRE Workshop 26/2/2007 | myExperiment | Slide 46 Take homes myExperiment is a Web 2.0 Environment for Scientists to share experiments Join us! David De Roure –dder@ecs.soton.ac.ukdder@ecs.soton.ac.uk Carole Goble –carole.goble@manchester.ac.ukcarole.goble@manchester.ac.uk

47. NeSC VRE Workshop Credits my Grid and CombeChem Matt Lee David Withers Don Cruickshank Rob Procter Alex Voss June Finch Ed Zaluska All the users inc. embedders 26/2/2007 | myExperiment | Slide 47