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David De Roure University of Southampton, UK Carole Goble The University of Manchester, UK

David De Roure University of Southampton, UK Carole Goble The University of Manchester, UK. A Web 2.0 Virtual Research Environment f or Collaboration and Sharing of Experiments. Motivation Realisation. myexperiment.org. E. Science laboris. Workflows are the new rock and roll.

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David De Roure University of Southampton, UK Carole Goble The University of Manchester, UK

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  1. David De Roure University of Southampton, UK Carole Goble The University of Manchester, UK A Web 2.0 Virtual Research Environment for Collaboration and Sharing of Experiments

  2. Motivation • Realisation myexperiment.org

  3. E. Science laboris • 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

  4. Taverna Workflow Workbench

  5. Taverna has averaged 40 downloads per day since 2006 41,344 sourceforge downloads by 29 November 2007 Ranked in sourceforge top 200 in June 2007

  6. Taverna domains • Systems biology • Proteomics • Gene/protein annotation • Microarray data analysis • Medical image analysis • Heart simulations • High throughput screening • Phenotypical studies • Phylogeny • Text mining • Plants, Mouse, Human • Astronomy

  7. Recycling, Reuse, 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.

  8. e-Services in the CLOUD Independent third party world-wide service providers of applications, tools and data sets. In the Cloud. 850 databases, 166 web servers Nucleic Acids Research Jan 2006 My local applications, tools and datasets. In the Enterprise. In the laboratory. Easily incorporate new service without coding. So even more services from the cloud and enterprise.

  9. e-Scientists in the CLOUD Individual life scientists, in under-resourced labs, who use other people’s applications, with little systems support. Exploratory workflows Developers (often) the users. Consumers are providers. A distributed, disconnected community of scientists.

  10. Scientific memes. Scientific virusesAccompany their published outcomes400+ Scufl workflows in the Web Cloud Kepler Ptolemy II Triana BPEL

  11. New Scientist

  12. openwetware.org

  13. Blogging The Lab • Blogging the lab

  14. Key evaluator and inspiration • Cat De Roure • Her idea. • 15 years old. • This is one of her MySpace pictures. • Facebook, LinkedIn, blah blah • Amazon, VivaLaDiva

  15. myExperiment.org is… • A market place. • A community social network. • A gateway to other publishing environments. • A federated repository • A platform for launching workflows. • Publishing self-describing Encapsulated myExperiment Objects. • Mindful publication. • Started March 2007. • Closed beta since July 2007 • Open beta November 2007

  16. myExperiment.org principles… • Make it easy to publish, easy to participate, easy to add value through mash-ups • Use familiar techniques • Shopping, Social networking • Use off the shelf, open source web tooling, not restrictive portals. Keep it funky, keep it flexible, keep it extensible. Assume other people will add functionality. • Ruby on Rails, Facebook platform • Aim it at young people. Make it fun and attractive. Say no to 1970s library interfaces! • Only do what users want

  17. The world isn’t just my workflows • Kepler, Triana, BPEL • Music Information Retrieval workflows • Experimental plans (chemistry) • And other stuff • Matlab scripts • Ontologies • Computational Economics • And the associated data!

  18. The Demo

  19. Parties 28th & 29th Sept 2006 Hand picked Taverna users + Taverna developers Facilitated by National Centre for e-Social Science AJAX based development Previous experiences from other projects: CombeChem, myTea. • A social networking environment for sharing any workflow • A Taverna workflow run environment • A multi-workflow launch environment 26/2/2007 | myExperiment | Slide 26

  20. Scoping Challenges Workflow warehouse / federation of repositoriesOpen Archives Initiative. Federated myExperiments. Sharepoint. Social space + organised rich siteSocial discourse + organised service / workflow space using curated semantics. Granularity and identifiersRolling-up provenance. Id resolution Open vs protected contentQuality, Reliability, Validation, Safety, Intellectual Property, Ownership, Secrecy, A duty of guardianship. Curation? Policing? Local data mixed with shared resources Desktop integrationGoogle gadgets for workflows. Interacting with workflows through Office products. Workflow execution(WHIP) Workflows Hosted in Portals project Evolving the myExperiment softwareCommunity development Enabling Scientists added valuethrough applications and collaborative tagging

  21. A Market Place: Shoe Shop? • Shopping for Workflows and Services and Data should be as easy as shopping for shoes. • Don’t need to train people. • Fuel for diagnostics. Find a similar workflow. • Organic growth good and bad. • We need good, organised metadata for automated use. • Impedance mismatch • Identity and Ontology Authority

  22. Challenge: Policy and Permissions without Tears

  23. Warehouse or Federation cloud laboratory project personal enterprise • Community web site, federated repository. • Multiple and My. • Publish what I want when I want within the group I want. • Mixed identity regimes: an identity authority • Open Archives Initiative. http://www.openarchives.org/ • The CombeChem project. http://www.combechem.org/

  24. A gateway to other publishing services • Tryps team already has a wiki • Mash up with Facebook and workflow hosting apps. • Bring functionality to the user. Cooperate! Don’t Control.

  25. Developers are Users Too. • How to Develop and Grow myExperiment? • Don’t just listen to the Scientist. • Get them to do the work!

  26. Hack Fests

  27. Management • Daily 5pm online meeting/telcon • Weekly management telcon • DDeR, Carole, Don, Jits, Rob • Monthly face-to-face • Hackfest, followed by • Management Meeting • Continuous user consultation • Duncan Hull, Danius Michaelides, Simon Coles, Paul Fisher, Jeremy Frey • Project Management Committee by email • Face 2 Face Team • DDeR • Carole • Ed • Don • Danius • Jits • Rob • Alex • Simon • Jeremy • Chris • Duncan • June • Katy • Stian • Antoon

  28. Web 2 Implementation

  29. Codebase development Enactment EMOs EvolveModel Versioning Wallace Trials (Open beta) OSP User Model System Model Carlin Carlin Trials (Closed beta) Nov Dec June Sep Mar

  30. Experiments are collections of stuff emo Mash up Application

  31. EMO Examples A workflow with its inputs and the products of executing it (including logs), perhaps multiple times Data from instruments, coupled with log book entries A collection of all the digital items associated with one experiment—including EMOs A collection of workflows with instructions and examples A reproducible academic paper with workflows and data

  32. EMO Challenges • How do I send an EMO by email? • Can I turn an EMO into a tarball? • Can I archive an EMO to a CDROM? • If I delete this file will it break anyone’s EMOs? • How do I trust an EMO? • How do I handle an EMO RESTfully? • Can my EMO link to objects outside the EMO? What happens when the parts are scattered across multiple stores? What happens if someone updates a part? How will my EMO be discovered on the Web? How can I work with an EMO offline? What is the provenance of the EMO and its parts? What happens if a part is unavailable?

  33. Our Approach • An EMO file is a Resource Map describing all the distinct parts contained in the EMO • Like a resource snapshot • EMOs map to the familiar folders and files interface Designed for compatibility with Linked Data and with Open Archives Initiative – Object Reuse and Exchange (OAI-ORE) which deals with compound object information and aims to build standardised and interoperable mechanisms

  34. Microsoft • Cool front end • Interface constructed using Silverlight • Desktop savvy • Feasibility of blending with desktop tools (e.g. excel) and exposing myExperiment objects through existing applications • Mashed up services • Demonstrate functionality mashups to build new services over the APIs including other science content in back end, EMOs and other content and information surfaced through other services • Research Information Centre • Windows workflows 24/5/2007 | myExperiment | Slide 48

  35. Timeline Closed Beta released in July 2007 Open Beta from November 2007 In “friends and family” trials now with bioinformaticians and chemists IntegratingTriana, talking with Kepler Enactment and EMOs coming next Music and social science in pipeline API available Open Source

  36. Take homes myExperiment is a Web 2.0 Environment for Scientists to share experiments Join us! David De Roure dder@ecs.soton.ac.uk Carole Goble carole.goble@manchester.ac.uk

  37. Credits • June Finch • Ed Zaluska • Jeremy Frey • Simon Coles • Danius Michaelides • Marco Roos • All the users inc. embedders myGrid and CombeChem Matt Lee David Withers Don Cruickshank David Newman Mark Borkum Rob Procter Alex Voss Duncan Hull Katy Wolstencroft

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