David De Roure University of Southampton, UK Carole Goble The University of Manchester, UK A Web 2.0 Virtual Research Environment OGF Semantic Grid Research Group

OGF21 Web 2.0 Workshop 1.Motivation 2.Design 3.Realisation 26/2/2007 | myExperiment | Slide 2 Overview

OGF21 Web 2.0 Workshop E. Science laboris 24/5/2007 | myExperiment | Slide 3 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. The challenge for biology is complexity and heterogeneity, not so much compute.

OGF21 Web 2.0 Workshop Taverna Workflow Workbench 24/5/2007 | myExperiment | Slide 4

OGF21 Web 2.0 Workshop Taverna domains 24/5/2007 | myExperiment | Slide 5 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

OGF21 Web 2.0 Workshop Recycling, Reuse, Repurposing 24/5/2007 | myExperiment | Slide 6 Paul meets Jo. Trypanosomiasis cattle workflow reused without change. Identified 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, by Jo, of candidate genes had failed to do this.

OGF21 Web 2.0 Workshop service operations All major providers Integration application for service providers like BioMOBY and BioMART 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.

OGF21 Web 2.0 Workshop 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. Decoupled suppliers and consumers of services and workflows. Scientists in an enterprise and in large projects Scientists out of the enterprise, in small projects or sole traders projects and sites, ~1000 individual users. Users throughout UK, USA, Europe, and SE Asia

39,326 total sourceforge downloads (4 October 2007). Ranked in sourceforge top 200 (June 07).

Kepler Triana BPEL Ptolemy II Scientific memes. Scientific viruses Accompany their published outcomes 400+ Scufl workflows in the Web Cloud

OGF21 Web 2.0 Workshop 26/2/2007 | myExperiment | Slide 11 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

OGF21 Web 2.0 Workshop 26/2/2007 | myExperiment | Slide 12 New Scientist

OGF21 Web 2.0 Workshop

26/2/2007 | myExperiment | Slide 14 openwetware.org

OGF21 Web 2.0 Workshop Key evaluator and inspiration 24/5/2007 | myExperiment | Slide 15 Cat De Roure Her idea. 15 years old. This is one of her MySpace pictures. Immediately understood it. Immediately could use it. “It’s like MySpace for science homework.”

OGF21 Web 2.0 Workshop myExperiment.org is… 24/5/2007 | myExperiment | Slide 16 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.

OGF21 Web 2.0 Workshop myExperiment.org principles… 24/5/2007 | myExperiment | Slide 17 Make it easy to publish, easy to participate, easy to add value to though mash-ups Use familiar techniques –Shopping, Social networking, gaming 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!

OGF21 Web 2.0 Workshop 26/2/2007 | myExperiment | Slide 18 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

Front End. A market place. A community social network. User Participation.

OGF21 Web 2.0 Workshop A Market Place: Shoe Shop? 24/5/2007 | myExperiment | Slide 20 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

Screen shot of bio Service shopping site

OGF21 Web 2.0 Workshop A Social Network and Collective Intelligence 24/5/2007 | myExperiment | Slide 22 Source of large amount of metadata. Open tagging, folksonomies, blogging, profiles, recommendations. Social network analysis and e-tracking are valuable intelligence. How do we avoid being deafened by the shouting? What are the incentive models for scientists?

OGF21 Web 2.0 Workshop Semantic Sweatshop 24/5/2007 | myExperiment | Slide 23 Service vocabularies and curation in the wild –Keywords and tagging only goes some of the way. –Curation Workflow metadata –Find a workflow that is similar to what I want or need; similar to this one. Or hers. Hmmmm. Recommendations, people profiles Fuel for discovery and diagnostics Pipeline from tag cloud to shop Semantic

OGF21 Web 2.0 Workshop Leveraging and Serving The Long Tail of Users in the Cloud 24/5/2007 | myExperiment | Slide 24 –Small labs or individuals –Specialist workflows, Niche –Expert and inexpert –Big labs & big groups –Common de facto workflows

Back End. Federated repositories. A gateway to other publishing environments. A platform for launching workflows. User Participation.

OGF21 Web 2.0 Workshop Warehouse or Federation 24/5/2007 | myExperiment | Slide 26 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. The CombeChem project. cloud enterprise personal laboratory project

OGF21 Web 2.0 Workshop A gateway to other publishing services 24/5/2007 | myExperiment | Slide 27 Tryps team already has a wiki Mash up with Facebook and workflow hosting apps. Bring functionality to the user. Cooperate! Don’t Control.

OGF21 Web 2.0 Workshop We Need You! Cooperate, Don't Control 24/5/2007 | myExperiment | Slide 28 A network of cooperating data services with simple interfaces which make it easy to work with content. Provides services Reuses the service of others. Support lightweight programming models so that it can easily be part of loosely coupled systems. You add a mashup! Workflows as content syndication?

OGF21 Web 2.0 Workshop A platform – popular request! 24/5/2007 | myExperiment | Slide 29 See a workflow? Launch it! Coming soon…. –The ability to execute workflows from myExperiment + integration of tools such as Taverna achieves increased value through usage – network effects. –And lets do that with Kepler, Triana etc –The WHIPs project for a workflow hosting portal environment. Funded by OMII-UK. Run by Triana! –Handling of results? Wiki pages? Workflows available through a variety of interfaces supporting workflow execution.

OGF21 Web 2.0 Workshop Web 2.0 Design Patterns 26/2/2007 | myExperiment | Slide 30 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

OGF21 Web 2.0 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 31

OGF21 Web 2.0 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 32

OGF21 Web 2.0 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 33

OGF21 Web 2.0 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 34

OGF21 Web 2.0 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 35

OGF21 Web 2.0 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 36

OGF21 Web 2.0 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 37

OGF21 Web 2.0 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 38

myExperiment makes it really easy for the next generation of scientists to contribute to a pool of scientific workflows, build communities and form relationships It enables scientists to share, re-use and repurpose workflows and reduce time-to-experiment, share expertise and avoid reinvention myexperiment.org

OGF21 Web 2.0 Workshop Hack Fest 26/2/2007 | myExperiment | Slide 40

OGF21 Web 2.0 Workshop Web 2 Implementation 24/5/2007 | myExperiment | Slide 41

OGF21 Web 2.0 Workshop

Timeline Closed Beta released in July 2007 Open Beta from November 2007 In “friends and family” trials now with bioinformaticians and chemists Linking up to Triana Enactment and EMOs coming next Music and social science in pipeline

OGF21 Web 2.0 Workshop 26/2/2007 | myExperiment | Slide 48 Take homes myExperiment is a Web 2.0 Environment for Scientists to share experiments Join us! David De Roure Carole Goble

OGF21 Web 2.0 Workshop Credits my Grid and CombeChem Matt Lee David Withers Don Cruickshank David Newman Mark Borkum Rob Procter Alex Voss Duncan Hull Katy Wolstencroft 26/2/2007 | myExperiment | Slide 49 June Finch Ed Zaluska Jeremy Frey Simon Coles Danius Michaelides Paul Fisher Marco Roos Stian Soiland All the users inc. embedders