David De Roure University of Southampton, UK Carole Goble The University of Manchester, UK A Web 2.0...
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Transcript of David De Roure University of Southampton, UK Carole Goble The University of Manchester, UK A Web 2.0...
David De RoureUniversity of Southampton, UK
Carole GobleThe University of Manchester, UK
A Web 2.0 Virtual Research Environment
OGF Semantic Grid Research Group
www.semanticgrid.org
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
3500+ 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.
200+ 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 virusesAccompany 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
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
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. http://www.openarchives.org/
The CombeChem project. http://www.combechem.org/
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
http://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html
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”
myExperiment 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 myExperiment and provide its unique value.
26/2/2007 | myExperiment | Slide 32
OGF21 Web 2.0 Workshop
3. Users Add Value
myExperiment 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
myExperiment aggregates user data as a side-effect of using the VRE.
The ability to execute workflows from myExperiment, and the integration of tools such as Taverna with myExperiment, further enable us to achieve increased value through usage.
26/2/2007 | myExperiment | Slide 34
OGF21 Web 2.0 Workshop
5. Some Rights Reserved
myExperiment 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
myExperiment 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
myExperiment 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 myExperiment 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
OGF21 Web 2.0 Workshop
OGF21 Web 2.0 Workshop
OGF21 Web 2.0 Workshop
OGF21 Web 2.0 Workshop
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 – [email protected]
Carole Goble – [email protected]
OGF21 Web 2.0 Workshop
Credits
myGrid 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