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


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.

The challenge for biology is complexity and heterogeneity, not so much compute.


Taverna Workflow Workbench



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


Recycling, Reuse, Repurposing


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.


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.


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


New Scientist


openwetware.org


Key evaluator and inspiration


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.”


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.


myExperiment.org principles…


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!


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.


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


A Social Network and Collective Intelligence


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?


Semantic Sweatshop


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


Leveraging and Serving The Long Tail of Users in the Cloud


– 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.


Warehouse or Federation


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


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.


We Need You! Cooperate, Don't Control


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?


A platform – popular request!


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.


Web 2.0 Design Patterns

http://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html


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


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.



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.



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.



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.



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.



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.



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.



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.


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


Hack Fest



Web 2 Implementation



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


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]


Credits

myGrid and CombeChem

Matt Lee

David Withers

Don Cruickshank

David Newman

Mark Borkum

Rob Procter

Alex Voss

Duncan Hull

Katy Wolstencroft


June Finch

Ed Zaluska

Jeremy Frey

Simon Coles

Danius Michaelides

Paul Fisher

Marco Roos

Stian Soiland

All the users inc. embedders

david de roure university of southampton, uk carole goble the university of manchester, uk a web 2.0...

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