PPT

myExperiment – Defining the Social Virtual Research Environment

David De Roure, Carole Goble, Jiten Bhagat,Don Cruickshank, Antoon Goderis,Danius Michaelides and David Newman

• What is it?• How we built it• Towards the e-Laboratory

scientists

LocalWeb

Repositories

Graduate Students

Undergraduate Students

Virtual Learning Environment

Technical Reports

Reprints

Peer-Reviewed Journal &

Conference Papers

Preprints &

Metadata

Certified Experimental

Results & Analyses

experimentation

Data, Metadata Provenance WorkflowsOntologies

Digital Libraries

The social process of Science 2.0

Kepler

Triana

BPEL

Ptolemy II

Taverna

Trident

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.

Reuse, Recycling, RepurposingReuse, Recycling, Repurposing

myExperiment.org is… “Facebook for Scientists”...but

different to Facebook! A community social network Fine control over sharing A federated repository A gateway to other publishing

environments A platform for launching

workflows

Started March 2007 Closed beta since July 2007 Open beta November 2007 Go to www.myexperiment.org to

access publicly available content or create an account

myExperiment.org is...myExperiment.org is...

myExperiment currently has 1331 registered users, 114 groups, 536 workflows, 147 files and 40 packs

myExperiment currently has 1331 registered users, 114 groups, 536 workflows, 147 files and 40 packs

myExperiment.org is…

User Profiles Groups Friends Sharing Tags Workflows Developer interface Credits and Attributions Fine control over privacy Packs Federation Enactment

myExperiment FeaturesmyExperiment Features

Ownership and AttributionOwnership and Attribution

The most important aspect of myExperimentDesigned by scientists

The most important aspect of myExperimentDesigned by scientists

PacksPacks

Packs allow you to collect different items together, like you might with a "wish list" or "shopping basket"

You can collect internal things (such as workflows, files and even other packs) as well as link to things outside myExperiment

Your packs can then be shared, tagged, discovered and discussed easily on myExperiment

• How we built it

24/5/2007 | myExperiment | Slide 19

Search Engine

reviewsratingsgroupsfriendships

tags

Enactor

filesworkflows

`

HTML

For DevelopersFor Developers

RDF Store

SPAR

QL

endp

oint

Managed REST API

face

book

iGoo

gle

andr

oid

XML

APIconfig

mySQL

profiles

packscredits

For DevelopersFor Developers

All the myExperiment services are accessible through simple RESTful programming interfaces use your existing environment and augment it with

myExperiment functionality build entirely new interfaces and functionality

mashups The open source Web 2.0 Software that powers the

myexperiment.org web site is downloadable so you can run your own myExperiment – perhaps for your own lab or projects

Go to wiki.myexperiment.org for information about our Developer Community

Google GadgetsGoogle Gadgets

Bringing myExperiment to the iGoogle userBringing myExperiment to the iGoogle user

Taverna PluginTaverna Plugin

Bringing myExperiment to the Taverna userBringing myExperiment to the Taverna user

FacebookFacebook

SilverlightSilverlight

Exporting packsExporting packs

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX myexp: <http://rdf.myexperiment.org/ontology#>PREFIX sioc: <http://rdfs.org/sioc/ns#>select ?friend1 ?friend2 ?acceptedat where {?z rdf:type<http://rdf.myexperiment.org/ontology#Friendship> . ?z myexp:has-requester?x .?x sioc:name ?friend1 . ?z myexp:has-accepter ?y . ?y sioc:name ?friend2 .?z myexp:accepted-at ?acceptedat }

All accepted Friendships including accepted-at time Semantically-Interlinked

Online Communities

SPARQL endpointSPARQL endpoint

1. Fit in, Don’t Force Change2. Jam today and more jam

tomorrow3. Just in Time and Just

Enough 4. Act Local, think Global 5. Enable Users to Add Value6. Design for Network Effects

1. Fit in, Don’t Force Change2. Jam today and more jam

tomorrow3. Just in Time and Just

Enough 4. Act Local, think Global 5. Enable Users to Add Value6. Design for Network Effects

Six Principles of Software Design to Empower ScientistsSix Principles of Software Design to Empower Scientists

1. Keep your Friends Close2. Embed3. Keep Sight of the Bigger

Picture4. Favours will be in your

Favour5. Know your users6. Expect and Anticipate

Change

1. Keep your Friends Close2. Embed3. Keep Sight of the Bigger

Picture4. Favours will be in your

Favour5. Know your users6. Expect and Anticipate

Change

De Roure, D. and Goble, C. (2009) Six Principles of Software Design to Empower Scientists. IEEE Software (in press)

• Towards the e-Laboratory

e-Laboratory Lifecyclee-Laboratory Lifecycle

Workflow Monitoring

Event Logging

Social Metadata

Annotation Service

Search

User Registration

Distributed Data Query

Job ExecutionNaming and Identity

Anonymisation

Text Mining

Research ObjectManagement

Assembling e-LaboratoriesAssembling e-LaboratoriesExample Core Services

An e-Lab is a set of components and resources An open system, not a software

monolith Utility of components

transcends their immediate application

We envisage an ecosystem of cooperating e-Laboratories

What are the e-Lab components and services?

What are the Research Objects?

Research ObjectsResearch Objects

Workflows and Services

Experts

Social by User Community

refinevalidate

refinevalidate

Self by Service Providers

seed seed

refinevalidate

seed

Automated

refinevalidate seed

Content Capture and CurationReuse and SymbiosisReuse and Symbiosis

1. It should facilitate the management and sharing of Research Objects – these are the digital commodities that are used and reused by researchers, ranging from data and methods to scholarly publications.

2. It should support the social model: producers of research objects should have incentives to make them available; consumers need to be able to discover and reuse them; all will benefit from self- and community-curation.

3. It should provide an open, extensible environment to permit ease of integration with other software, tools and services, and benefit from participative contribution of software.

4. It should provide a platform to action research, for example to deliver research objects to remote services and software. It should be straightforward to create customised, task specific tools and environments.

Defining the Social Virtual Research EnvironmentDefining the Social Virtual Research Environment

ReflectionsReflections

myExperiment provides social infrastructure – it facilitates sharing and enables scientists to collaborate in order to compete

myExperiment has growing community and growing content Supports Taverna, Trident, UsefulChem, ... Kepler, Meandre next Scale makes discovery more difficult and easier! Could share R, matlab, statistical models, spreadsheets

We are targetting how we believe research will be conducted in the future, through the assembly of e-Laboratories which share Research Objects

Contact

David De Rouredder@ecs.soton.ac.uk

Carole Goblecarole.goble@manchester.ac.uk

Further infowiki.myexperiment.org

Thanks

The myGrid Family, National Centre for e-Social Science,CombeChem, Scientific Workflow Community