PPT - Designing the myExperiment Virtual Research Environment for

David De RoureUniversity of Southampton, UK

Carole Goble and Robert StevensThe University of Manchester, UK

Designing the myExperimentVirtual Research Environment for the Social Sharing of Workflows

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Motivation

Realisation

myexperiment.org

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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

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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.

Taverna downloads

41,344 sourceforge downloads by 29 November 2007Ranked in sourceforge top 200 in June 2007

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Taverna downloads per day

20072006200520042003

40

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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

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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.

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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.

Kepler

Triana

BPEL

Ptolemy II

Scientific memes. Scientific virusesAccompany their published outcomes

400+ Scufl workflows in the Web Cloud


New Scientist

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openwetware.org

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Blogging The Lab

Blogging the lab

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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

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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

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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!

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The Demo

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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.

1. A social networking environment for sharing any workflow

2. A Taverna workflow run environment

3. A multi-workflow launch environment


Scoping Challenges

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

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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

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Challenge: Policy and Permissions without Tears

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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

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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.

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Developers are Users Too.

How to Develop and Grow myExperiment?

Don’t just listen to the Scientist.

Get them to do the work!

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Web 2 Implementation


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Hack Fests


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CarlinCarlin Trials

(Closed beta)

System Model

User Model

Wallace Trials (Open beta)

EvolveModel

Mar

June

Sep

Nov

OS

PV

ersi

onin

g

Dec

Ena

ctm

ent

EM

Os

Codebase development

`

users

descriptions

groups

friendships

SearchAPI

tags

Enactor

Enactor API

Workflow API

blobsworkflows

Social NetAPI

TAG API

EMO

API

OwnershipSharing

API

EPrintsDSpaceFedoraS3SRB

EMOmanifest

HTMLXML

Snapshot map of resources with their relationships and versions

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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


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Our Approach

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


• 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

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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


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]

mailto:[email protected]

mailto:[email protected]

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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

Marco Roos

All the users inc. embedders

Documents

PPT - Designing the myExperiment Virtual Research Environment for