David De Roure
University of Southampton, UK
Carole Goble and Robert Stevens
The University of Manchester, UK
Designing th...
JISC VRE Workshop 26/2/2007 | myExperiment | Slide 2
 Motivation
 Realisation
myexperiment.org
JISC VRE Workshop
E. Science laboris
24/5/2007 | myExperiment | Slide 3
 Workflows are the new rock and roll.
 Machinery...
JISC VRE Workshop
Recycling, Reuse, Repurposing
24/5/2007 | myExperiment | Slide 4
 Paul writes workflows for identifying...
Taverna downloads
41,344 sourceforge downloads by 29 November 2007
Ranked in sourceforge top 200 in June 2007
JISC VRE Workshop
Taverna downloads per day
20072006200520042003
40
JISC VRE Workshop
Taverna domains
24/5/2007 | myExperiment | Slide 8
 Systems biology
 Proteomics
 Gene/protein annotat...
JISC VRE Workshop
e-Services in the CLOUD
 Independent third party world-
wide service providers of
applications, tools a...
JISC VRE Workshop
e-Scientists in the CLOUD
 Individual life
scientists, in under-
resourced labs, who
use other people’s...
Kepler
Triana
BPEL
Ptolemy II
Scientific memes. Scientific viruses
Accompany their published outcomes
400+ Scufl workflows...
JISC VRE Workshop 26/2/2007 | myExperiment | Slide 12
New Scientist
JISC VRE Workshop
JISC VRE Workshop 26/2/2007 | myExperiment | Slide 16
openwetware.org
JISC VRE Workshop
Blogging The Lab
 Blogging the lab
JISC VRE Workshop
Key evaluator and inspiration
24/5/2007 | myExperiment | Slide 18
 Cat De Roure
 Her idea.
 15 years ...
JISC VRE Workshop
myExperiment.org is…
24/5/2007 | myExperiment | Slide 19
 A market place.
 A community social network....
JISC VRE Workshop
The world isn’t just my workflows
 Kepler, Triana, BPEL
 Music Information Retrieval
workflows
 Exper...
JISC VRE Workshop
The Demo
JISC VRE Workshop
JISC VRE Workshop
JISC VRE Workshop
JISC VRE Workshop
JISC VRE Workshop 26/2/2007 | myExperiment | Slide 27
Parties
 28th & 29th Sept 2006
 Hand picked Taverna users
+ Tavern...
JISC VRE Workshop 26/2/2007 | myExperiment | Slide 28
Scoping Challenges
 Workflow warehouse / federation of repositories...
JISC VRE Workshop
A Market Place: Shoe Shop?
24/5/2007 | myExperiment | Slide 30
 Shopping for Workflows and
Services and...
JISC VRE Workshop
Challenge: Policy and Permissions
without Tears
JISC VRE Workshop
Warehouse or Federation
24/5/2007 | myExperiment | Slide 37
 Community web site, federated
repository.
...
JISC VRE Workshop
A gateway to other publishing services
24/5/2007 | myExperiment | Slide 38
 Tryps team already has a wi...
JISC VRE Workshop
Developers are Users Too.
 How to Develop and Grow myExperiment?
 Don’t just listen to the Scientist.
...
JISC VRE Workshop
Web 2 Implementation
24/5/2007 | myExperiment | Slide 42
JISC VRE Workshop
Hack Fests
26/2/2007 | myExperiment | Slide 43
JISC VRE Workshop
26/2/2007 | myExperiment | Slide 44
Carlin
Carlin Trials
(Closed beta)
System
Model
User Model
Wallace T...
`
users
descriptions
groups
friendships
tags
Enactor
blobs
workflows
HTML
XML
Snapshot map
of resources
with their
relatio...
JISC VRE Workshop
EMO Examples
 A workflow with its inputs and
the products of executing it
(including logs), perhaps
mul...
JISC VRE Workshop
Our Approach
 Designed for compatibility with Linked Data and with Open
Archives Initiative – Object Re...
JISC VRE Workshop
Timeline
 Closed Beta released in July 2007
 Open Beta from November 2007
 In “friends and family” tr...
JISC VRE Workshop 26/2/2007 | myExperiment | Slide 61
Take homes
 myExperiment is a Web 2.0 Environment
for Scientists to...
JISC VRE Workshop
Credits
 myGrid and CombeChem
 Matt Lee
 David Withers
 Don Cruickshank
 David Newman
 Mark Borkum...
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PPT - Designing the myExperiment Virtual Research Environment for ...

  1. 1. David De Roure University of Southampton, UK Carole Goble and Robert Stevens The University of Manchester, UK Designing the myExperiment Virtual Research Environment for the Social Sharing of Workflows
  2. 2. JISC VRE Workshop 26/2/2007 | myExperiment | Slide 2  Motivation  Realisation myexperiment.org
  3. 3. JISC VRE 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
  4. 4. JISC VRE Workshop Recycling, Reuse, Repurposing 24/5/2007 | myExperiment | Slide 4  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.
  5. 5. Taverna downloads 41,344 sourceforge downloads by 29 November 2007 Ranked in sourceforge top 200 in June 2007
  6. 6. JISC VRE Workshop Taverna downloads per day 20072006200520042003 40
  7. 7. JISC VRE Workshop Taverna domains 24/5/2007 | myExperiment | Slide 8  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
  8. 8. JISC VRE Workshop 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.
  9. 9. JISC VRE 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.
  10. 10. Kepler Triana BPEL Ptolemy II Scientific memes. Scientific viruses Accompany their published outcomes 400+ Scufl workflows in the Web Cloud
  11. 11. JISC VRE Workshop 26/2/2007 | myExperiment | Slide 12 New Scientist
  12. 12. JISC VRE Workshop
  13. 13. JISC VRE Workshop 26/2/2007 | myExperiment | Slide 16 openwetware.org
  14. 14. JISC VRE Workshop Blogging The Lab  Blogging the lab
  15. 15. JISC VRE Workshop Key evaluator and inspiration 24/5/2007 | myExperiment | Slide 18  Cat De Roure  Her idea.  15 years old.  This is one of her MySpace pictures.  Facebook, LinkedIn, blah blah  Amazon, VivaLaDiva
  16. 16. JISC VRE Workshop myExperiment.org is… 24/5/2007 | myExperiment | Slide 19  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
  17. 17. JISC VRE Workshop 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!
  18. 18. JISC VRE Workshop The Demo
  19. 19. JISC VRE Workshop
  20. 20. JISC VRE Workshop
  21. 21. JISC VRE Workshop
  22. 22. JISC VRE Workshop
  23. 23. JISC VRE Workshop 26/2/2007 | myExperiment | Slide 27 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
  24. 24. JISC VRE Workshop 26/2/2007 | myExperiment | Slide 28 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
  25. 25. JISC VRE Workshop A Market Place: Shoe Shop? 24/5/2007 | myExperiment | Slide 30  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
  26. 26. JISC VRE Workshop Challenge: Policy and Permissions without Tears
  27. 27. JISC VRE Workshop Warehouse or Federation 24/5/2007 | myExperiment | Slide 37  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
  28. 28. JISC VRE Workshop A gateway to other publishing services 24/5/2007 | myExperiment | Slide 38  Tryps team already has a wiki  Mash up with Facebook and workflow hosting apps.  Bring functionality to the user. Cooperate! Don’t Control.
  29. 29. JISC VRE Workshop Developers are Users Too.  How to Develop and Grow myExperiment?  Don’t just listen to the Scientist.  Get them to do the work!
  30. 30. JISC VRE Workshop Web 2 Implementation 24/5/2007 | myExperiment | Slide 42
  31. 31. JISC VRE Workshop Hack Fests 26/2/2007 | myExperiment | Slide 43
  32. 32. JISC VRE Workshop 26/2/2007 | myExperiment | Slide 44 Carlin Carlin Trials (Closed beta) System Model User Model Wallace Trials (Open beta) Evolve Model Mar June Sep Nov OSP Versioning Dec Enactment EMOs Codebase development
  33. 33. ` users descriptions groups friendships tags Enactor blobs workflows HTML XML Snapshot map of resources with their relationships and versions
  34. 34. JISC VRE Workshop 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 24/5/2007 | myExperiment | Slide 47
  35. 35. JISC VRE Workshop 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 24/5/2007 | myExperiment | Slide 49 • 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
  36. 36. JISC VRE Workshop 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
  37. 37. JISC VRE Workshop 26/2/2007 | myExperiment | Slide 61 Take homes  myExperiment is a Web 2.0 Environment for Scientists to share experiments  Join us!  David De Roure – dder@ecs.soton.ac.uk  Carole Goble – carole.goble@manchester.ac.uk
  38. 38. JISC VRE 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 62  June Finch  Ed Zaluska  Jeremy Frey  Simon Coles  Danius Michaelides  Marco Roos  All the users inc. embedders
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