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 Graduate Students Undergraduate Students experimentation Data, Metadata Provenance Workflows Ontologies Digital Libraries The social process of Science 2.0 Local Web Repositories Virtual Learning Environment Technical Reports Reprints Peer-Reviewed Journal & Conference Papers Preprints & Metadata Certified Experimental Results & Analyses
Taverna Trident Kepler Triana BPEL Ptolemy II
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, Repurposing
“ 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 currently has 1331 registered users, 114 groups, 536 workflows, 147 files and 40 packs
Credits and Attributions
Fine control over privacy
Ownership and Attribution The most important aspect of myExperiment Designed by scientists
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
HTML For Developers mySQL Search Engine reviews ratings groups friendships tags Enactor files workflows ` RDF Store SPARQL endpoint Managed REST API facebook iGoogle android XML API config profiles packs credits
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 Gadgets Bringing myExperiment to the iGoogle user
Taverna Plugin Bringing myExperiment to the Taverna user
Six Principles of Software Design to Empower Scientists
Keep your Friends Close
Keep Sight of the Bigger Picture
Favours will be in your Favour
Know your users
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
Workflow Monitoring Event Logging Social Metadata Annotation Service Search User Registration Distributed Data Query Job Execution Naming and Identity Anonymisation Text Mining Research Object Management Assembling e-Laboratories Example 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?
Content Capture and Curation Workflows and Services Experts Social by User Community refine validate refine validate Self by Service Providers seed seed refine validate seed Automated refine validate seed Reuse and Symbiosis
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.
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.
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.
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 Environment
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
David De Roure
The myGrid Family, National Centre for e-Social Science, CombeChem, Scientific Workflow Community