Jiten Bhagat University of Manchester David De Roure – University of Southampton Carole Goble – University of Manchester Don Cruickshank – University of Southampton Marco Roos – University of Amsterdam www.myexperiment.org myExperiment: social software for sharing workflows
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, reuse and repurpose workflows and reduce time-to-experiment, share expertise and avoid reinvention.
Use myExperiment to… Build packs of related content Share your workflows and files Control access to your workflows and files Find workflows and files that others have shared Maintain and use different versions of workflows Tag and rate workflows and files Write reviews and comments Have discussions and collaborate Create and join groups of similar interests Find people and make friends Send messages to other people on myExperiment Build your profile and reputation
Execute workflows directly within myExperiment
(if you have access to a remote Taverna enactor)
Reuse and repurpose workflows (and other files!)
16 months old
Built on Ruby on Rails
Source code hosted on RubyForge
2 core developers
50% in Southampton, 50% in Manchester
User driven design and development
Mar 2007 – start of project Jul 2007 – closed beta Nov 2007 – open beta
Vitals – July 2008
959 active users
1429 unique IP visits in last month
248 group memberships
296 workflow entries, 425 workflow versions
12 packs (with 237 total entries)
myExperiment has over 950 users (over 1400 unique IP visits last month) , 80 groups, 290 workflows, 100 files and 10 packs … with over 46,000 downloads of workflows/files
SETTING THE CONTEXT
Why do we need an environment like myExperiment?
Taverna Workflow Workbench
Taverna enables the interoperation between databases and tools by providing a toolkit for composing, executing and managing workflow experiments
Access to local and remote resources and analysis tools
Automation of data flow
Iteration over large data sets
Part of the myGrid project
Who uses Taverna?
Microarray data analysis
Medical image analysis
High throughput screening
ISMB07 – 6 posters, 2 demos,
1 BOF, 1 tutorial
Taverna Kepler Triana BPEL Ptolemy II
Encapsulating your Experiment
Workflows are protocols and records.
Explicit and precise descriptions of a scientific protocol
Scientific transparency. Easier to explain, share, relocate, reuse and repurpose and remember.
Provenance of results for credibility.
Workflows are know-how.
Specialists create applications; experts design and set parameters; inexperienced punch above their weight with sophisticated protocols
Workflows are collaborations.
Multi-disciplinary workflows promote even broader collaborations.
Workflow design is challenging and labour-intensive.
Reuse is highly desirable.
Reuse is a challenge
especially for individuals or small groups, decoupled from each other and acting independently.
workflows that cover processes outside of expertise.
workflows from a common pool of components.
workflows shared across discipline boundaries.
when inexperienced scientists need to leverage the expertise of others.
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.
As Taverna’s popularity increased we observed a workflow exchange activity emerging amongst our users and a strong desire for a place were workflows could be collected and opened to peer review.
myExperiment enables scientists to discover , reuse and repurpose workflows, and to enact them from a web page using a remote enactment service.
See the internals of a workflow
Aids decision making when deciding on reuse/repurposing
myExperiment focuses on the special requirements of scientists, providing support for: ownership , credit and attribution , licensing , visibility and sharing .
Just Enough Sharing….
myExperiment can provide a central location for workflows from one community/group
myExperiment allows you to say
Who can look at your workflow
Who can download your workflow
Who can modify your workflow
Who can run your workflow
myExperiment aids reuse because workflows can be discovered not just by what they do but based on how they are used by the community , with tags and reviews adding to the ‘collective intelligence’.
Workflows have friends (and social metadata) too!
Emphasising social networking around the workflows.
Attributions show what workflows/files it’s based on (= reuse/repurpose).
myExperiment is not just about workflows, it’s about sharing digital objects, which include data, results, provenance information, tags, associated documentation, etc. … collected together to form scientific research objects , for example to record an experiment.
myExperiment functionality can be accessed through simple RESTful APIs so that it can be accessed through existing interfaces, including wikis, web pages… and Taverna. Also enables the creation of other interfaces such as Google Gadgets, myExperiment add-ons for sites such as Facebook and functionality mashups over myExperiment.
One click' workflow launch from myExperiment to Taverna (using WHIP).
Browse the example workflows mantained and curated by a member of the Taverna team (Alan Williams).
Browse the latest workflows from myExperiment.
Search for workflows from myExperiment.
View a dynamic and resizeable tag cloud from myExperiment.
Get workflows based on a tag.
'Preview' a workflow - get more information from myExperiment about a workflow.
Open a workflow in design mode (when in the myExperiment section of the plugin).
Import a workflow into a current workflow in design mode.
myExperiment is an open source codebase (released under the BSD licence). Individuals and laboratories are free to install their own myExperiment instances.
Anyone can download and set up their own myExperiment - http://rubyforge.org/projects/myexperiment/
We have a new wiki to support external developers and their projects – http://wiki.myexperiment.org/
Ability to "subscribe" to a workflow or group
so that you can be updated whenever something new happens or something is updated (eg: a new comment or new tag is set).
Ability to attach documents and data to workflow entries in myExperiment.
Uploading Taverna 2, Triana, Trident and Pipeline Pilot workflows.
More group collaboration features
Group wiki pages
Ability to aggregate external blog content and associate it with your user profile
Future – BioCatalogue
Fully curated catalogue of Web services
Building on the work carried out for myExperiment
Come meet us at ISMB
Demo: Tues 22 nd July, 14:15
Stand: Booth 20, Manchester Bioinformatics
For more information… http://www.myexperiment.org http://wiki.myexperiment.org http://rubyforge.org/projects/myexperiment/ Mailing list - [email_address] http://www.mygrid.org.uk http://www.biocatalogue.org Mailing list - [email_address]