Bhagat Myexperiment Bosc2008

Jiten BhagatUniversity of Manchester

David De Roure – University of SouthamptonCarole Goble – University of Manchester

Don Cruickshank – University of SouthamptonMarco Roos – University of Amsterdam

www.myexperiment.org

myExperiment: social software for sharing workflows

myExperiment: social software for sharing workflows

Sales PitchSales Pitch

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.

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

Use myExperiment to…Use myExperiment to…

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!)

Bare FactsBare Facts

• 16 months old

• Built on Ruby on Rails

• BSD License

• Source code hosted on RubyForge– Publicly available

• 2 core developers– 50% in Southampton,

50% in Manchester

• User driven design and development

Mar 2007 – start of projectJul 2007 – closed betaNov 2007 – open beta

Mar 2007 – start of projectJul 2007 – closed betaNov 2007 – open beta

Vitals – July 2008Vitals – July 2008

– 959 active users– 1429 unique IP visits in last month– 82 groups– 248 group memberships– 296 workflow entries, 425 workflow versions– 101 files– 1382 taggings– 46,427 downloads– 77,393 viewings– 408 creditations– 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

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 CONTEXTSETTING THE CONTEXT

Why do we need an environment like myExperiment?

Taverna Workflow WorkbenchTaverna 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

Part of the myGrid project

Who uses Taverna? Who uses Taverna? 350+ organisations40,000+ downloads

Users worldwide • Systems biology• Proteomics• Gene/protein annotation• Microarray data analysis• Medical image analysis• Heart simulations• High throughput screening• Genotype/Phenotype studies• Health Informatics• Astronomy• Chemoinformatics• Data integration

• ISMB07 – 6 posters, 2 demos,

1 BOF, 1 tutorial

Kepler

Triana

BPEL

Ptolemy II

Taverna

Encapsulating your ExperimentEncapsulating 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.

But…But…

• 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.

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.

Recycling, Reuse, RepurposingRecycling, Reuse, Repurposing

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.

Workflow ComponentsWorkflow Components

• See the internals of a workflow

• Aids decision making when deciding on reuse/repurposing

Workflow EnactmentWorkflow Enactment

myExperiment focuses on the special requirements of scientists, providing support for:

ownership,

credit and attribution,

licensing,

visibility and sharing.

Workflow UploadWorkflow Upload

Just Enough 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!

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.

PacksPacks

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.

Google GadgetsGoogle Gadgets

Taverna PluginTaverna Plugin • 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.

Developer SupportDeveloper Support

• 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/

FutureFuture

• 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 announcements– Group discussions– Group wiki pages

• Ability to aggregate external blog content and associate it with your user profile

Future – BioCatalogueFuture – BioCatalogue

• Fully curated catalogue of Web services

• Building on the work carried out for myExperiment

http://www.biocatalogue.org/

AcknowledgementsAcknowledgements

Come meet us at ISMBCome meet us at ISMB

• Demo: Tues 22nd 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 - myexperiment-discuss@nongnu.org

http://www.mygrid.org.uk

http://www.biocatalogue.orgMailing list - biocatalogue-friends@listserv.manchester.ac.uk