Post on 29-Dec-2015
Designing, Executing, Reusing and Sharing Workflows: Taverna and
myExperiment Supporting the in silico Experiment Life Cycle
Katy WolstencroftPaul Fisher
University of Manchester
Workflow Environments
Taverna Workflow design and
execution environment Access to local and
remote resources and analysis tools
Automation of data flow Iteration over large data
sets 50,000 downloads Used by 350+
organisations
myExperiment Workflow sharing and
publishing environment Web 2.0 Social network Sharing workflows,
expertise, knowledge and/or data
964 users 301 workflows
Taverna
For bioinformaticians, NOT biologists Used for
Data gathering annotation pipelines, data integration, model
population Data analysis
microarray, proteomics, Data mining and knowledge integration
Ontology building
myExperiment
Supports bioinformaticians but also enables biologists to run ready-made workflows
Intended for ANY workflows, not just Taverna Already working with Triana
Allows “just enough” sharing between groups/communities Who can look at your workflow Who can download your workflow Who can modify your workflow Who can run your workflow
myGrid Development
Started 2001 – EPSRC E-Science project
2005 – OMII-UK
myExperiment - started 2007 Open Source Funded until after 2010
Speed and Scalability
Taverna 2 enactor Support for long running workflows Large scale data – industrial bioinformatics Data streaming Passing data by reference Integration with established computing
platforms
Extensibility and Ease of Use
Drag and drop workflow building More content – greater pool of workflows in
myExperiment More components – gathering together
commonly used groups of services Shim libraries – for combining incompatible
services Service and workflow annotation checking
Curation by Experts
Curation by the Community
Automated Curation
refinevalidate
refinevalidate
Curation by Developers
seed seed
refinevalidate
seed
BioCatalogueJoint Manchester-EBI
Toolkits “Taverna Inside”
Workflows under the hood e-Laboratories (portals)
Systems Biology, e-Health Dashboards
configurable platforms for small biological communities
Visualisation clients that call workflows in the background
Toolkits “Taverna Inside”Workflow development pipeline
Workflows developed by bioinformaticians
Enacted locally
E-Labs, Dashboards and 3rd party clients
Social support for bioinformaticians to find and reuse workflows and expertiseAccess to ready made workflows for biologists
Workflows enacted locally Taverna remote execution service (T-Rex)
Social support to find and reuse workflows and expertise
CONFIGURABLE access to ready made workflows for biologists
Workflows embedded in applications and combined with data management systems
Come and see us Booth 20 Manchester Bioinformatics
Development is user driven – we need your input!
Try out myExperiment Try out Taverna and T2 Try out the new drag and drop interface Do you want workflows behind your tools? ….and come and tell us what you think
http://www.myexperiment.org http://taverna.sourceforge.net