Taverna Workflows for Systems Biology

Katy WolstencroftSchool of Computer Science

University of Manchester

What is a Taverna Workflow?

Workflow management system

Sophisticated analysis pipelines

A set of services to analyse or manage data (either local or remote)

Data flow through services

Control of service invocation

Interoperability, Integration and Collaboration

Access to distributed and local resources

Iteration over data sets Automation of data flow Agile methods development Extensible Experimental protocols

Taverna Workflows

Workflows are ideal for…

High throughput analysis Transcriptomics, proteomics, Next Gen

sequencing, etc Data integration, data interoperation Data management

Model construction Data format manipulation

Systems Biology

Workflow engine to run workflows

List of services

Construct and visualise workflows

Taverna Workbench

Web ServicesWeb Services e.g. KEGG

ProgramminglibrariesProgramminglibraries

e.g. libSBML

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32.Taverna: a tool for building and running workflows of services.Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T.

Freely availableopen source

Current Version 2.2

70,000+ downloads across version

Part of the myGrid Toolkit

Taverna Workbench

myGrid Open Suite of Tools

Client User InterfacesWorkflow GUI Workbench

Workflow Repository

Service CatalogueThird Party Tools

Programming and APIs

Web Portal

Activity and Service Plug-in Manager

Provenance Store

Workflow Server

Open Provenance

Model

Secure Service Access

Examples of Workflows for Systems Biology

Escherichia coli : From cDNA Microarray Raw Data to Pathways and Published Abstracts

Identify differentially expressed genesusing t-test with RPeter Li, MCISB

SysMO SUMO: Systems Understanding of Microbial Oxygen responses

Afsaneh Maleki-Dizaji, University of Sheffield

High Throughput Experiments

Wei Tan Univ. Chicago, CABIG

Using gene-expression patterns associated with two lymphoma types to predict the type of an unknown sample

Workflows for Model Building

Results from experiments in systems biology -> related to mathematical models in SBML

Workflows can link data and models

Workflows can create models

SBML

Location of components

Species

Reactions

Model construction workflow

Input: list of ORFs

Output: SBML file

1. Get reaction info

3. Create species

2. Create compartments

4. Create reactions

Get

ann

otat

ions

Peter Li et al, MCISB, myGrid

Integrating libSBML into Taverna

Peter Li et al, MCISB, myGrid

Workflows for Data Integration

Read enzyme names from

SBML

Read enzyme names from

SBML

Query maxd database using enzyme names

Query maxd database using enzyme names

Calculate colours based on gene

expn level

Calculate colours based on gene

expn level

Create new SBML model

with new colour nodes

Create new SBML model

with new colour nodes

Mapping transcriptomic data onto SBML models

HUMAN Microarray CEL file to candidate pathways

Reuse, Recycle, Repurpose Workflows

From cDNA Microarray Raw Data to Pathways and Published Abstracts

SUMO

Metware: Workflows for metabolomics, Netherlands/GermanySteffen Neumann, Leibniz Institute of Plant Biochemistry

Workflows through web interface

Reuse, Recycle, Replay Workflows

Workflows in e-Laboratories

SysMO SEEK e-Laboratory for

interlinking and sharing data, models, SOPS and workflows for Systems Biology in Europe

Workflows for data analysis

Summary

Informatics in Systems Biology relies on data integration and large-scale data analysis

Taverna workflows are a mechanism for linking together resources and analyses

myExperiment allows you to reuse workflows and benefit from others work

More information

Taverna http://www.taverna.org.uk

myExperiment http://www.myexperiment.org http://wiki.myexperiment.org

BioCatalogue http://www.biocatalogue.org

SysMO-SEEK http://www.sysmo-db.org