Taverna Workflows for Systems Biology Katy Wolstencroft School 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 Services e.g. KEGG Scripts e.g. beanshell, R Programming libraries Programming libraries e.g. libSBML

Nucleic Acids Res Jul 1;34(Web Server issue):W 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 available open source Current Version ,000+ downloads across version Part of the myGrid Toolkit Taverna Workbench

myGrid Open Suite of Tools Client User Interfaces Workflow GUI Workbench Workflow Repository Service Catalogue Third 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 genes using t-test with R Peter 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 annotations 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 Query maxd database using enzyme names Calculate colours based on gene expn level 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/Germany Steffen 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 myExperiment BioCatalogue SysMO-SEEK