Taverna Workflows for Systems Biology Katy Wolstencroft School of Computer Science University of Manchester.
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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
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