Taverna Workflow

A suite of tools for bioinformatics• Fully featured, extensible and scalable

scientific workflow management system– Workbench, server, portal– Standards-compliant provenance collection – Immediate ingest of web services– Grid services, Beanshell scripts, R-scripts,

BioMOBY services…• Web 2.0 social collaboration

environments (“E-Labs”) for sharing– Methods, workflows– Systems biology data, models and SOPS– Statistical methods

• Curated catalogue of Web Services

Taverna Open Suite of Tools

Client User InterfacesWorkflow GUI Workbench

Workflow Repository

Service CatalogueThird Party Tools

Programming and APIs

Web PortalActivity and Service

Plug-in Manager

Provenance Store

Workflow Server

Open Provenance

Model

Secure Service Access

1000s of Servicesdeveloped by the community

Any SOAP based service, REST services soonGrid Services, R Scripts, Beanshell scripts, Java programs, BioMart queries

• Gene expression• SNP arrays and aCGH• Proteomics• Pathway analysis • Systems biology model

building• Proteomics• Sequence analys• Protein structure prediction• Gene/protein annotation • Microarray data analysis

• QSAR studies• Medical image analysis• Epidemiology• Model simulation• High throughput screening• Phenotypical studies• Phylogeny• Statistical analysis• Text mining• Data retrieval and formatting• QTL studies

CDK

Taverna SoftwareRelease Information• Taverna first released 2004. • Current versions 1.7.2 and Taverna 2.1.2• Currently 1500 + users per month, 350+ organizations, ~40

countries, 80000+ downloads across versionsAvailability• Freely available, open source LGPL• On Windows, Mac OS, and Linux platformsResources• http://www.taverna.org.uk, http://www.mygrid.org.uk• User and developer workshops, documentation, email help

desk• Collaborations with numerous groups including NCI’s cancer

biomedical informatics grid (caBIG), EMBL-EBI, NCBI, Concept Web Alliance, Bio2RDF

myExperiment• A Web 2.0 community for

sharing, discovering and reusing workflows and other scientific methods.

• A platform for launching workflows

• Launched late 2007. • Currently: 3272 members, 223

groups, 1024 workflows, 306 files and 97 packs, 56 different countries.

• 10+ workflow systems: Taverna, Pipeline pilot, BioExtract, Kepler

• ~ 3000 unique hits per month

REST APIsLinked Open DataSoftware Open source BSD

Systems Biology and myGridSysMO-SEEK• e-Laboratory for interlinking

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

• ISA-TAB & SBML/MIRIAM compliant

ONDEX• Network based analysis

environment for Systems Biology

• Uses Taverna workflows and text mining

http://www.ondex.org/http://www.sysmo-db.org/

Performing Taverna KDA and Pathways pipeline

• A demonstration Taverna Pipeline (workflow)

• Calculate a differentially expressed genes in a TCGA dataset

• Perform KDA using a Sage breast cancer network model and the gene list from the differentially expressed genes

• Reformats the KDA output for Cytoscape

• Launches Cytoscape to visualize the results

• Extracts gene names from TCGA dataset

• Finds pathways for these genes in KEGG using workflow deposited in myExperiment.

Taverna pathway pipeline demo