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 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

1000s of Services developed by the community Any SOAP based service, REST services soon Grid 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 Software Release Information Taverna first released Current versions and Taverna Currently users per month, 350+ organizations, ~40 countries, downloads across versions Availability Freely available, open source LGPL On Windows, Mac OS, and Linux platforms Resources User and developer workshops, documentation, 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 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 APIs Linked Open Data Software Open source BSD

Systems Biology and myGrid SysMO-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

myGrid Taverna provides another strong environment for the analysis of Sage data and linking data with external analytics and data resources, including text mining with publications SysMO-SEEK, myExperiment and BioCatalogue are community collaboration resources for sharing Sage methods, models and data ONDEX is a potentially powerful network analysis tool for Sage Bionetworks

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

Taverna Workflow Key Driver Analysis Download files Sage Cytoscape Reformat Map to KEGG gene ids Find KEGG Pathways Re-format results Extract Entrez ids View Results Download files