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Taverna Workflow

Taverna Workflow. Taverna. 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

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Taverna Workflow

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  1. Taverna Workflow

  2. Taverna 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

  3. Taverna Open Suite of Tools Workflow Repository Client User Interfaces Workflow GUI Workbench Third Party Tools Service Catalogue Provenance Store Workflow Server Web Portal Activity and Service Plug-in Manager Open Provenance Model Programming and APIs Secure Service Access

  4. 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 1000s of Servicesdeveloped by the communityAny SOAP based service, REST services soonGrid Services, R Scripts, Beanshell scripts, Java programs, BioMart queries CDK

  5. Taverna Software Release 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 versions Availability • Freely available, open source LGPL • On Windows, Mac OS, and Linux platforms Resources • 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

  6. 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 APIs Linked Open Data Software Open source BSD

  7. Systems Biology and myGrid ONDEX • Network based analysis environment for Systems Biology • Uses Taverna workflows and text mining SysMO-SEEK • e-Laboratory for interlinking and sharing data, models, SOPS and workflows for Systems Biology in Europe • ISA-TAB & SBML/MIRIAM compliant http://www.ondex.org/ http://www.sysmo-db.org/

  8. 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.

  9. Taverna pathway pipeline demo Taverna

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