Taverna Workflow

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Taverna Workflow

description

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 - PowerPoint PPT Presentation

Transcript of Taverna Workflow

Page 1: Taverna Workflow

Taverna Workflow

Page 2: 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

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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

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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

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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

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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

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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/

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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.

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Taverna pathway pipeline demo