taverna workflow. a suite of tools for bioinformatics fully featured, extensible and scalable...
TRANSCRIPT
![Page 1: Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,](https://reader036.vdocuments.mx/reader036/viewer/2022070410/56649ebf5503460f94bca923/html5/thumbnails/1.jpg)
Taverna Workflow
![Page 2: Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,](https://reader036.vdocuments.mx/reader036/viewer/2022070410/56649ebf5503460f94bca923/html5/thumbnails/2.jpg)
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
![Page 3: Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,](https://reader036.vdocuments.mx/reader036/viewer/2022070410/56649ebf5503460f94bca923/html5/thumbnails/3.jpg)
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
![Page 4: Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,](https://reader036.vdocuments.mx/reader036/viewer/2022070410/56649ebf5503460f94bca923/html5/thumbnails/4.jpg)
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
![Page 5: Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,](https://reader036.vdocuments.mx/reader036/viewer/2022070410/56649ebf5503460f94bca923/html5/thumbnails/5.jpg)
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
![Page 6: Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,](https://reader036.vdocuments.mx/reader036/viewer/2022070410/56649ebf5503460f94bca923/html5/thumbnails/6.jpg)
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
![Page 7: Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,](https://reader036.vdocuments.mx/reader036/viewer/2022070410/56649ebf5503460f94bca923/html5/thumbnails/7.jpg)
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/
![Page 8: Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,](https://reader036.vdocuments.mx/reader036/viewer/2022070410/56649ebf5503460f94bca923/html5/thumbnails/8.jpg)
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.
![Page 9: Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,](https://reader036.vdocuments.mx/reader036/viewer/2022070410/56649ebf5503460f94bca923/html5/thumbnails/9.jpg)
Taverna pathway pipeline demo