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Taverna Roadmap

Taverna Roadmap. Shoaib Sufi myGrid Project Manager. Sources of Influence. Projects SCAPE – Digital preservation BioVel – Biodiversity science CA4LS – Next Generation Sequencing Wf4ever – Workflow preservation Astronomy & Bioinformatics focus e-Lico – Data mining – (Kidney function data)

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Taverna Roadmap

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  1. Taverna Roadmap Shoaib Sufi myGrid Project Manager

  2. Sources of Influence • Projects • SCAPE – Digital preservation • BioVel – Biodiversity science • CA4LS – Next Generation Sequencing • Wf4ever – Workflow preservation Astronomy & Bioinformatics focus • e-Lico – Data mining – (Kidney function data) • NeISS – Social Simulation • Collaboration • IMPACT – Digital preservation • HELIO – Solar physics • Taverna - Galaxy – Bioinformatics • ViBRANT – Biodiversity • User communities • Super users requests (experts e.g. Andrea Wiggins) • User requests • Carole • Feedback from conference attendance • Developer community • What are other projects doing • Developer requests and contributions (integration) • Useful to do / take into account • Clouds • Semantic Web • Other promising or proven technologies

  3. Taverna 2.3 Server Release 1 (November 2011) • Hardened, debugged and tested • Improved large input and output data handling • Security support • User authentication to the Server • Secure service invocation from inside workflows • Workflow run access control • Improved job management and accounting trails • Notification of workflow finishing using various mechanisms

  4. Taverna 3 • Why – Standards compliance (OSGi), aid reuse • Taverna 3 Platform OSGi beta and Command Line Tool (January 2012) • Re-engineering the Taverna Engine using OSGi • Support programmatic access to the Taverna Core • New Run/Execution Manager and Edits API • Embeddable in applications for executing workflows • Taverna 3 Platform OSGi and Command Line Tool (July 2012) • Stabilized and hardened • Plugin-enabled • Taverna 3 Platform OSGi and Workbench alpha (July 2012) • Based on the Taverna 3 Platform OSGi • Taverna 3 Platform OSGi and Server beta (July 2012) • Based on the Taverna 3 Platform OSGi

  5. Draft Taverna 3 features • Better user-interaction during workflow run • - Improved interaction with visualizing tools and services • ‘Blackboard’ support • Improved workflow diagram • Mark as boring • More obvious looping & iteration strategy • Data • JSON related services (create, search, extract) (in 2.x also) • XML related service (create via templates) (in 2.x also) • Table support (structured objects) • Services • Choice of languages for in-workflow-programming via Java Scripting framework • A better ‘bean shell’ (e.g. python or other languages supported by JVM) • Components (semantically annotated workflows as pipeline steps) • - Components creation/deletion • - Components registry • Enhanced execution • Ability to change WSDL bindings • Intelligent re-run/resume of workflows (use results before error occurred) • Tarpit mitigation – i.e. XSD caching (2.x also)

  6. Taverna 3 features continued … • Improved Provenance • More efficient provenance capture • More detailed provenance capture • Export of Provenance in OPM and W3 PROV serialisation • Research Object support • via SCUFL 2 Data bundle: • Workflow • Provenance • Data • In • Out • Intermediate • Manifest • Control flow • Branching support (if/else) • Better looping (explicit while)

  7. Taverna 3 features continued(2) … • Domain specific support (from projects req’s) • Astronomy • VOTable visualisation support (Workbench) • VOTable local workers support (Engine) • Opens way for Table support +XML template use case • SAMP support (Workbench) local blackboard • Biodiversity • Asynchronous input support • Sensor data • Relevant to other instruments producing continuous data • Security • Single Sign On • Server • Pause/resume • Fine grained monitoring and feedback for a running workflow. • Where is it upto

  8. SCUFL2 – the new workflow format • SCUFL2 Language Specification (January 2012) • Taverna workflow language specification more like SCUFL from Taverna 1.7.x to replace the current t2flow serialisation format • Easier for third party use • A packaged format with annotation support • SCUFL2 Tools beta (January 2012) • Tools for conversion from t2flow to SCUFL2 • SCUFL2 Tools Release (July 2012) • A stabilised and fully tested version • Plugin for the Taverna Workbench 2.3 • Plugin for the Taverna Server 2.3 • Other SCULF2 tooling • workflows to Hadoop/MapReduce (SCAPE project) • Workflows to Wf4ever abstract workflow format • Processers and links (no activities) – Skeleton workflow • Conversion from abstract format to SCULF2 (won’t execute but act as template)

  9. Cloudy with a chance of Taverna • Taverna Infrastructure Virtual Appliance • Taverna Server Virtual Machine (VM) (December 2011) • Including Taverna 2.3 Server and management interface • Amazon Machine Interface (AMI) (December 2011) • Including Taverna 2.3 Server and management interface

  10. KISS – Taverna keeping it simple • (December 2011 alpha) • Web based interface • Connecting workflows • Hides complex iterations/looping/config in ‘components’ • Build ‘component’ workflows in Taverna Workbench and then deploy in KISS • Simple install and one config file containing workflow definitions for a particular domain/instance • Uses Wireit • Will shortly have a Baclava data viewer • Alpha (uses command line) • Multi user support Q1 2012 • Will use Taverna Server

  11. Plugins • Data Mining plugin (December 2011) • Makes all the RapidMiner (www.rapidminer.com) services available in Taverna • more than 500 operators for data integration and transformation, data mining, evaluation, and visualization • Automatic workflow building via metadata and goals • SPARQL plugin (2.x and 3) • Query RDF data sources (e.g Linked Data)

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