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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

Taverna Roadmap

Shoaib Sufi

myGrid Project Manager

sources of influence
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
taverna 2 3 server release 1 november 2011
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
taverna 3
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
draft taverna 3 features
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)
taverna 3 features continued
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)
taverna 3 features continued 2
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
scufl2 the new workflow format
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)
cloudy with a chance of taverna
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
kiss taverna keeping it simple
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
plugins
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)