Taverna

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Taverna
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Taverna

• Workflow development and enactment environment
• Allow users to construct such models from
  libraries of available components in a graphical
  editing environment with semantic support
• Publish process definitions as scientific
  methods, enact and automatically scale to large
  data sets, multiple runs
• Automatically collect enactment metadata
  workflow provenance.
• Originally intertwined in myGrid project started
  in 2001
• Release 1.0 24 January 2005
• Current version of Taverna 1.2 ? more modular
• Vast group of developers

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Modular architecture
Haystack Provenance Browser

• Open domain services and resources
• Open community
• Open application
• Open model and open data
• Open architecture
• Service Oriented Architecture
• Loosely coupled
• Web services based
• Assemble your own components
• Designed to work together

Feta Semantic Discovery
Pedro
Gateway Portal
Grimoire Registry
Taverna WfDE
Freefluo WfEE
Event Notification
LSID
Info. Model
mIR
Soaplab Gowlab
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Technologies

• XScufl Simple conceptual unified flow language
  in XML, produced by the Scufl Workbench
• Freefluo workflow enactment engine for
  workflows in either WSFL or Scufl
• SOAP and WSDL
• BeanShell An interpreter for Java, scripting
  engine to allow arbitrary Java scripts to be
  invoked on workflow data

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Taverna Highlights

• Language, Platform, and Domain independent
• Services available as remote and local components
• Visual interface
• Workflow graph
• Visualisers
• Access to computing clusters such as at EBI via
  services (no administrative overhead)
• Workflow exchange through XML (XScufl)
• Provenance
• Personalisation

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Taverna Features

• Implicit Iteration
• Conditional Branching
• Beanshell scripting
• Scavengers
• Control links for temporal constraints i.e.
  synchronization

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Functional analysis workflow
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and the result
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What can be integrated

• Web services defined by WSDL
• Pathport, BIND, Gene Ontology, DBFetch, FASTA,
  InterproScan, NCBI eUtils
• Complex analysis services conforming to Life
  Science Analysis Engine (LSAE) specification
• EMBOSS, Jess, any arbitrary legacy C, PERL or
  Shell script
• BioMoby services (www.biomoby.org)
• PlaNeT, IRI, Spanish Bioinformatics Network,
  Genome Prairie
• Biomart Database Queries
• Ensembl, DbSNP, VEGA
• Local embedded scripts via Java, Perl, Python,
  Ruby etc.
• Seqhound Genomic data warehouse
• Genbank, LocusLink, GO
• Styx Grid Service
• Environmental eScience, ocean temperature
  analysis etc
• Arbitrary 3rd Party APIs i.e. BioJava, JUMBO,
  caBIG

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Biological question Differentially expressed
genes Sample class prediction etc.
Experimental design
Microarray experiment
Wet Lab
16-bit TIFF files
Digital
Feature Extraction
(Rfg, Rbg), (Gfg, Gbg)
Normalization
R, G
Estimation
Testing
Clustering
Discrimination
Biological verification and interpretation
Courtesy of Nicola Armstrong CMB, Eurandom
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VL-e wishlist applied to Taverna

• Present
• Absent
• Potential or Intention

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Functional Wishlist

• Language, Platform (not browser), and Domain
  independent
• Encapsulation of procedures for novice users and
  best practice
• Access to DBMS a service on(/from) which a
  workflow entity can store(/retrieve) data
• Access to databases from workflow
  (storage/retrieval/querying) (ODBC)
• Integration of 3rd party software the ability to
  integrate existing software packages in a
  workflow (R, Matlab, VTK, ITK, FSL, etc.)
• Discovery and invocation of existing web-services
  developed/maintained by others (e.g. EMBOSS)
• Typing mechanism for input/output data connected
  entities in a workflow should only be allowed to
  exchange data if the type of the data produced by
  the outputting-module is of the same type as is
  consumed by the inputting-module
• Fan-in ( the input data of an entity can come
  from multiple entities) andfan-out ( the output
  of an entity can be passed to multiple entities)

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User interface and SW Engineering wishlist

• User-friendly (graphical, sensible defaults,
  wizards)
• Interactive graph editing of workflow diagram
• Encapsulation the ability to create hierarchies
  of workflow), copy/paste (topologies are
  first-class objects being able to load a
  topology as if it is a module)
• Capture workflow, provenance
• Based on well-established standards (i.e. Grid
  software, easy to install, maintain)
• Software engineering maintainability of
  dependency on 3rd party software
• Open source
• Semantic annotation of web services as well as
  the data produced by a given module
• Visualization from a service component
• Interaction with (the visualization from) a
  service component, especially selections

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Run-time wishlist

• Execution of workflow, controlled (e.g. stepwise
  useful in debugging)
• Distributed execution (e.g. across a Grid of
  systems)
• Interactive, dynamic execution of workflow,
  Dynamic workflow (execution is not predetermined)
• Monitoring execution of workflow, gathering
  information on execution of workflow (metadata)
  (also from inside a workflow)
• Maintain history/log of executed workflow for
  later scrutinyReproduction of experiment
• Checkpointing both data (as a BLOB) and
  process checkpointing
• nohup execution (being able to execute a
  workflow in the background, without having to
  be logged in all the time)
• Control flow (while/for/if-then-else,
  parallel/sequential/recursion, execute the same
  workflow with multiple different input, parameter
  sweeping, gathering/collecting of result)
• Resource brokering given the description of
  resources required by a workflow entity and the
  description of abilities provided by a resource
  the (automatic) brokering of and entity onto a
  resource
• Quality-of-Service fault tolerant, stable, high
  availability, dependable

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Conclusion

• Taverna provides a foundation for the further
  implementation of semantic annotation and
  provenance.