Taverna and BioMOBY

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Taverna and BioMOBY

• Savita Shrivastava
• Lab presentation
• September 16th, 2005

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A Life Science Scenario
GeneID
Over expressed genes
DNA Sequence
Microarray data
Protein Sequence

• "To answer most interesting biological problems,
  you need to combine data from many data sources,"

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A Life Science Scenario contd.

• Repeat the discovery process
• The same chain of services to be applied to
  different data sets
• Publish the methodology
• Preserve as much information about how services
  were used
• Trace the data to support a conclusion

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The Problem

• Finding the available resources on the web
• What and who?
• How to use it?
• What Input and output data types?
• How to create an analysis pipeline (take the
  output from one analysis and send it to another
  resource/website for further analysis)?

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The Problem contd.

• Diversity and complexity of information
• Data-intensive
• Compute-intensive
• Diversity and autonomy of the biological
  community
• Currently 5000 public data repositories and
  applications
• Different formats, interfaces, structures, and
  coverage
• Reliability

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The Problem contd.

• Writing scripts

Code for translation of a DNA sequence
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The Problem contd.
Code for getting Secondary Structure
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The Problem contd.
Code for Signal peptide and Transmembrane region
prediction
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The Problem contd.
Code for creating analysis pipeline
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The Solution - Workflow Techniques

• What is a workflow?
• A set of components/services and relation between
  them
• Defines a complex process from simple building
  blocks
• Transfers information from the output of one
  component to the input of another

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Terminology

• What is a Component?
• Any command line analysis tool or
• A script written in any programming language
• Consumes an input and produce an output
• What are Services?
• All services are also Component
• Components hosted on remote machine and
  accessible through internet

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Advantage of Workflow Technology

• Analysis processes in a structured, repeatable
  and verifiable way
• Applications are centralized to a common
  interface
• Automate the high through put data analysis to
  accelerate the pace and reduce overall costs

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Advantage of Workflow Technology

• Users are freed from component management
• No high performance computing hardware
• Provenance
• Who, what, where, why, when, how?
• The traceability of knowledge as it is evolves
  and as it is derived.
• Implications for recording which services invoked
  on what data, when with what parameters.
• No programming and command line work, just mouse
  clicks and Drag and Drop

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Taverna Workbench

• Designed for a biologist
• Allow users to construct complex analysis
  workflows
• Components are located in both remote and local
  machine
• Implicit iteration support

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Taverna Workbench

• Result browsing and data encapsulation
• Provenance recording
• Fault tolerance features

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Availability

• http//taverna.sourceforge.net/
• Available for Windows, Linux, Mac and Sun
• Download and unzip the file
• Requires Java (1.4 and above) to run
• Tutorial is available on website.

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Workbench Window
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Advanced Model Explorer Window
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Available Services
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Workflow Diagram
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Run Workflow
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Enactor Invocation
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Enactor Invocation-Result
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Enactor Invocation-Report
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BioMOBY Services in Taverna

• http//www.biomoby.org
• gt230 services registered and growing!!!
• 70 independent service providers
• List and details of all the MOBY services on-
• http//mobycentral.icapture.ubc.ca/cgi-bin/list.se
  rvices.cgi

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What is BioMOBY?
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• Information discovery system
• Discovers and retrieves related piece of data
  from multiple hosts and services
• Provides a common format for the retrieved data
  representation regardless of its origin.

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Three Components of MOBY

• MOBY-Central
• MOBY-Servers
• MOBY-Clients

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MOBY-Central(A central registry of the services)

• Responsible for cataloguing the services provided
  by all MOBY-Servers
• Respond to queries about these services from
  MOBY-Client
• MOBY-Central stores only the information about
  the services available, and the URL of the
  service specification

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MOBY-Servers(Provide one or more services)

• Create a service e.g. database lookup
  retrieval, sequence alignment, Blast homology
  search, etc.
• MOBY-Servers register themselves with
  MOBY-Central as providing service X using
  input(s) Y and generating output(s) Z.

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MOBY-Clients(The end-users computer )

• Identify type of data
• Generate the query to MOBY-central
• Receives the list of potential services and
  returned data types,
• Selection of the desired service.
• Initiates contact with the service, submits a
  properly formatted query, and receives/interprets
  the service response.

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MOBY uses ontology

• Object ontology types of input/output objects
• Service ontology types of services
• - Analysis
• - Parsing
• - Registration
• - Retrieval
• - Resolution
• Service relationships
• Service lt-- Analysis lt-- Alignment
  lt-- BLAST lt--

WU BLAST NCBI BLAST
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What does MOBY provide?

• A library that makes it easy to write new web
  services
• A library of calls to discover existing services
  according to
• The name of the service
• What input is required
• What output is produced
• Keywords in the description of the service
• Who wrote the service
• Calls to register new data types, existing types
  include
• GenericSequence
• DNASequence
• Keyword
• FASTA
• Calls to register new services
• You do not need to install your own MOBY-Central

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How the service providers register with MOBY
Central

• A service name
• Service name from service type hierarchy
• Input/Output object (s) by name from the
  Object-type hierarchy
• A URI identifying the service provider
• The URL to the service script
• A human readable description of the service
• There are many tools available on homepage of
  BioMOBY to create services

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Summary of MOBY's capabilities

• Easy to write web services using the MOBY library
  
• Services can be written by anyone, anywhere
• Anyone can registers their services with MOBY
  Central
• Anyone can query MOBY Central to discover and
  learn about any service

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MOBY clients

• Gbrowse_moby
• http//mobycentral.icapture.ubc.ca/cgi-bin/gbro
  wse_moby
• Taverna
• http//taverna.sourceforge.net/

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A Simple Workflow
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• Thanks