Bioinformatics Workflows

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Bioinformatics Workflows

• Chris Wroe
• (based on material from the myGrid team
• May Tassabehji / Hannah Tipney
• Medical Genetics, St Marys)

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Bioinformatics pipelines on the web
RepeatMasker
BLASTn
Twinscan

• Copying and pasting from one web based
  application to annotation by hand
• Advantages quick, easy access to distributed
  resources
• Disadvantages time consuming, error prone, tacit
  procedure so difficult to share both protocol and
  results

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Automating pipelines

• Using Perl/ Matlab scripts to implement a
  pipeline
• Advantages automation, quick to write,
  significant community resources (e.g. BioPerl)
• Disadvantages hard to explain, hard to relocate,
  hard to tinker with.

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Workflows
Predicted genes out
Sequence in
RepeatMasker Web service
BLASTn Web Service
TwinscanWeb Service

• Simple scripting language aims to specify how
  steps of a pipeline link together
• High level picture of the pipeline separated from
  any low level fiddling
• Application logic and low level fiddling
  encapsulated in remote web services
• Advantages automation, quick to write, easier
  to explain, share, relocate, and record
  provenance of results in a standard way

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Workflow components in myGrid

• Scufl Simple Conceptual Unified Flow Language
• Developed by myGrid members at EBI.
• Designed to be as simple as possible, just enough
  features to support bioinformatics workflows
• Taverna a tool for writing, running workflows
  and examining results.
• (http//taverna.sourceforge.net)
• FreeFluo workflow engine to run workflows
• (http//freefluo.sourceforge.net)

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Workflow use

• Newcastle University (Anil Wipat, Peter Li)
• Affymetrix Microarray Analysis Workflow
• Gene annotation workflow
• Manchester University May Tassabehji, PhD
  student Hannah Tipney, Medical Gentics, St Marys
  (Wellcome Trust Funded)
• Gene alerting service workflow (GAS)
• Gene and protein annotation workflow
• And others

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Workflow experience

• Easy to get started with Taverna (1-2 hours
  tutorial)
• Sharing does happen
• Cuts down the time taken to perform one pipeline
  from 2wks to 2 hours

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Workflow experience outstanding
issues

• Early days web services rare significant time
  take to wrap applications as web services
  (licensing, installation, maintenance)
• Soaplab and Gowlab try to help (http//industry.eb
  i.ac.uk/soaplab)
• Fiddly bits dont go away Many shim services
  needed to ensure the output of one step fits the
  expected input of another
• Automation produces many results in a short
  amount of time. Issues of result management and
  display

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Other workflow systems

• Commercial bioinformatics drug discovery
• Incogen VIBE
• TurboWorx Pipeline Pilot
• eScience
• DiscoveryNet (bioinformatics proprietary)
• Keppler ( US ecology)
• Triana (UK Physics astronomy, signal processing)

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Workflow standards

• Cant have enough of them! All currently come
  from e-Business rather than science community
• BPEL Business Process Execution Language
• WS Orchestration
• XML Process Definition Language (XPDL)
• Business Process Markup Language (BPML)