Portals and myGrid

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Portals and myGrid
Stefan Rennick EgglestoneMixed Reality
LaboratoryUniversity of Nottingham
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Introduction to myGrid

• a computer science pilot project working in the
  field of bioinformatics
• a consortium of the European Bioinformatics
  Institute, IT Innovations, 5 universities and
  some industrial partners
• ends June 2005 and other projects will develope
  infrastructure further

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Presentation aims

• Introduce myGrid
• Introduce bioinformatics
• Introduce portal work in myGrid
• Show some screenshots of portlets

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Introduction to bioinformatics

• how to store, process and publish large volumes
  of biological data
• large databases, access and analysis services
• composite processes involve multiple databases
  and services
• Automation through workflows

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Data in bioinformatics

• Commonly genetic sequences
• DNA GCGCATAGCGATGA
• Protein MAHPLGPHGVANA
• Meta information
• Species, chromosome
• Interesting features
• Equipment used
• First published paper referring to sequence

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Data storage

• 3 international databases aim to store all DNA
  sequences (EMBL, GenBank, DDBJ)
• Protein sequences in SwissProt
• Journals require submission before publication
• Smaller databases hold specialist information

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Using bioinformatics data

• Database access services
• Fetch sequence for given ID
• Fetch similar sequences
• Sequence analysis
• Look for interesting regions of sequence
• Sequence prediction
• Predict proteins generated by DNA sequence

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Service interface types

• Web-page
• Command-line tool set
• Programming language library client
• SOAP web-service with WSDL interface

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Using services

• Often need to combine services with different
  interface types
• Cut-and-paste from web-page to file and run
  command-line tool
• Repetitive and time-consuming
• Can be automated using scripts

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Workflows
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myGrid workflow technology

• Freefluo workflow enactor
• Taverna graphical workbench allowing users to
• Author workflows
• Enact and browse results
• myGrid Information Repository

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Authoring a workflow
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Enacting a workflow
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Browsing results
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Including services in workflows

• Service invocation done by processor
• Generic processor for SOAP/WSDL web-services
• Custom processor can wrap custom client
• SOAPlab exposes command-line tools as web-service

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Portal in myGrid

• Taverna/Freefluo is production workflow system,
  so interface cant be hacked around with
• Some interface limitiations
• Difficult to start new workflow running using
  results of enactment
• Complex interface, so takes time to master

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Text services work

• If enactment of a workflow produces a SwissProt
  protein sequence record, can extract from this
  PubMed ID of first paper referring to this
  protein
• Add extra workflow stages which look up related
  papers
• Might like to re-run these stages as a separate
  workflow on any new papers found

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Input form
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Monitoring progress
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Results
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MIR portal work

• Taverna/Freefluo/MIR interface caters for expert
  user
• Large numbers of users who wont write workflows
  but might enact them
• Provide a simpler workflow enactment interface
• Portal useful all biologists have browser on
  their desk

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Collections of workflows
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View workflow
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View workflow results
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View individual output param
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Further details

• www.mygrid.org.uk
• Twiki.mygrid.org.uk
• Stefan Rennick Egglestone (sre_at_cs.nott.ac.uk0
• Ian Roberts (i.roberts_at_dcs.sheff.ac.uk)
• Presentation and notes will be at
  www.mrl.nott.ac.uk/sre