Version 4 (modified by yshigemo, 7 years ago)

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Workflow Workgroup

Here I hope to learn from Taverna, Remora, MOWServ etc. other existing workflow frameworks which utilize various webservices.

Existing Workflow Engines

Desktop/Rich Client Applicaiotns:

Web Applications:

Discussion Items

  • What is the current bottleneck to create bioinformatics workflows?
  • What kind of workflows have been created? (see examples below)
  • What kind of services are missing yet?
  • ID mapping problem
    • Some usufl services are already there:
    • Need standard API!
    • One-to-many/many-to-one mapping problem
  • Data format conversion
  • Job management
  • Remote and local execution
  • Grid integration

Example Workflows and Current Isuues

  • Network/Pathway Analysis (suppose client is  Cytoscape)
    1. Load Networks from various kinds of data sources:
    2. Load annotations:
      • Local files (XML docs/text file/Excel worksheet)
      • Web services (BioMart?, NCBI Gene, PICR, KEGG)
      • Gene Ontology
      • Gene Expression data
    3. Analyze the networks by plugins
    4. Visualize the result
    5. Generate publishable quality images
  • Questions:
    • How can we (at least partially) automate this by connecting to other workflow engins?
    • Scripting vs Visual Programming
  • (Please add your typical workflows here...) Sample workflows in Web API for Bioinformatics (WABI)

 http://www.xml.nig.ac.jp/workflow/index.html