Version 9 (modified by standley, 10 years ago)

I have added two workflows that I would like to implement during the Hackathon with help from the Taverna, DDBj, and other experts.

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? (see wishlist below)
  • 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

Workflow Wishlist

  • Obtaining a sequence family and/or profile associated with a PDB entry
    • This would involve:
      1. Get FASTA file for PDB chain (from RCSB-PDB, MSD-EBI, or PDBj)
      2. Get family and/or profile (from NCBI, UNIPROT or DDBJ)
  • Build phylogenetic tree from set of sequence and structure alignments
    • This is trickier then the above example, but one approach would be:
      1. Cluster sequences using clustalw (from NCBI,EBI, DDBJ)
      2. Collect the PDB IDs for each sequence that has a structure (from RCSB-PDB, MSD-EBI, or PDBj:Sequence Navigator)
      3. Compute all-on-all structure alignments for those sequences with structures (from MSD-EBI:SSM or PDBj:ASH)
      4. Now, combine all the sequence scores and structure scores (if available) into a single distance matrix
      5. Compute tree from distance matrix