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 Applications:

•  Taverna
•  Bio-jETI
•  Kepler

Web Applications:

•  Remora
•  MOWServ
•  IWWE&M (INB Web Workflow Enactor and Manager)

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)
• Reusing existing workflows as virtual services.
• The naïve end-user problem
  • How are you giving a end-user GUI for your workflows?
• ID mapping problem
  • Some usufl services are already there:
    •  BioMart
    •  PICR
  • Need standard API!
  • One-to-many/many-to-one mapping problem
• Data format conversion
• Job management
• Remote and local execution
• Grid integration
  • One possible solution to provide grid access from simple web service API:  NBCR Opal Toolkit

Example Workflows and Current Isuues

• Network/Pathway Analysis (suppose client is  Cytoscape)
  1. Load Networks from various kinds of data sources:
     • local files
     • web services ( IntAct, etc.)
     • manually download from web applications ( STRING,  BioGRID, etc.)
     • NLP(Natual Language Processiong)-based data miner ( Agilent Litelature Search)
  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
     •  MCODE
     • jActiveModules
  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
  •  http://www.myexperiment.org
  •  http://ubio.bioinfo.cnio.es/biotools/IWWEM/workflowmanager.html

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