= 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:
 * [http://taverna.sourceforge.net/ Taverna]
 * [http://jeti.cs.uni-dortmund.de/biojeti/ Bio-jETI]
 * [http://www.kepler-project.org/Wiki.jsp?page=KeplerProject Kepler]

Web Applications:
 * [http://lipm-bioinfo.toulouse.inra.fr/remora/cgi/remora.cgi Remora]
 * [http://www.inab.org/MOWServ/ MOWServ]
 * [http://ubio.bioinfo.cnio.es/biotools/IWWEM/workflowmanager.html 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)
  * ID mapping problem
    * Some usufl services are already there:
      * [http://www.biomart.org/ BioMart]
      * [http://www.ebi.ac.uk/Tools/picr/ 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: [http://nbcr.net/software/opal/ NBCR Opal Toolkit]

== Example Workflows and Current Isuues ==
 * Network/Pathway Analysis (suppose client is [http://www.cytoscape.org/ Cytoscape])
  1. Load Networks from various kinds of data sources:
    * local files
    * web services ([http://www.ebi.ac.uk/intact/site/index.jsf IntAct], etc.)
    * manually download from web applications ([http://string.embl.de/ STRING], [http://www.thebiogrid.org/ BioGRID], etc.)
    * NLP(Natual Language Processiong)-based data miner ([http://www.agilent.com/labs/research/litsearch.html Agilent Litelature Search])
  1. Load annotations:
    * Local files (XML docs/text file/Excel worksheet)
    * Web services (BioMart, NCBI Gene, PICR, KEGG)
    * Gene Ontology
    * Gene Expression data
  1. Analyze the networks by plugins
    * [http://baderlab.org/Software/MCODE MCODE]
    * jActiveModules
  1. Visualize the result
  1. 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