Changes between Version 8 and Version 9 of Workflow_workgroup

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Timestamp:
2008/02/04 14:38:13 (17 years ago)
Author:
standley
Comment:

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

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  • Workflow_workgroup

    v8 v9  
    1717 
    1818  * What kind of workflows have been created?  (see examples below) 
    19   * What kind of services are missing yet? 
     19  * What kind of services are missing yet? (see wishlist below) 
    2020  * ID mapping problem 
    2121    * Some usufl services are already there: 
    … …  
    5555    * Sample workflows in Web API for Bioinformatics (WABI) 
    5656    * http://www.xml.nig.ac.jp/workflow/index.html 
     57    * http://www.myexperiment.org 
     58 
     59== Workflow Wishlist == 
     60 * Obtaining a sequence family and/or profile associated with a PDB entry  
     61   * This would involve: 
     62     1. Get FASTA file for PDB chain (from RCSB-PDB, MSD-EBI, or PDBj) 
     63     2. Get family and/or profile (from NCBI, UNIPROT or DDBJ) 
     64 
     65 * Build phylogenetic tree from set of sequence and structure alignments 
     66   * This is trickier then the above example, but one approach would be: 
     67     1. Cluster sequences using clustalw (from NCBI,EBI, DDBJ) 
     68     2. Collect the PDB IDs for each sequence that has a structure (from RCSB-PDB, MSD-EBI, or PDBj:Sequence Navigator) 
     69     3. Compute all-on-all structure alignments for those sequences with structures (from MSD-EBI:SSM or PDBj:ASH) 
     70     4. Now, combine all the sequence scores and structure scores (if available) into a single distance matrix 
     71     5. Compute tree from distance matrix 
     72  
     73