Changes between Version 1 and Version 2 of Workflow_workgroup

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Timestamp:
2008/02/02 07:29:06 (16 years ago)
Author:
kono
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  • Workflow_workgroup

    v1 v2  
    1 = Workflow workgroup = 
     1= Workflow Workgroup = 
    22 
    33Here I hope to learn from Taverna, Remora, MOWServ etc. other existing workflow frameworks which utilize various webservices. 
    44 
     5== Existing Workflow Engines == 
     6Desktop/Rich Client Applicaiotns: 
     7 * [http://taverna.sourceforge.net/ Taverna] 
     8 * [http://jeti.cs.uni-dortmund.de/biojeti/ Bio-jETI] 
     9 * [http://www.kepler-project.org/Wiki.jsp?page=KeplerProject Kepler] 
     10 
     11Web Applications: 
     12 * [http://lipm-bioinfo.toulouse.inra.fr/remora/cgi/remora.cgi Remora] 
     13 * [http://www.inab.org/MOWServ/ MOWServ] 
     14 
     15== Discussion Items == 
    516 * What is the current bottleneck to create bioinformatics workflows? 
    6   * What kind of workflows have been created? 
     17 
     18  * What kind of workflows have been created?  (see examples below) 
    719  * What kind of services are missing yet? 
    8   * ID problem 
     20  * ID mapping problem 
     21    * Some usufl services are already there: 
     22      * [http://www.biomart.org/ BioMart] 
     23      * [http://www.ebi.ac.uk/Tools/picr/ PICR] 
     24    * Need standard API! 
     25    * One-to-many/many-to-one mapping problem 
    926  * Data format conversion 
    1027  * Job management 
    … …  
    1229  * Grid integration 
    1330 
     31== Example Workflows and Current Isuues == 
     32 * Network/Pathway Analysis (suppose client is [http://www.cytoscape.org/ Cytoscape]) 
     33  1. Load Networks from various kinds of data sources: 
     34    * local files 
     35    * web services ([http://www.ebi.ac.uk/intact/site/index.jsf IntAct], etc.) 
     36    * manually download from web applications ([http://string.embl.de/ STRING], [http://www.thebiogrid.org/ BioGRID], etc.) 
     37    * NLP(Natual Language Processiong)-based data miner ([http://www.agilent.com/labs/research/litsearch.html Agilent Litelature Search]) 
     38  1. Load annotations: 
     39    * Local files (XML docs/text file/Excel worksheet) 
     40    * Web services (BioMart, NCBI Gene, PICR, KEGG) 
     41    * Gene Ontology 
     42    * Gene Expression data 
     43  1. Analyze the networks by plugins 
     44    * [http://baderlab.org/Software/MCODE MCODE] 
     45    * jActiveModules 
     46  1. Visualize the result 
     47  1. Generate publishable quality images 
    1448 
     49    * Questions: 
     50      * How can we (at least partially) automate this by connecting to other workflow engins? 
     51      * Scripting vs Visual Programming 
     52 
     53  * (Please add your typical workflows here...) 
     54