Changes between Version 1 and Version 2 of Workflow_workgroup

Timestamp:

2008/02/02 07:29:06 (17 years ago)

Author:

kono

Comment:

--

Workflow_workgroup

@@ -1 @@
-= Workflow workgroup =
+= 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]
+
+== Discussion Items ==
  * What is the current bottleneck to create bioinformatics workflows?
-  * What kind of workflows have been created?
+
+  * What kind of workflows have been created?  (see examples below)
   * What kind of services are missing yet?
-  * ID problem
+  * 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
@@ -12 +29 @@
   * Grid integration
 
+== 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...)
+