Changes between Version 5 and Version 6 of DAS

Timestamp:

2011-02-01T10:41:33+01:00 (14 years ago)

Author:

jvelde

Comment:

--

DAS

@@ -53 +53 @@
 
 The last two can be done by eg. IFRAMing an existing client and entering our application URL to the list of sources, making use of existing software and source listings.
+
+=== Older explanation, more technical, outdated locations ===
+
+In short:
+
+1) Template/example servlet for DAS data in XGAP
+2) Connecting the servlet to a DAS client
+3) Querying XGAP data within the servlet
+4) The data mapping possibilities
+5) Constructing the complete servlet
+6) The visualization tool we want to integrate
+
+
+In long:
+
+
+1)
+In the xgap_1_3_distro project, go to:
+handwritten -> java -> mydas -> DasServlet.java
+
+We set the MIME type to indicate what we are serving:
+response.setContentType("application/x-das-features+xml");
+
+After that we print data to the output stream:
+printExample(out);
+
+This servlet is mapped to the URL '/xgap_1_3_distro/das', see:
+WebContent/WEB-INF/web.xml
+
+Later on you can parse variables to the servlet like this:
+URL: xgap_1_3_distro/atted?locus=At4g08470
+String gene = req.getString("locus");
+
+For an advanced example, see:
+handwritten -> java -> plugins -> matrixmanager ->
+MatrixManagerDownloadServlet.java
+
+
+2)
+Go to the Ensembl genome browser:
+http://www.ensembl.org/index.html
+
+To enter the view, select an organism, eg 'Human'
+
+Now select:
+Manage your data -> Custom data -> Attach DAS
+
+In the box behind "or other DAS server", input the URL with your IP
+instead of 'localhost', ie.
+http://145.39.234.55:8080/xgap_1_3_distro/das
+
+
+3)
+XGAP should now serve some example data that can be interpreted by the
+Ensembl DAS client :) I will test this tomorrow, here at the UMCG the
+firewalls prevent external computers to reach my IP.
+
+If you look at bit closer at the MatrixManager servlet you notice we
+instantiate the database:
+db = (JDBCDatabase) this.getDatabase();
+
+After which we can run queries using find, eg. this retrieves all
+markers in the database:
+db.find(Marker.class);
+
+
+4)
+Now the idea is to take a close look at the DAS specifications: (I
+also took the example data from here)
+http://www.biodas.org/documents/das2/das2_get.html
+
+And identify which parts of DAS and XGAP overlap. (XGAP datamodel
+basics: http://www.xgap.org/wiki/XgapDataModel)
+
+
+5)
+After we know what to serve out, we can build the servlet. I think it
+should look like this:
+
+- Depending on arguments, query a part of the current XGAP database
+(eg. marker positions and QTL peak data)
+- Using the mydas-1.6.0 library:
+- Construct DAS objects from the queried XGAP objects
+- Create DAS xml format from these objects and serve out
+
+
+6)
+That would already be great. Next we can look at different viewers and
+how to integrate them into an XGAP plugin. Tampering with Freemarker
+templates can be very tedious so if you have a nice idea I can work
+this out.
+
+A customizable viewer that we should possibly use is Gbrowse:
+http://gmod.org/wiki/GBrowse
+
+And then we can let biologists drool over pictures such as these :)
+http://gmod.org/w/images/b/b6/Gbrowse_screenshot1.gif