Milestone 5

 

In the previous milestones, you have successfully created and populated databases for a set of protein data. With this organization, a Rosetta analysis can be carried out through SQL queries and the results can be verified and stored as a table. Computation accounts for a large part of the research, an equally important part is to present and share this data with science community.

 

In this milestone, you are going to practice presenting results you have computed through web interface. These will include several key steps:

 

1.      Create an web interface to handle user requests

2.      Establish the connection with database server

3.      retrieve user requested data from database

4.      Parse the query results in a human readable format (such as a web page)

 

The steps 2 though 4 are similar to what you have been accomplished for the previous milestones.  

 

A sample code of query possible gene fusion events by accession number through Java applets. You can try this applet through links in following page

 

http://www.cs.utexas.edu/~mobios/cs329e/rosetta/RosettaAnalysis.htm

 

The source code is also furnished at class website.

 

After submitting an accession number 'acc' in the search box, the applet will conduct following query to the Postgres through JDBC:

 

SELECT * FROM t_genefusionevent g, t_protein p

WHERE

              p.accessionnumber='acc'

     AND ( p.t_protein_id =g.t_protein_id

        OR   p.t_protein_id =g.t_protein_t_protein_id

        OR   p.t_protein_id = g.t_localalignment_t_protein_id);

 

This query will return a list of possible gene fusion event that involves the given acessionnumber. Then the applet will get the detailed information of each protein and associated GO functions and present the results in a tabulate web page.

 

Your job is to extend/modify this applet to enable one of the following query:

 

Search by gene name (t_protein.name)

 

Search by gene function (t_gofunction.function)

 

Search by gene sequence (t_protein.sequence)

 

……

 

You should turn in screenshots of successfully running your applet through browser.

 

Note:

  1. A web interface can be created in various ways, if you are familiar with other language such as PHP, perl and JSP etc, you are welcome to accomplish this milestone using other than means instead of java applet.

 

  1. You should download the complete zip file, unzip and working in the zip file directory.

 

 

  1. Due to the security restriction, the applet can only connect to the Postgres installed in the same machine.

 

  1. Although applet is also a java file, you must embedded it into an html file for it to run. I suggest you make a duplicate copy and rename both webpage and applet files.

 

  1. An easier way to test your applet file is using a utility comes with java installation:

appletviewer

You can start the command prompt, navigate to the directory, and type

appletviewer  HTML_FILE_NAME

  

      6.  As usual, you have to change the provided code accordingly to your set up.


      7.  You can visit here to check if your browser can properly run the applet. Then you can download the provide source files, unzip, change the correspoding database connection settings in Rosetta.java, recompile and load the demo.html in browser to see if it works on your computer.