Difference between revisions of "Ksherbina Project Notebook"

Revision as of 07:33, 15 November 2013

Week 12

Starting the Set Up of the Testing Environment

1. Downloaded the following software onto my personal computer:
   • Latest version of GenMAPP Builder (gmbuilder2.0-b71) from SourceForge
   • Java SE 7u45
   • Eclipse IDE for Java EE Developers
2. Created an account on SourceForge.

Import/Export of Gene Database

1. Downloaded the UniProt XML for C. trachomatis serovar A strain HAR-13: Uniprot XML C.trachomatis serovar A KS 20131114.xml
2. Downloaded the GOA file for C. trachomatis serovar A: 22183.C trachomatis A KS 20131114.goa
3. Created a new database in pgAdminIII: CT_KS_20131114_gmb2b71
   • Created tables in the database by executing the script in the file gmbuilder.sql.
4. Launched gmbuilder-32bit.bat:
5. Configured the database in gmbuilder:
   • Host or address: localhost
   • Port number: 5432
   • Database name: CT_KS_20131114_gmb2b71
   • Username: postgres
   • Password: <password of the PostgreSQL database created above>
6. Imported the UniProt XML file into the PostgreSQL database through gmbuilder.
7. Imported the OBO-XML file into the PostgreSQL database through gmbuilder.
   • gmbuilder was not able to completely process the data. See the testing report below for details.
8. Imported the GOA file into into the PostgreSQL database through gmbuilder.
   • I did not begin the actual export of the database due to the problem with processing the OBO-XML file.

Testing Report

Version of GenMAPP Builder: 2.0b71

Computer on which export was run: Personal computer

Postgres Database name: CT_KS_20131114_gmb2b71

UniProt XML filename: Uniprot_XML_C.trachomatis_serovar_A_KS_20131114.xml

• UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2013_11
• Time taken to import: 1.70 min

GO OBO-XML filename: Go_daily-termdb_v2_HD_20131107.obo-xml

• GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the GO Download page has been unzipped):
• Time taken to import: 9.29 min
• Time taken to process: Could no complete the process. The following error came up when gmbuilder was processing the 81000 term:

ERROR edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder  - java.util.concurrent.ExecutionException:java.lang.OutOfMemoryError:
Java heap space

GOA filename: 22183.C_trachomatis_A_KS_20131114.goa

• GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site):
• Time taken to import: 0.02 min

Name of .gdb file:

• Time taken to export .gdb:
• Upload your file and link to it here.

Note:

Creating Custom Species Profile

1. On one of the class computers in the first row, I launched Eclipse with Subclipse.
2. Went to Window > Open Perspective > Other > SVN Repository Exploring.
3. Defined a new subversion by clicking on Add Repository and adding the URL https://svn.code.sf.net/p/xmlpipedb/code. Clicked Finish.
4. Double-clicked on trunk, right-clicked on gmbuilder, and chose Checkout....
5. Created a new project (chose Check out as a project configured using the New Project Wizard).
6. Went to Window > Preferences > Java > Installed JREs. Added a new environment with JDK.
7. Double-clicked on the project folder.
8. Double-clicked on the lib folder.
9. Shift-clicked and selected all files in the lib folder and then control-clicked on every file inside the lib folder whose name does not end in .jar. Right-click on one of them and choose Build Path > Add to Build Path from the popup menu that comes up.
10. Created a species profile called ChlamydiaTrachomatisSerovarA.
    • Dondi modified the name to ChlamydiaTrachomatisSerovarAUniProtSpeciesProfile.
11. Customized the species profile.

• Opened the new profile and added the lines of code as specified in "Customize the Species Profile" directions.

• Still need to insert the species-specific URL that returns a web page describing a gene for that species.

Week 13