Ksherbina Project Notebook
From LMU BioDB 2013
| Assignment Description | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 15 |
| Class Journal | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | |||||
| Individual Journal | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 |
| Other | Week 5: Database Wiki |
| Final Project | Team H(oo)KD Project Page | Journal Club Presentation | Project Individual Journal |
Contents |
Week 12
Starting the Set Up of the Testing Environment
- 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
- Created an account on SourceForge.
Import/Export of Gene Database
- Downloaded the UniProt XML for C. trachomatis serovar A strain HAR-13: Uniprot XML C.trachomatis serovar A KS 20131114.xml
- Downloaded the GOA file for C. trachomatis serovar A: 22183.C trachomatis A KS 20131114.goa
- Created a new database in pgAdminIII: CT_KS_20131114_gmb2b71
- Created tables in the database by executing the script in the file gmbuilder.sql.
- Launched gmbuilder-32bit.bat:
- 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>
- Imported the UniProt XML file into the PostgreSQL database through gmbuilder.
- 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.
- 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
- On one of the class computers in the first row, I launched Eclipse with Subclipse.
- Went to Window > Open Perspective > Other > SVN Repository Exploring.
- Defined a new subversion by clicking on Add Repository and adding the URL https://svn.code.sf.net/p/xmlpipedb/code. Clicked Finish.
- Double-clicked on trunk, right-clicked on gmbuilder, and chose Checkout....
- Created a new project (chose Check out as a project configured using the New Project Wizard).
- Went to Window > Preferences > Java > Installed JREs. Added a new environment with JDK.
- Double-clicked on the project folder.
- Double-clicked on the lib folder.
- 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.
- Created a species profile called ChlamydiaTrachomatisSerovarA.
- Dondi modified the name to ChlamydiaTrachomatisSerovarAUniProtSpeciesProfile.
- Customized the species profile.
