Difference between revisions of "Ksherbina Project Notebook"
From LMU BioDB 2013
(→Testing Report: Had to reimport GO OBO-XML file so changed the time taken to import) |
(→Testing Report: Recorded error with processing obo-xml file. Recorded time it took to) |
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| Line 37: | Line 37: | ||
* Time taken to import: 1.70 min | * Time taken to import: 1.70 min | ||
| − | GO OBO-XML filename: Go_daily-termdb_v2_HD_20131107 | + | 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 [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): | * GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped): | ||
* Time taken to import: 9.29 min | * Time taken to import: 9.29 min | ||
| − | * Time taken to process: | + | * 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: | + | GOA filename: 22183.C_trachomatis_A_KS_20131114.goa |
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): | * GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): | ||
| − | * Time taken to import: | + | * Time taken to import: 0.02 min |
Name of .gdb file: | Name of .gdb file: | ||
Revision as of 05:56, 15 November 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
Setting Up 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>
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:
