Difference between revisions of "Ksherbina Project Notebook"
From LMU BioDB 2013
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#Downloaded the [http://www.uniprot.org/uniprot/?query=organism:315277+keyword:181 UniProt XML] for ''C. trachomatis'' serovar A strain HAR-13: [[Media:Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]] | #Downloaded the [http://www.uniprot.org/uniprot/?query=organism:315277+keyword:181 UniProt XML] for ''C. trachomatis'' serovar A strain HAR-13: [[Media:Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]] | ||
#Downloaded the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ GOA file] for ''C. trachomatis'' serovar A: [[Media:22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]] | #Downloaded the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ GOA file] for ''C. trachomatis'' serovar A: [[Media:22183.C trachomatis A KS 20131114.goa|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''. | ||
====Testing Report==== | ====Testing Report==== | ||
Revision as of 01:17, 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.
Testing Report
Version of GenMAPP Builder:
Computer on which export was run:
Postgres Database name:
UniProt XML filename:
- UniProt XML version (The version information can be found at the UniProt News Page):
- Time taken to import: 1.05 min
GO OBO-XML filename:
- 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:
- Time taken to process:
GOA filename:
- 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:
Name of .gdb file:
- Time taken to export .gdb:
- Upload your file and link to it here.
Note:
