Difference between revisions of "Taur.vil Week 12"

Revision as of 18:37, 14 November 2013

Week 12 Individual Journal

Downloaded GM Builder 2.0b71 for my personal computer from [1]
On my personal computer created new database in PgAdminIII titled: tATK_G54_20131113
Ran SQL, opened gmbuilder.sql and executed
- Produced the expect 159 tables
Configured gmbuilder-32bit.bat to connect with the database
Imported the XML file 20131107_UniProtXML_tATK_G54_AJV.xml which can be found on our team page.
- Took 2.98 minutes
Imported the goa file 20131107_UniProtXML_tATK_G54_AJV.goa (also on our team page)
- Took 0.05 minutes
Downloaded the compressed go-obo file 20131107_GO-OBO_tATK_KM.gz from the team page.
- Extracted files using 7zip and imported extracted file into gmbuilder
- Took 12.64 minutes to import and 10.63 minutes to process
Exported file to title: 20131113_G45export_tATK_TPV.gdb
- Took less than 2h
Uploaded export to wiki: Media:20131113 G45export tATK TPV.gdb

Created new database in pgAdminIII titled: tATK_R6_20131113
Ran SQL, opened gmbuilder.sql and executed
- Produced the expect 159 tables
Configured gmbuilder-32bit.bat to connect with the database
Imported the XML file 20131105_UniProtXML_tATK_R6_AJV.xml which can be found on our team page.
- Import took 5.16 minutes
Imported go-obo file extracted during G54
- Took 12.67min to upload and 10.06min to process.
Imported goa file 20131107_UniProtXML_tATK_R6_AJV.goa
- Import took 0.04min
Exported file to 20131113_R6export_tATK_TPV.gdb
- Took less than an hour
Uploaded export to wiki: Media:20131113 R6export tATK TPV.gdb

Opened Eclipse
Window-->Open Perspective-->Other-->SVN Repository Exploring
- added url: https://svn.code.sf.net/p/xmlpipedb/code
Opened SVN repository
Opened trunk
Checked out gmbuilder folder
Created new java project called tATK_gmbuilder1
Verified that it was running java jdk
Selected all .jar files in lib and added to build path
- Formed referenced libraries section
ran build.xml in ant build...
- selected clean and dist
- Built in 4s

Please Remember the Harassing of Deities is Strictly Prohibited

Never Forget Samson

@@ Line 33: / Line 33: @@
 **Took less than an hour
 *Uploaded export to wiki: [[Media:20131113 R6export tATK TPV.gdb]]
+===SourceForge===
+*Created source forge acount
+**User: taur-vil
+===14 Nov 2013 in class===
+====Building first database====
+*Opened Eclipse
+*Window-->Open Perspective-->Other-->SVN Repository Exploring
+**added url: https://svn.code.sf.net/p/xmlpipedb/code
+*Opened SVN repository
+*Opened trunk
+*Checked out gmbuilder folder
+*Created new java project called tATK_gmbuilder1
+*Verified that it was running java jdk
+*Selected all .jar files in lib and added to build path
+**Formed referenced libraries section
+*ran build.xml in ant build...
+**selected clean and dist
+**Built in 4s
+====Adding species profile to GenMAPP builder code database====
+*Two taxon IDs: 373153 for straind D39
+*171101 for R6
+*Created profile called StreptococcusPneumoniaeR6UniprotSpeciesProfile
+*Edited code within profile to define a constructor for the species profile page
+*Insert override into code (see bellow for edits needed)
+*In source, organize imports*
+======work with QA======
+*Need to work out what the placeholder for gene IDs are in the mod
 {{Taur.vil}}