Difference between revisions of "Taur.vil Week 12"

Revision as of 18:45, 14 November 2013

Week 12 Individual Journal

Lab Journal

G54

• 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

R6

• 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

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)
• Did a team synchronize to include the work from everyone else in the lab

work with QA

• Need to work out what the placeholder for gene IDs are in the mod

By Tauras Vilgalys

As part of Biological Databases

Please Remember the Harassing of Deities is Strictly Prohibited

Never Forget Samson