View source for Taur.vil Week 12

[[Week_12| Week 12]] Individual Journal for work on [[Streptococcus pneumoniae]]

==Week 12 Reflection==
#The key accomplishments this week were: 1) doing a first export for each of our three data sets, 2) learning how to edit gmbuilder, and 3) Kevin starting to work with the experimental data and understand how it's put together. 
#Next week, we hope to 1) test whether the first export was successful, work to resolve errors, and try to run an export for all 3 sub-strains at once and 2) for Kevin to actually understand what is going on with the raw research data and why it is organized so weirdly.
#This week, we saw that we worked well had as a group, could divide labor well, and that everybody was competent enough to make progress working independently and with group members. 
#The largest weakness we have is scheduling. It's often hard for us to meet, so we'll have to plan our outside of class meetings well ahead of time. We also have an issue of direction, I observed that without a firm idea of purpose and an immediate goal, none of us work that efficiently necessitating firm direction and clear intermediate goals.

==Lab Journal==
===G54===
*Downloaded GM Builder 2.0b71 for my personal computer from [http://sourceforge.net/projects/xmlpipedb/files/GenMAPP%20Builder/]
*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 [[Streptococcus pneumoniae|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 [[Streptococcus pneumoniae|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
*Model organism database; replace gene ID with a tilde
*Upload gmbuilder 72
*build a copy, run it off an import, run the export using custom profile

{{Taur.vil}}


[[Category: Journal Entry]]
[[Category: Individual Homework]]
[[Category: Team ATK]]
[[Category: Streptococcus pneumoniae]]