Anuvarsh Week 14

Electronic Lab Notebook

Goals

• Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
• Finish GenMAPP Builder
  • * Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
• Start writing README and scientific paper (parts of deliverables).

Build 2

• The last build was a dry run and had no customizations. This build will include a customized species profile.

Created the Species Profile

• Exposed the contents of the src folder.
• Right-clicked on the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package and choose New > Class from the popup menu.
• In the dialog that appeared:
  • Name: BurkholderiaCenocepaciaUniProtSpeciesProfile
  • Superclass: edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile
• Clicked Finish.
• There was a BurkholderiaCenocepaciaUniProtSpeciesProfile.java file within the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package

Customizing the Species Profile

• In the java file created in the previous step, the following code was added:
  • 
• The 6 digit code in the constructor refers to the taxon of B. cenocepacia. This code was found on the NCBI Taxonomy Browser.
• The link towards the bottom of the code refers to the page on the model organism database with gene information where the ~ at the end of the link would be replaced with each gene name.

Added the Species Profile to the Catalog of Known Species Profiles

• I navigated to the file UniProtDatabaseProfile.java under the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package.
• I modified the already existing code by adding a line at the bottom of the following block of code towards the top of the page indicating the B. cenocepacia profile.
  • 

Created Build and Tested

• Created a new build by:
  1. Switched to Eclipse’s Java perspective.
  2. Edited the GenMAPPBuilder.java source code to identify the distribution that you are about to create by setting the VERSION string (located at approximately line 83) to a sufficiently descriptive value.
  3. Opened the gmbuilder project by clicking on the gray triangle to the left of its name.
  4. Right-clicked on build.xml and choose Run As > Ant Build... (the one with the ellipses) from the menu that appears.
  5. In the Edit Configuration dialog that appeared, uncheck dist if it is already checked.
  6. Checked on the clean and dist items in the Targets tab. The Target execution order section near the bottom of the dialog said clean, dist.
  7. Clicked the Run button. The computer will work for a bit. You will see some messages scroll up on the Console tab if that tab is visible, as seen below:
     • 
• Tested the new build with the QA and determined that the build did not create a functional gene database because the gmbuilder was attempting to collect gene names from OrderedLocusNames, but gene names were stored in the ORF table.

• Link to the build: gmbuilder-genialomics-12012015-build-2.zip

Build 3

• In order to modify the GenMAPPBuilder to collect gene names from the ORF table, the following code was added to the customized species profile:
  • 
• This code is meant to override the function that collects gene names from OrderedLocusNames.
• After completing this change in code, the build was created and tested just as before.
• Link to the build: gmbuilder-genialomics-12032015-build-3.zip

Build 4

• After testing the previous build, the QA noticed that the ORF data did not appear in the Tally Engine. This is because the Tally Engine was unmodified.

Customized the IDs that the Tally Engine Counts

1. Determined which IDs (outside of the defaults that the tally engine already counts) you would like to count. In this case, ORF ID's wanted to be counted.
2. Under edu.lmu.xmlpipedb.gmbuilder.resource.properties, opened gmbuilder.properties.
3. Locate the block of text below (near the bottom).

#
# wizard.properties
#

• First, marked out the section that denotes the customization for your species:

# Burkholderia Cenocepacia

• Next, rewrote your species name without spaces and all lowercase (burkholderacenocepacia). Specifid the number of additional custom IDs to count as follows:

burkholderiacenocepacia_level_amount=1

• Now, I specified three things: an element, a query, and a name. Each of these items is numbered, starting from 0. Each item number is called a level.

# Burkholderia cenocepacia
burkholderiacenocepacia_level_amount=1
burkholderiacenocepacia_element_level0=uniprot/entry/gene/name&type&ORF
burkholderiacenocepacia_query_level0=select count(*) from genenametype where type = 'ORF';
speciesname_query_level0=ORF

• A build was created just as before, and tested.
• All genes were found as expected, so the QA and I determined that this build was a success.

• Link to the build: gmbuilder-genialomics-12032015-build-4.zip

Other Links

User Page: Anindita Varshneya
Class Page: BIOL/CMSI 367: Biological Databases, Fall 2015
Group Page: GÉNialOMICS

Assignment Pages

Week 1 Assignment
Week 2 Assignment
Week 3 Assignment
Week 4 Assignment
Week 5 Assignment
Week 6 Assignment
Week 7 Assignment
Week 8 Assignment
Week 9 Assignment
Week 10 Assignment
Week 11 Assignment
Week 12 Assignment
No Week 13 Assignment
Week 14 Assignment
Week 15 Assignment

Individual Journals

Individual Journal Week 2
Individual Journal Week 3
Individual Journal Week 4
Individual Journal Week 5
Individual Journal Week 6
Individual Journal Week 7
Individual Journal Week 8
Individual Journal Week 9
Individual Journal Week 10
Individual Journal Week 11
Individual Journal Week 12
Individual Journal Week 14
Individual Journal Week 15

Shared Journals

Class Journal Week 1
Class Journal Week 2
Class Journal Week 3
Class Journal Week 4
Class Journal Week 5
Class Journal Week 6
Class Journal Week 7
Class Journal Week 8
Class Journal Week 9
GÉNialOMICS Journal Week 10
GÉNialOMICS Journal Week 11
GÉNialOMICS Journal Week 12
GÉNialOMICS Journal Week 14
GÉNialOMICS Journal Week 15

GÉNialOMICS Links

Weekly Group Assignments	Shared Group Journals	Project Links	Team Members
Week 10 Week 11 Week 12 Week 14 Week 15	GÉNialOMICS Week 10 GÉNialOMICS Week 11 GÉNialOMICS Week 12 GÉNialOMICS Week 14 GÉNialOMICS Week 15	GENialOMICS Home Page GENialOMICS Deliverables Gene Database Project Overview Instructions for Project Deliverables Project Manager Guild Page GenMAPP User Guild Page Quality Assurance Guild Page Coder Guild Page	Project Manager/Coder: Anu Varshneya Quality Assurance: Brandon Litvak GenMAPP User: Veronica Pacheco GenMAPP User: Kevin Wyllie