Difference between revisions of "Anuvarsh Week 14"
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=Electronic Lab Notebook= | =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: | ||
| + | ** [[Image:Build-2-code-AV-12032015.png]] | ||
| + | * The 6 digit code in the constructor refers to the taxon of B. cenocepacia. This code was found on the [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=216591 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 <code>~</code> 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. | ||
| + | ** [[Image:Add-species-to-customs-list-AV.png]] | ||
{{Template:Anuvarsh}} | {{Template:Anuvarsh}} | ||
==GÉNialOMICS Links== | ==GÉNialOMICS Links== | ||
{{Template:GÉNialOMICS}} | {{Template:GÉNialOMICS}} | ||
Revision as of 20:39, 6 December 2015
Contents
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.
-
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
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 |
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