Difference between revisions of "Bklein7 Week 15"

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(added screenshots)
(updated electronic lab notebook- tally engine)
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==Processes to Document==
 
==Processes to Document==
−
*TallyEngine customization
 
−
*ReadMe file (finish editing)
 
 
*Gene Database Testing Report
 
*Gene Database Testing Report
 
*[[File:Dist cw20151210.zip]]
 
*[[File:Dist cw20151210.zip]]
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**create new gtr if necessary
 
**create new gtr if necessary
 
*deliverables!
 
*deliverables!
−
**start with the readme file
+
**ReadMe file (finish editing)
 
*EC question
 
*EC question
  
−
==Coding Progress==
+
 
−
===Species Export Customization===
+
==TallyEngine Customization==
 +
In GenMAPP Builder version 3.0.0 Build 5 - cw20151203, the ''Bordetella pertussis'' species profile was customized to import 11 ORF gene IDs that were not exported in previous versions. To account for this change, the TallyEngine was customized for ''Bordetella pertussis'' to count "ORF" gene listings separately from "Ordered Locus Names". To do this, I followed the procedure documented below:
 +
 
 +
* First, I determined that I wanted to count the "ordered locus" IDs and "ORF" IDs from the ''gene/name'' tag in the UniProt XML file.
 +
** In the relational database ''bpertussis_cw20151203_gmb3build5'', gene IDs were defined by the type "ordered locus" or "ORF" in the table "genenametype".
 +
* Next, I opened our team's branch of GenMAPP Builder in Eclipse.
 +
* Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', I opened ''gmbuilder.properties''.
 +
* I located the block of text below (it was near the bottom).
 +
#
 +
# wizard.properties
 +
#
 +
* I added the necessary customizations above this block of text. The resulting code was as follows:
 +
# Bordetella pertussis
 +
bordetellapertussis_level_amount=1
 +
 +
bordetellapertussis_element_level0=uniprot/entry/gene/name&type&ORF
 +
 +
bordetellapertussis_query_level0=select count(*) from genenametype where type = 'ORF';
 +
 +
bordetellapertussis_table_name_level0=ORF
 +
 +
#
 +
# wizard.properties
 +
#
 +
* I committed and pushed the changes in the code to Github and then created a new distribution of GenMAPP Builder. This distribution was uploaded as an updated version of the following file: *[[File:Dist cw20151203.zip]].
 +
* Using the updated build of GenMAPP Builder present in the distribution folder, I connected to the relational database ''bpertussis_cw20151203_gmb3build5'' and ran the TallyEngine. The results are pictured below:
 +
**[[File: Tallyenginecustomization_cw20151203.png]]
 +
***The TallyEngine results successfully reflected the customizations I made to the TallyEngine, listing all 11 ORF genes in addition to the 3435 "Ordered Locus Names" gene IDs present in the ''Bordetella pertussis'' gene database.
 +
 
 +
== ==
 +
 
 +
 
 +
 
 
==Links==
 
==Links==
 
{{Template:Bklein7}}
 
{{Template:Bklein7}}
  
 
[[Category:Journal Entry]] [[Category: Group Projects]] [[Category: Class Whoopers]]
 
[[Category:Journal Entry]] [[Category: Group Projects]] [[Category: Class Whoopers]]

Revision as of 00:53, 14 December 2015

Processes to Document

To Do

  • update this page
  • identify and resolve issue with bp3167a
    • recode, push/commit, import/export if necessary
    • create new gtr if necessary
  • deliverables!
    • ReadMe file (finish editing)
  • EC question


TallyEngine Customization

In GenMAPP Builder version 3.0.0 Build 5 - cw20151203, the Bordetella pertussis species profile was customized to import 11 ORF gene IDs that were not exported in previous versions. To account for this change, the TallyEngine was customized for Bordetella pertussis to count "ORF" gene listings separately from "Ordered Locus Names". To do this, I followed the procedure documented below:

  • First, I determined that I wanted to count the "ordered locus" IDs and "ORF" IDs from the gene/name tag in the UniProt XML file.
    • In the relational database bpertussis_cw20151203_gmb3build5, gene IDs were defined by the type "ordered locus" or "ORF" in the table "genenametype".
  • Next, I opened our team's branch of GenMAPP Builder in Eclipse.
  • Under edu.lmu.xmlpipedb.gmbuilder.resource.properties, I opened gmbuilder.properties.
  • I located the block of text below (it was near the bottom).
#
# wizard.properties
#
  • I added the necessary customizations above this block of text. The resulting code was as follows:
# Bordetella pertussis
bordetellapertussis_level_amount=1

bordetellapertussis_element_level0=uniprot/entry/gene/name&type&ORF

bordetellapertussis_query_level0=select count(*) from genenametype where type = 'ORF'; 

bordetellapertussis_table_name_level0=ORF

#
# wizard.properties
#
  • I committed and pushed the changes in the code to Github and then created a new distribution of GenMAPP Builder. This distribution was uploaded as an updated version of the following file: *File:Dist cw20151203.zip.
  • Using the updated build of GenMAPP Builder present in the distribution folder, I connected to the relational database bpertussis_cw20151203_gmb3build5 and ran the TallyEngine. The results are pictured below:
    • Tallyenginecustomization cw20151203.png
      • The TallyEngine results successfully reflected the customizations I made to the TallyEngine, listing all 11 ORF genes in addition to the 3435 "Ordered Locus Names" gene IDs present in the Bordetella pertussis gene database.

Links

Assignments Pages

Individual Journal Entries

Shared Journal Entries

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