Difference between revisions of "Bordetella Pertussis GenMAPP Analysis Deliverables"

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(→‎Group Files and Datasets: uploaded the ribosome pathway mapp created in genmapp)
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== Group Files and Datasets ==
 
== Group Files and Datasets ==
  
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* GenMAPP Gene Database for assigned species (''.gdb''): [[File:Bpertussis-std cw20151210.zip]]
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* GenMAPP Gene Database for assigned species: [[Media:Bpertussis-std cw20151210.zip]]
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* ReadMe file to accompany the Gene Database (''.pdf'')
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* ReadMe file to accompany the Gene Database: [[Media:ReadMe bpertussis-std cw20151210.docx]]
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** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
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** [[Media:Bpertussis genedatabase schema cw20151210.jpg|Gene Database Schema diagram (also included in ReadMe)]]
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** [https://github.com/lmu-bioinformatics/xmlpipedb/blob/readme/GenMAPP%20Gene%20Databases/V.%20cholerae/V.%20cholerae%2020101022/ReadMe.md Sample ReadMe in markdown (a work in progress)]
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* Gene Database Testing Report for final submitted Gene Database: [[Media:Gdb testingreport cw20151210.pdf]]
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** Include Gene Database Schema diagram in ReadMe
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* Processed and analyzed DNA microarray dataset: [[Media:Bpertussis compiledrawdata cw20151208.xlsx]]
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*** Sample schema in Adobe Illustrator format:  [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
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* Data file used for import into GenMAPP: [[Media:Bpertussis compiledrawdata cw20151208.txt]]
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* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
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* GenMAPP Expression Dataset file: [[Media:Bpertussis compiledrawdata cw20151218.gex]]
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* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx''): [[File:Bpertussis compiledrawdata cw20151208.xlsx]]
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* Exceptions file of data imported into GenMAPP: [[Media:Bpertussis compiledrawdata cw20151218.EX.txt]]
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* Data file used for import into GenMAPP (''.txt'' or ''.csv''): [[File:Bpertussis compiledrawdata cw20151208.txt]]
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* Raw MAPPFinder results files:  
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* GenMAPP Expression Dataset file (''.gex''): [[File:Bpertussis expressiondataset cw20151213.gex]]
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** [[Media:Bpertussis mappfinderresults cw20151218-Criterion0-GO.txt|Increased]]
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* Exceptions file of data imported into GenMAPP (''.EX.txt''): [[File:Bpertussis expressiondataset exceptions cw20151213.EX.txt]]
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** [[Media:Bpertussis mappfinderresults cw20151218-Criterion1-GO.txt|Decreased]]
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* Raw MAPPFinder results files (''-GO.txt''):  
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* ''.gmf'' file: [[Media:Bpertussis compiledrawdata cw20151218.gmf]]
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** [[File:Bpertussis mappfinderresults cw20151213-criterion0-GO.txt]]
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* Filtered MAPPFinder Results:
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** [[File:Bpertussis mappfinderresults cw20151213-criterion1-GO.txt]]
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** [[Media:Bpertussis mappfinderresults cw20151218-Criterion0-GO - Filtered.xlsx|Increased]]
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* ''.gmf'' file: [[File:Bpertussis compiledrawdata cw20151213.gmf]]
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** [[Media:Bpertussis mappfinderresults cw20151218-Criterion1-GO - Filtered.xlsx|Decreased]]
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* Filtered MAPPFinder Results (''.xls'' or ''.xlsx''): [[File:Bpertussis mappfinderresults filtered cw20151213-Criterion1-GO.xlsx]]
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* Sample MAPP file of a relevant biological pathway for your species: [[Media: Bpertussis ribosomepathway cw20151218.mapp]]
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* Sample MAPP file of a relevant biological pathway for your species (''.mapp''): [[File:Bpertussis ribosomepathway cw20151215.mapp]]
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* Group Report: [[File:Bpertussis groupreport cw20151218.pdf]] ''version 2''
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* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
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* PowerPoint presentation: [[Media:Bpertussis findings powerpoint.pdf]]
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* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)
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==Team Information & Links==
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{{Template:Class Whoopers}}

Latest revision as of 03:20, 19 December 2015

Group Files and Datasets

Team Information & Links

GenMAPP Analysis of Bordetella pertussis Microarray Data

Gene Database Project Links
Overview Deliverables Reference Format Guilds Project Manager GenMAPP User Quality Assurance Coder
Teams Heavy Metal HaterZ The Class Whoopers GÉNialOMICS Oregon Trail Survivors

Journal Entries

Class Whoopers Individual Journal Entries
Brandon Klein Week 11 Week 12 Week 14 Week 15
Lena Olufson Week 11 Week 12 Week 14 Week 15
Mahrad Saeedi Week 11 Week 12 Week 14 Week 15
Team Entries Week 11 Week 12 Week 14 Week 15

Group Members

Team Weekly Assignments

  • Week 10 Creation of page and combined annotated bibliography (midnight 11/10)
  • Week 11 (midnight 11/17)
  • Week 12 (midnight 11/24)
  • Week 14 (midnight 12/8)
  • Week 15 (midnight 12/15)
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