LMU BioDB 2015 - User contributions [en]

GENialOMICS Deliverables

2015-12-18T23:00:55Z

Anuvarsh: /* Group Files and Datasets */ added final report

[[Image: Genialomics-banner.jpg | center | 1055px]]
 

= Group Files and Datasets =

* [[Media:Bc-Std GEN Build4 20151204.zip|GenMAPP Gene Database for assigned species (''.gdb'') (compressed)]]
* [[Media:ReadMe_Bc-Std_GEN_Build4_20151214_final.pdf|ReadMe file to accompany the Gene Database (''.pdf'')]]
** [[Media: Genialomics-DatabaseSchema-20151211.pdf|Gene Database Schema Diagram]]
* [[media:GÉNialOMICS_Gene_Database_Testing_Report_(Build_4_Export)_-_LMU_BioDB_2015.pdf|Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)]]
* [[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')]]
* [[media:For_genMAPP_KWVP20151205.txt|Data file used for import into GenMAPP (''.txt'' or ''.csv'')]]
* [[media:KWVP20151205.gex|GenMAPP Expression Dataset file (''.gex'')]]
* [[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file of data imported into GenMAPP (''.EX.txt'')]]
* Raw MAPPFinder results files (''-GO.txt'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|Increase]]
** [[media:KWVP_MAPPfinder_20151208-decrease-GO.txt|Decrease]]
* [[media:KWVP20151205.gmf|''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.xlsx|Increase]]
** [[media:Vpkwmappfinder20151205-Criterion1-GO-decreased.xlsx|Decrease]]
*[[media:Oxphosmappkwvp20151212.mapp|Sample MAPP file of a relevant biological pathway for your species (''.mapp'')]]
* [[Media:BioDBFinalReport-Genialomics.pdf | Group Report]]
* [[Media:Genialomics-BioDBFinalPresentation.pdf|Final PowerPoint presentation]]

==Individual Assessments and Reflections==
*[[Media:ReflectionForFinalProject-AV.pdf | Anindita Varshneya]]

 

{{Template:GÉNialOMICS}}

File:BioDBFinalReport-Genialomics.pdf

2015-12-18T22:59:52Z

Anuvarsh:

File:ReflectionForFinalProject-AV.pdf

2015-12-18T21:54:13Z

Anuvarsh: Anuvarsh uploaded a new version of File:ReflectionForFinalProject-AV.pdf

File:ReflectionForFinalProject-AV.pdf

2015-12-18T21:53:05Z

Anuvarsh: Anuvarsh uploaded a new version of File:ReflectionForFinalProject-AV.pdf

GENialOMICS Deliverables

2015-12-18T21:45:34Z

Anuvarsh: /* Group Files and Datasets */ added my reflection

[[Image: Genialomics-banner.jpg | center | 1055px]]
 

= Group Files and Datasets =

* [[Media:Bc-Std GEN Build4 20151204.zip|GenMAPP Gene Database for assigned species (''.gdb'') (compressed)]]
* [[Media:ReadMe_Bc-Std_GEN_Build4_20151214_final.pdf|ReadMe file to accompany the Gene Database (''.pdf'')]]
** [[Media: Genialomics-DatabaseSchema-20151211.pdf|Gene Database Schema Diagram]]
* [[media:GÉNialOMICS_Gene_Database_Testing_Report_(Build_4_Export)_-_LMU_BioDB_2015.pdf|Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)]]
* [[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')]]
* [[media:For_genMAPP_KWVP20151205.txt|Data file used for import into GenMAPP (''.txt'' or ''.csv'')]]
* [[media:KWVP20151205.gex|GenMAPP Expression Dataset file (''.gex'')]]
* [[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file of data imported into GenMAPP (''.EX.txt'')]]
* Raw MAPPFinder results files (''-GO.txt'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|Increase]]
** [[media:KWVP_MAPPfinder_20151208-decrease-GO.txt|Decrease]]
* [[media:KWVP20151205.gmf|''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.xlsx|Increase]]
** [[media:Vpkwmappfinder20151205-Criterion1-GO-decreased.xlsx|Decrease]]
*[[media:Oxphosmappkwvp20151212.mapp|Sample MAPP file of a relevant biological pathway for your species (''.mapp'')]]
* [[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'')
* [[Media:Genialomics-BioDBFinalPresentation.pdf|Final PowerPoint presentation]]

==Individual Assessments and Reflections==
*[[Media:ReflectionForFinalProject-AV.pdf | Anindita Varshneya]]

 

{{Template:GÉNialOMICS}}

File:ReflectionForFinalProject-AV.pdf

2015-12-18T21:44:35Z

Anuvarsh:

Anuvarsh Week 15

2015-12-15T07:49:56Z

Anuvarsh: /* Created ReadMe file */ added link to final readme

=Electronic Lab Notebook=
==Created a new build to fix problem in GenMAPP Builder==
* A modification was mistakenly made last week in Build 5 that returned ORF data into PostGres instead of OrderedLocusNames data. This mistake obviously led to no data being transported into any of the tables that relied on OrderedLocusNames data to be present.
* Brandon recognized this issue, and because this was the only change applied to Build 5, Build 5 was completely deleted, and the final running version of GenMAPP Builder was reverted back to Build 4.
* An image representing the fixed change can be seen here:
** [[Image:Build-3-code-AV.png]]

==Contributed to final presentation and practiced speaking==
* The presentation was started in class on Thursday, December 10, 2015. I began adding information regarding GenMAPP Builder, and Brandon began adding information regarding the production of the database.
* Kevin and Veronica began adding their slides on the Google Drive Presentation before we met.
* Kevin Wyllie, Veronica Pacheco, and I met on Saturday, December 12, 2015 to continue adding slides and talking about the information we want to include in the presentation.
* On Monday, December 14, 2015, Kyle, Veronica, Brandon, and I met to finish off the presentation and practice the entire talk.
* The final presentation can be accessed here: [[Media: Genialomics-BioDBFinalPresentation.pdf | Final Presentation]]

Began drafting final report of findings from this project.
==Created ReadMe file==
* An example ReadMe file was provided (ReadMe for V. cholera) on the [[Gene_Database_Project_Deliverables | Deliverables Instructions Page]].
* This ReadMe file was modified to incorporate information regarding our species, B. cenocepacia.
* I went through and modified most of the data on the example ReadMe file so that it represented data about our database.
* After making those changes, I sent the file to Brandon who added in links regarding each of the different databases that we used.
* The final ReadMe for our database can be accessed here: [[Media:ReadMe_Bc-Std_GEN_Build4_20151214_final.pdf|Final ReadMe]]

==Modified Gene Database Schema for B. cenocepacia.==
* An example Gene Database Schema was provided (for V. cholera) on the [[Gene_Database_Project_Deliverables | Deliverables Instructions Page]].
* After analyzing the gene database schema and cross checking it with the tables created by our own database, Brandon and I were able to determine that this schema also represented the data produced by our own database.
* A descriptive title corresponding to the title of our ReadMe file was added to the schema document via PowerPoint.
* The final Gene Database Schema for our database can be accessed here: [[Media: Genialomics-DatabaseSchema-20151211.pdf | B. cenocepacia Gene Database Schema]]

{{Template:Anuvarsh}}
==Genialomics Links==
{{Template:GÉNialOMICS}}

GENialOMICS Deliverables

2015-12-15T07:40:51Z

Anuvarsh: /* Group Files and Datasets */ added schema link

[[Image: Genialomics-banner.jpg | center | 1055px]]
 

= Group Files and Datasets =

* [[Media:Bc-Std GEN Build4 20151204.zip|GenMAPP Gene Database for assigned species (''.gdb'') (compressed)]]
* [[Media:ReadMe_Bc-Std_GEN_Build4_20151214_final.pdf|ReadMe file to accompany the Gene Database (''.pdf'')]]
** [[Media: Genialomics-DatabaseSchema-20151211.pdf|Gene Database Schema Diagram]]
* [[media:GÉNialOMICS_Gene_Database_Testing_Report_(Build_4_Export)_-_LMU_BioDB_2015.pdf|Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)]]
* [[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')]]
* [[media:For_genMAPP_KWVP20151205.txt|Data file used for import into GenMAPP (''.txt'' or ''.csv'')]]
* [[media:KWVP20151205.gex|GenMAPP Expression Dataset file (''.gex'')]]
* [[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file of data imported into GenMAPP (''.EX.txt'')]]
* Raw MAPPFinder results files (''-GO.txt'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|Increase]]
** [[media:KWVP_MAPPfinder_20151208-decrease-GO.txt|Decrease]]
* [[media:KWVP20151205.gmf|''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.xlsx|Increase]]
** [[media:Vpkwmappfinder20151205-Criterion1-GO-decreased.xlsx|Decrease]]
*[[media:Oxphosmappkwvp20151212.mapp|Sample MAPP file of a relevant biological pathway for your species (''.mapp'')]]
* [[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'')
* [[Media:Genialomics-BioDBFinalPresentation.pdf|Final PowerPoint presentation]]

 
{{Template:GÉNialOMICS}}

GENialOMICS Deliverables

2015-12-15T07:39:09Z

Anuvarsh: fixed spacing issues

[[Image: Genialomics-banner.jpg | center | 1055px]]
 

= Group Files and Datasets =

* [[Media:Bc-Std GEN Build4 20151204.zip|GenMAPP Gene Database for assigned species (''.gdb'') (compressed)]]
* [[Media:ReadMe_Bc-Std_GEN_Build4_20151214_final.pdf|ReadMe file to accompany the Gene Database (''.pdf'')]]
** ReadMe includes Gene Database Schema Diagram
* [[media:GÉNialOMICS_Gene_Database_Testing_Report_(Build_4_Export)_-_LMU_BioDB_2015.pdf|Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)]]
* [[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')]]
* [[media:For_genMAPP_KWVP20151205.txt|Data file used for import into GenMAPP (''.txt'' or ''.csv'')]]
* [[media:KWVP20151205.gex|GenMAPP Expression Dataset file (''.gex'')]]
* [[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file of data imported into GenMAPP (''.EX.txt'')]]
* Raw MAPPFinder results files (''-GO.txt'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|Increase]]
** [[media:KWVP_MAPPfinder_20151208-decrease-GO.txt|Decrease]]
* [[media:KWVP20151205.gmf|''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.xlsx|Increase]]
** [[media:Vpkwmappfinder20151205-Criterion1-GO-decreased.xlsx|Decrease]]
*[[media:Oxphosmappkwvp20151212.mapp|Sample MAPP file of a relevant biological pathway for your species (''.mapp'')]]
* [[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'')
* [[Media:Genialomics-BioDBFinalPresentation.pdf|Final PowerPoint presentation]]

 
{{Template:GÉNialOMICS}}

GENialOMICS Deliverables

2015-12-15T07:38:39Z

Anuvarsh: added header and template

[[Image: Genialomics-banner.jpg | center | 1055px]]
 

= Group Files and Datasets =

* [[Media:Bc-Std GEN Build4 20151204.zip|GenMAPP Gene Database for assigned species (''.gdb'') (compressed)]]
* [[Media:ReadMe_Bc-Std_GEN_Build4_20151214_final.pdf|ReadMe file to accompany the Gene Database (''.pdf'')]]
** ReadMe includes Gene Database Schema Diagram
* [[media:GÉNialOMICS_Gene_Database_Testing_Report_(Build_4_Export)_-_LMU_BioDB_2015.pdf|Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)]]
* [[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')]]
* [[media:For_genMAPP_KWVP20151205.txt|Data file used for import into GenMAPP (''.txt'' or ''.csv'')]]
* [[media:KWVP20151205.gex|GenMAPP Expression Dataset file (''.gex'')]]
* [[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file of data imported into GenMAPP (''.EX.txt'')]]
* Raw MAPPFinder results files (''-GO.txt'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|Increase]]
** [[media:KWVP_MAPPfinder_20151208-decrease-GO.txt|Decrease]]
* [[media:KWVP20151205.gmf|''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.xlsx|Increase]]
** [[media:Vpkwmappfinder20151205-Criterion1-GO-decreased.xlsx|Decrease]]
*[[media:Oxphosmappkwvp20151212.mapp|Sample MAPP file of a relevant biological pathway for your species (''.mapp'')]]
* [[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'')
* [[Media:Genialomics-BioDBFinalPresentation.pdf|Final PowerPoint presentation]]

{{Template:GÉNialOMICS}}

Template:GÉNialOMICS

2015-12-15T07:37:00Z

Anuvarsh: bolded link to deliverables

{|class="wikitable" style="margin: auto;"
|-
! Weekly Group Assignments
! Shared Group Journals
! Project Links
! Team Members
|-
|
{| class="wikitable"
|-
*[[Week_10|Week 10]]
*[[Week_11|Week 11]]
*[[Week_12|Week 12]]
*[[Week_14|Week 14]]
*[[Week_15|Week 15]]
|}
|
{| class="wikitable"
|-
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_10 GÉNialOMICS Week 10]
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_11 GÉNialOMICS Week 11]
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_12 GÉNialOMICS Week 12]
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_14 GÉNialOMICS Week 14]
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_15 GÉNialOMICS Week 15]
|}
|
{| class="wikitable"
|-
*[[GENialOMICS|GENialOMICS Home Page]]
*[[GENialOMICS Deliverables|'''GENialOMICS Deliverables''']]
*[[Gene Database Project|Gene Database Project Overview]]
*[[Gene Database Project Deliverables|Instructions for Project Deliverables]]
*[[Project Manager|Project Manager Guild Page]]
*[[GenMAPP User|GenMAPP User Guild Page]]
*[[Quality Assurance|Quality Assurance Guild Page]]
*[[Coder|Coder Guild Page]]
|}
|
{| class="wikitable"
|-
*[[User:Anuvarsh |Project Manager/Coder: Anu Varshneya]]
*[[User:Blitvak |Quality Assurance: Brandon Litvak]]
*[[User:Vpachec3 |GenMAPP User: Veronica Pacheco]]
*[[User:Kwyllie |GenMAPP User: Kevin Wyllie]]

[[Category:Group Projects]]
[[Category:GÉNialOMICS]]
|}
|}

Anuvarsh Week 15

2015-12-15T00:27:46Z

Anuvarsh: progress from this week was added

=Electronic Lab Notebook=
==Created a new build to fix problem in GenMAPP Builder==
* A modification was mistakenly made last week in Build 5 that returned ORF data into PostGres instead of OrderedLocusNames data. This mistake obviously led to no data being transported into any of the tables that relied on OrderedLocusNames data to be present.
* Brandon recognized this issue, and because this was the only change applied to Build 5, Build 5 was completely deleted, and the final running version of GenMAPP Builder was reverted back to Build 4.
* An image representing the fixed change can be seen here:
** [[Image:Build-3-code-AV.png]]

==Contributed to final presentation and practiced speaking==
* The presentation was started in class on Thursday, December 10, 2015. I began adding information regarding GenMAPP Builder, and Brandon began adding information regarding the production of the database.
* Kevin and Veronica began adding their slides on the Google Drive Presentation before we met.
* Kevin Wyllie, Veronica Pacheco, and I met on Saturday, December 12, 2015 to continue adding slides and talking about the information we want to include in the presentation.
* On Monday, December 14, 2015, Kyle, Veronica, Brandon, and I met to finish off the presentation and practice the entire talk.
* The final presentation can be accessed here: [[Media: Genialomics-BioDBFinalPresentation.pdf | Final Presentation]]

Began drafting final report of findings from this project.
==Created ReadMe file==
* An example ReadMe file was provided (ReadMe for V. cholera) on the [[Gene_Database_Project_Deliverables | Deliverables Instructions Page]].
* This ReadMe file was modified to incorporate information regarding our species, B. cenocepacia.
* I went through and modified most of the data on the example ReadMe file so that it represented data about our database.
* After making those changes, I sent the file to Brandon who added in links regarding each of the different databases that we used.
* The final ReadMe for our database can be accessed here:

==Modified Gene Database Schema for B. cenocepacia.==
* An example Gene Database Schema was provided (for V. cholera) on the [[Gene_Database_Project_Deliverables | Deliverables Instructions Page]].
* After analyzing the gene database schema and cross checking it with the tables created by our own database, Brandon and I were able to determine that this schema also represented the data produced by our own database.
* A descriptive title corresponding to the title of our ReadMe file was added to the schema document via PowerPoint.
* The final Gene Database Schema for our database can be accessed here: [[Media: Genialomics-DatabaseSchema-20151211.pdf | B. cenocepacia Gene Database Schema]]

{{Template:Anuvarsh}}
==Genialomics Links==
{{Template:GÉNialOMICS}}

GENialOMICS

2015-12-15T00:06:46Z

Anuvarsh: /* Individual Goals and Progress */ added final bits of progress

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
* Work with Anu to fix any issues with the final gene database
* Finish presentation
* Prepare for presentation
* Work on final paper
* Conduct final checks on last export (check testing report, make any adjustments)
|
''Work with Kevin Wyllie''
* Finish example MAPPs (one for increase and decrease).
* Create sanity check table (with P-values).
* Upload deliverables.
* Begin PowerPoint.
* Begin report.
|
''Work with Veronica Pacheco''
* Finish example MAPPs (one for increase and decrease).
* Create sanity check table (with P-values).
* Upload deliverables.
* Begin PowerPoint.
* Begin report.
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine.
* Contributed to final presentation and practiced speaking.
* Began drafting final report of findings from this project.
* Created ReadMe file.
* Modified Gene Database Schema for B. cenocepacia.
|
* Checked final export: everything appears in order
* Checked new build of GenMAPP builder
* Realized why the UniProt count of 6994 is so different from the one reported by our database (difference between protein entry/gene name)
|
* Finished example MAPP (decided do chose one pathway, oxidative phosphorylation).
* Created sanity check table (with P-values)
* Uploaded deliverables
* Began and finished PowerPoint.
* Began report.
|
* Finished example MAPP (decided do chose one pathway, oxidative phosphorylation).
* Created sanity check table (with P-values)
* Uploaded deliverables
* Began and finished PowerPoint.
* Began report.
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[Media:gmbuilder-genialomics-20151210-build-5.zip | gmbuilder-genialomics-20151210-build-5.zip]] 
[[Media:Genialomics-DatabaseSchema-20151211.pdf | Genialomics-DatabaseSchema-20151211.pdf]]
|
|
|
* Generated sanity check table.
* Upload deliverables.
|}

==Other Progress==
* On December 14, 2015, GENialOMICS completed a presentation summarizing their methods and findings.
** [[Media:Genialomics-BioDBFinalPresentation.pdf | GENialOMICS Final Presentation]]

=Deliverables=
*See [[GENialOMICS Deliverables|GENialOMICS Deliverables]]
=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

GENialOMICS

2015-12-15T00:05:53Z

Anuvarsh: /* Individual Goals and Progress */ updated anu's progress

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
* Work with Anu to fix any issues with the final gene database
* Finish presentation
* Prepare for presentation
* Work on final paper
* Conduct final checks on last export (check testing report, make any adjustments)
|
''Work with Kevin Wyllie''
* Finish example MAPPs (one for increase and decrease).
* Create sanity check table (with P-values).
* Upload deliverables.
* Begin PowerPoint.
* Begin report.
|
''Work with Veronica Pacheco''
* Finish example MAPPs (one for increase and decrease).
* Create sanity check table (with P-values).
* Upload deliverables.
* Begin PowerPoint.
* Begin report.
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine.
* Contributed to final presentation and practiced speaking.
* Began drafting final report of findings from this project.
|
* Checked final export: everything appears in order
* Checked new build of GenMAPP builder
* Realized why the UniProt count of 6994 is so different from the one reported by our database (difference between protein entry/gene name)
|
* Finished example MAPP (decided do chose one pathway, oxidative phosphorylation).
* Created sanity check table (with P-values)
* Uploaded deliverables
* Began and finished PowerPoint.
* Began report.
|
* Finished example MAPP (decided do chose one pathway, oxidative phosphorylation).
* Created sanity check table (with P-values)
* Uploaded deliverables
* Began and finished PowerPoint.
* Began report.
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[Media:gmbuilder-genialomics-20151210-build-5.zip | gmbuilder-genialomics-20151210-build-5.zip]] 
[[Media:Genialomics-DatabaseSchema-20151211.pdf | Genialomics-DatabaseSchema-20151211.pdf]]
|
|
|
* Generated sanity check table.
* Upload deliverables.
|}

==Other Progress==
* On December 14, 2015, GENialOMICS completed a presentation summarizing their methods and findings.
** [[Media:Genialomics-BioDBFinalPresentation.pdf | GENialOMICS Final Presentation]]

=Deliverables=
*See [[GENialOMICS Deliverables|GENialOMICS Deliverables]]
=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

GENialOMICS

2015-12-15T00:04:06Z

Anuvarsh: /* Group Deliverables */ removed this section

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
* Work with Anu to fix any issues with the final gene database
* Finish presentation
* Prepare for presentation
* Work on final paper
* Conduct final checks on last export (check testing report, make any adjustments)
|
''Work with Kevin Wyllie''
* Finish example MAPPs (one for increase and decrease).
* Create sanity check table (with P-values).
* Upload deliverables.
* Begin PowerPoint.
* Begin report.
|
''Work with Veronica Pacheco''
* Finish example MAPPs (one for increase and decrease).
* Create sanity check table (with P-values).
* Upload deliverables.
* Begin PowerPoint.
* Begin report.
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine
|
* Checked final export: everything appears in order
* Checked new build of GenMAPP builder
* Realized why the UniProt count of 6994 is so different from the one reported by our database (difference between protein entry/gene name)
|
* Finished example MAPP (decided do chose one pathway, oxidative phosphorylation).
* Created sanity check table (with P-values)
* Uploaded deliverables
* Began and finished PowerPoint.
* Began report.
|
* Finished example MAPP (decided do chose one pathway, oxidative phosphorylation).
* Created sanity check table (with P-values)
* Uploaded deliverables
* Began and finished PowerPoint.
* Began report.
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[Media:gmbuilder-genialomics-20151210-build-5.zip | gmbuilder-genialomics-20151210-build-5.zip]] 
[[Media:Genialomics-DatabaseSchema-20151211.pdf | Genialomics-DatabaseSchema-20151211.pdf]]
|
|
|
* Generated sanity check table.
* Upload deliverables.
|}

==Other Progress==
* On December 14, 2015, GENialOMICS completed a presentation summarizing their methods and findings.
** [[Media:Genialomics-BioDBFinalPresentation.pdf | GENialOMICS Final Presentation]]

=Deliverables=
*See [[GENialOMICS Deliverables|GENialOMICS Deliverables]]
=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

GENialOMICS Deliverables

2015-12-15T00:00:24Z

Anuvarsh: /* Group Files and Datasets */ added presentation

== Group Files and Datasets ==

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Include Gene Database Schema diagram in ReadMe
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* [[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')]]
* [[media:For_genMAPP_KWVP20151205.txt|Data file used for import into GenMAPP (''.txt'' or ''.csv'')]]
* [[media:KWVP20151205.gex|GenMAPP Expression Dataset file (''.gex'')]]
* [[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file of data imported into GenMAPP (''.EX.txt'')]]
* Raw MAPPFinder results files (''-GO.txt'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|Increase]]
** [[media:KWVP_MAPPfinder_20151208-decrease-GO.txt|Decrease]]
* [[media:KWVP20151205.gmf|''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.xlsx|Increase]]
** [[media:Vpkwmappfinder20151205-Criterion1-GO-decreased.xlsx|Decrease]]
*[[media:Oxphosmappkwvp20151212.mapp|Sample MAPP file of a relevant biological pathway for your species (''.mapp'')]]
* [[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'')
* [[Media:Genialomics-BioDBFinalPresentation.pdf|Final PowerPoint presentation]]

GENialOMICS

2015-12-14T23:59:48Z

Anuvarsh: /* Other Progress */ added link to final presentation

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
* Work with Anu to fix any issues with the final gene database
* Finish presentation
* Prepare for presentation
* Work on final paper
* Conduct final checks on last export (check testing report, make any adjustments)
|
''Work with Kevin Wyllie''
|
''Work with Veronica Pacheco''
* Finish example MAPPs (one for increase and decrease).
* Create sanity check table (with P-values).
* Upload deliverables.
* Begin PowerPoint.
* Begin report.
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine
|
* Checked final export: everything appears in order
* Checked new build of GenMAPP builder
* Realized why the UniProt count of 6994 is so different from the one reported by our database (difference between protein entry/gene name)
|
|
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[Media:gmbuilder-genialomics-20151210-build-5.zip | gmbuilder-genialomics-20151210-build-5.zip]] 
[[Media:Genialomics-DatabaseSchema-20151211.pdf | Genialomics-DatabaseSchema-20151211.pdf]]
|
|
|
* Generated sanity check table.
* Upload deliverables.
|}

==Other Progress==
* On December 14, 2015, GENialOMICS completed a presentation summarizing their methods and findings.
** [[Media:Genialomics-BioDBFinalPresentation.pdf | GENialOMICS Final Presentation]]

=Deliverables=
*See [[GENialOMICS Deliverables|GENialOMICS Deliverables]]
=== Group Deliverables ===
* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

File:Genialomics-BioDBFinalPresentation.pdf

2015-12-14T23:58:16Z

Anuvarsh:

File:Build-3-code-AV.png

2015-12-13T00:21:20Z

Anuvarsh: Anuvarsh uploaded a new version of File:Build-3-code-AV.png

File:Build-3-code-AV.png

2015-12-13T00:20:54Z

Anuvarsh: Anuvarsh uploaded a new version of File:Build-3-code-AV.png

GENialOMICS

2015-12-11T18:16:02Z

Anuvarsh: /* Individual Goals and Progress */ added schema draft

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
|
''Work with Kevin Wyllie''
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine
|
|
|
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[Media:gmbuilder-genialomics-20151210-build-5.zip | gmbuilder-genialomics-20151210-build-5.zip]] 
[[Media:Genialomics-DatabaseSchema-20151211.pdf | Genialomics-DatabaseSchema-20151211.pdf]]
|
|
|
|}

==Other Progress==

=Deliverables=
=== Group Deliverables ===

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

File:Genialomics-DatabaseSchema-20151211.pdf

2015-12-11T17:55:49Z

Anuvarsh:

GENialOMICS

2015-12-11T17:50:55Z

Anuvarsh: /* Individual Goals and Progress */ fixed typo in file name

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
|
''Work with Kevin Wyllie''
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine
|
|
|
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[Media:gmbuilder-genialomics-20151210-build-5.zip | gmbuilder-genialomics-20151210-build-5.zip]]
|
|
|
|}

==Other Progress==

=Deliverables=
=== Group Deliverables ===

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

File:Gmbuilder-genialomics-20151210-build-5.zip

2015-12-11T17:49:34Z

Anuvarsh:

GENialOMICS

2015-12-11T17:47:54Z

Anuvarsh: /* Individual Goals and Progress */ updated date on file

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
|
''Work with Kevin Wyllie''
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine
|
|
|
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[Media:Gmbuilder-genialmocis-121015-build-5.zip | gmbuilder-genialomcis-20151210-build-5.zip]]
|
|
|
|}

==Other Progress==

=Deliverables=
=== Group Deliverables ===

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

GENialOMICS

2015-12-11T17:46:46Z

Anuvarsh: /* Individual Goals and Progress */ updated links

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
|
''Work with Kevin Wyllie''
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine
|
|
|
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[Media:Gmbuilder-genialmocis-121015-build-5.zip | gmbuilder-genialomcis-121015-build-5.zip]]
|
|
|
|}

==Other Progress==

=Deliverables=
=== Group Deliverables ===

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

GENialOMICS

2015-12-11T17:46:04Z

Anuvarsh: /* Individual Goals and Progress */ updated links

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
|
''Work with Kevin Wyllie''
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine
|
|
|
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[Media:Gmbuilder-genialmocis-121015-build-5.zip | gmbuilder-genialmocis-121015-build-5.zip]]
|
|
|
|}

==Other Progress==

=Deliverables=
=== Group Deliverables ===

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

GENialOMICS Deliverables

2015-12-11T17:23:32Z

Anuvarsh: added list of deliverables to attach

Template:GÉNialOMICS

2015-12-11T17:22:13Z

Anuvarsh: added deliverables link

{|class="wikitable" style="margin: auto;"
|-
! Weekly Group Assignments
! Shared Group Journals
! Project Links
! Team Members
|-
|
{| class="wikitable"
|-
*[[Week_10|Week 10]]
*[[Week_11|Week 11]]
*[[Week_12|Week 12]]
*[[Week_14|Week 14]]
*[[Week_15|Week 15]]
|}
|
{| class="wikitable"
|-
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_10 GÉNialOMICS Week 10]
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_11 GÉNialOMICS Week 11]
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_12 GÉNialOMICS Week 12]
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_14 GÉNialOMICS Week 14]
*[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_15 GÉNialOMICS Week 15]
|}
|
{| class="wikitable"
|-
*[[GENialOMICS|GENialOMICS Home Page]]
*[[GENialOMICS Deliverables|GENialOMICS Deliverables]]
*[[Gene Database Project|Gene Database Project Overview]]
*[[Gene Database Project Deliverables|Instructions for Project Deliverables]]
*[[Project Manager|Project Manager Guild Page]]
*[[GenMAPP User|GenMAPP User Guild Page]]
*[[Quality Assurance|Quality Assurance Guild Page]]
*[[Coder|Coder Guild Page]]
|}
|
{| class="wikitable"
|-
*[[User:Anuvarsh |Project Manager/Coder: Anu Varshneya]]
*[[User:Blitvak |Quality Assurance: Brandon Litvak]]
*[[User:Vpachec3 |GenMAPP User: Veronica Pacheco]]
*[[User:Kwyllie |GenMAPP User: Kevin Wyllie]]

[[Category:Group Projects]]
[[Category:GÉNialOMICS]]
|}
|}

GENialOMICS

2015-12-11T04:54:29Z

Anuvarsh: /* Individual Goals and Progress */ removed left-over writing from last week

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
|
''Work with Kevin Wyllie''
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine
|
|
|
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[File:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip|ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[File:Gmbuilder-genialmocis-121015-build-5.zip|gmbuilder-genialmocis-121015-build-5.zip]]
|
|
|
|}

==Other Progress==

=Deliverables=
=== Group Deliverables ===

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

GENialOMICS

2015-12-11T04:53:47Z

Anuvarsh: added new build

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Fix any problems with the build
* Finish presentation
* Start paper
|
|
''Work with Kevin Wyllie''
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Progress'''
|
* Created a new build to fix problem in TallyEngine
|
|
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 15]]
|
*[[Blitvak Week 15]]
|
*[[Vpachec3 Week 15]]
|
*[[Kevin Wyllie Week 15]]
|-
!scope="row"|'''Files Used/Created'''
|
[[File:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip|ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip]] 
[[File:Gmbuilder-genialmocis-121015-build-5.zip|gmbuilder-genialmocis-121015-build-5.zip]]
|
|
|
|}

==Other Progress==

=Deliverables=
=== Group Deliverables ===

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

File:Gmbuilder-genialmocis-121015-build-5.zip

2015-12-11T04:53:21Z

Anuvarsh:

GENialOMICS

2015-12-09T00:01:30Z

Anuvarsh: /* Week 14 */ added week 15

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Create testing reports on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
* It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder)
* Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder
* Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found
* Completed gene database test reports for builds 2, 3, and 4
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Build 2 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Build 3 Export Testing Report]]
*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Build 4 Export Testing Report]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:GEN BL14 20151201.zip|Files from work done on 12/01/15]]
*[[Media:GEN BL14 20151203.zip|Files from work done on 12/03/15]]
*[[Media:GEN BL14 20151204.zip|Files from work done on 12/04/15]]
*[[Media:GEN BL14 20151207.zip|Files from work done on 12/07/15]]
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.txt|txt form of the forGenMAPP sheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

===Kevin Wyllie===
# What worked?
#* Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
# What didn't work?
#* Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
# What will I do next to fix what didn't work?
#* We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

===Veronica Pacheco===
#What worked?
#* Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
#What didn't work?
#*What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
#What will I do next to fix what didn't work?
#*Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

===Brandon Litvak===
#What worked?
#*I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
#What didn't work?
#*At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
#What will I do next to fix what didn't work?
#*We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

=Week 15=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
|
|
''Work with Kevin Wyllie''
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Progress'''
|
|
|
|
''Work with Veronica Pacheco''
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
[[File:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip|ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip]]
|
|
|
|}

==Other Progress==

=Deliverables=
=== Group Deliverables ===

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

File:ReadMe Bc-Std GEN Build4 20151204.doc.zip

2015-12-09T00:00:50Z

Anuvarsh:

GENialOMICS

2015-12-08T05:59:01Z

Anuvarsh: /* Week 14 */ added my reflection

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Perform testing report on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
|
''Work with Kevin Wyllie''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|
''Work with Veronica Pacheco''
*Performed the statistical analysis in Excel.
*Formatted the gene expression data for import into GenMAPP.
*Imported data into GenMAPP, created ColorSets, and ran MAPPFinder.
*Documented and took screenshots on test runs with GenMAPP.
*Sent the EX.txt file to Brandon and also uploaded on wiki
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
| see Kevin's section -->
|
*[[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|Final processed/formatted microarray data spreadsheet]]
*[[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

==Reflections==
===Anu Varshneya===
*What worked?
**In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
*What didn't work?
**I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
*What will I do next to fix what didn't work?
**Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

=Deliverables=
=== Group Deliverables ===

* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** [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)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[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'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

GENialOMICS

2015-12-06T21:29:50Z

Anuvarsh: /* Individual Goals and Progress */ added anu's progress

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
* Perform database export on the second build and other builds of the customized genMAPP builder
* Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine
* Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1
* Perform testing report on any builds created for the week.
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
* Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Finished third build.
* Customized Tally Engine to collect counts for ORF ID's.
* Finished fourth build.
|
|
|
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
|
| [[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
|}

==Other Progress==

=Deliverables=

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.

Template:Anuvarsh

2015-12-06T21:26:28Z

Anuvarsh: /* Shared Journals */ updated links to genialomics journal

=Other Links=

User Page: [[User:Anuvarsh|Anindita Varshneya]] 
Class Page: [[Main_Page|BIOL/CMSI 367: Biological Databases, Fall 2015]] 
Group Page: [[GENialOMICS|GÉNialOMICS]]

==Assignment Pages==

[[Week_1|Week 1 Assignment]] 
[[Week_2|Week 2 Assignment]] 
[[Week_3|Week 3 Assignment]] 
[[Week_4|Week 4 Assignment]] 
[[Week_5|Week 5 Assignment]] 
[[Week_6|Week 6 Assignment]] 
[[Week_7|Week 7 Assignment]] 
[[Week_8|Week 8 Assignment]] 
[[Week_9|Week 9 Assignment]] 
[[Week_10|Week 10 Assignment]] 
[[Week_11|Week 11 Assignment]] 
[[Week_12|Week 12 Assignment]] 
''No Week 13 Assignment'' 
[[Week_14|Week 14 Assignment]] 
[[Week_15|Week 15 Assignment]] 

==Individual Journals==

[[Anuvarsh_Week_2|Individual Journal Week 2]] 
[[Anuvarsh_Week_3|Individual Journal Week 3]] 
[[Anuvarsh_Week_4|Individual Journal Week 4]] 
[[Anuvarsh_Week_5|Individual Journal Week 5]] 
[[Anuvarsh_Week_6|Individual Journal Week 6]] 
[[Anuvarsh_Week_7|Individual Journal Week 7]] 
[[Anuvarsh_Week_8|Individual Journal Week 8]] 
[[Anuvarsh_Week_9|Individual Journal Week 9]] 
[[Anuvarsh_Week_10|Individual Journal Week 10]] 
[[Anuvarsh_Week_11|Individual Journal Week 11]] 
[[Anuvarsh_Week_12|Individual Journal Week 12]] 
[[Anuvarsh_Week_14|Individual Journal Week 14]] 
[[Anuvarsh_Week_15|Individual Journal Week 15]] 

==Shared Journals==

[[Class_Journal_Week_1|Class Journal Week 1]] 
[[Class_Journal_Week_2|Class Journal Week 2]] 
[[Class_Journal_Week_3|Class Journal Week 3]] 
[[Class_Journal_Week_4|Class Journal Week 4]] 
[[Class_Journal_Week_5|Class Journal Week 5]] 
[[Class_Journal_Week_6|Class Journal Week 6]] 
[[Class_Journal_Week_7|Class Journal Week 7]] 
[[Class_Journal_Week_8|Class Journal Week 8]] 
[[Class_Journal_Week_9|Class Journal Week 9]] 
[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_10 GÉNialOMICS Journal Week 10] 
[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_11 GÉNialOMICS Journal Week 11] 
[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_12 GÉNialOMICS Journal Week 12] 
[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_14 GÉNialOMICS Journal Week 14] 
[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/GENialOMICS#Week_15 GÉNialOMICS Journal Week 15] 

[[Category:Journal Entry]]

Anuvarsh Week 14

2015-12-06T21:24:24Z

Anuvarsh: /* Build 4 */ added link to build

=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]]
===Created Build and Tested===
* Created a new build by:
*# Switched to Eclipse’s Java perspective.
*# 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.
*# Opened the gmbuilder project by clicking on the gray triangle to the left of its name.
*# Right-clicked on build.xml and choose Run As > Ant Build... (the one with the ellipses) from the menu that appears.
*# In the Edit Configuration dialog that appeared, uncheck dist if it is already checked.
*# 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.
*# 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:
*#* [[Image:Build-2-console-AV.png]]
* 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: [[Media:gmbuilder-genialomics-12012015-build-2.zip | 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:
** [[Image:Build-3-code-AV.png]]
* 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: [[Media:gmbuilder-genialomics-12032015-build-3.zip | 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===
# 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.
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', opened ''gmbuilder.properties''.
# 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: [[Media: gmbuilder-genialomics-12032015-build-4.zip | gmbuilder-genialomics-12032015-build-4.zip]]

{{Template:Anuvarsh}}

==GÉNialOMICS Links==
{{Template:GÉNialOMICS}}

Anuvarsh Week 14

2015-12-06T21:23:47Z

Anuvarsh: /* Build 3 */ added link to build

=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]]
===Created Build and Tested===
* Created a new build by:
*# Switched to Eclipse’s Java perspective.
*# 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.
*# Opened the gmbuilder project by clicking on the gray triangle to the left of its name.
*# Right-clicked on build.xml and choose Run As > Ant Build... (the one with the ellipses) from the menu that appears.
*# In the Edit Configuration dialog that appeared, uncheck dist if it is already checked.
*# 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.
*# 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:
*#* [[Image:Build-2-console-AV.png]]
* 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: [[Media:gmbuilder-genialomics-12012015-build-2.zip | 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:
** [[Image:Build-3-code-AV.png]]
* 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: [[Media:gmbuilder-genialomics-12032015-build-3.zip | 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===
# 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.
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', opened ''gmbuilder.properties''.
# 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.

{{Template:Anuvarsh}}
==GÉNialOMICS Links==
{{Template:GÉNialOMICS}}

Anuvarsh Week 14

2015-12-06T21:23:11Z

Anuvarsh: /* Build 2 */ added link to build

=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]]
===Created Build and Tested===
* Created a new build by:
*# Switched to Eclipse’s Java perspective.
*# 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.
*# Opened the gmbuilder project by clicking on the gray triangle to the left of its name.
*# Right-clicked on build.xml and choose Run As > Ant Build... (the one with the ellipses) from the menu that appears.
*# In the Edit Configuration dialog that appeared, uncheck dist if it is already checked.
*# 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.
*# 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:
*#* [[Image:Build-2-console-AV.png]]
* 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: [[Media:gmbuilder-genialomics-12012015-build-2.zip | 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:
** [[Image:Build-3-code-AV.png]]
* 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.

==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===
# 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.
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', opened ''gmbuilder.properties''.
# 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.

{{Template:Anuvarsh}}
==GÉNialOMICS Links==
{{Template:GÉNialOMICS}}

File:Gmbuilder-genialomics-12032015-build-4.zip

2015-12-06T21:21:58Z

Anuvarsh: Anuvarsh uploaded a new version of File:Gmbuilder-genialomics-12032015-build-4.zip

Anuvarsh Week 14

2015-12-06T21:16:27Z

Anuvarsh: /* Electronic Lab Notebook */ finished ELN

=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]]
===Created Build and Tested===
* Created a new build by:
*# Switched to Eclipse’s Java perspective.
*# 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.
*# Opened the gmbuilder project by clicking on the gray triangle to the left of its name.
*# Right-clicked on build.xml and choose Run As > Ant Build... (the one with the ellipses) from the menu that appears.
*# In the Edit Configuration dialog that appeared, uncheck dist if it is already checked.
*# 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.
*# 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:
*#* [[Image:Build-2-console-AV.png]]
* 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.

==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:
** [[Image:Build-3-code-AV.png]]
* 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.

==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===
# 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.
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', opened ''gmbuilder.properties''.
# 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.

{{Template:Anuvarsh}}
==GÉNialOMICS Links==
{{Template:GÉNialOMICS}}

File:Build-3-code-AV.png

2015-12-06T21:07:51Z

Anuvarsh: Anuvarsh uploaded a new version of File:Build-3-code-AV.png

File:Build-3-code-AV.png

2015-12-06T21:00:18Z

Anuvarsh: Anuvarsh uploaded a new version of File:Build-3-code-AV.png

File:Build-3-code-AV.png

2015-12-06T20:57:09Z

Anuvarsh:

File:Build-2-console-AV.png

2015-12-06T20:49:13Z

Anuvarsh:

Anuvarsh Week 14

2015-12-06T20:39:19Z

Anuvarsh: /* Electronic Lab Notebook */ started adding information to ELN

File:Add-species-to-customs-list-AV.png

2015-12-06T20:38:43Z

Anuvarsh:

File:Build-2-code-AV-12032015.png

2015-12-06T20:24:07Z

Anuvarsh:

GENialOMICS

2015-12-04T00:05:27Z

Anuvarsh: /* Week 14 */ added deliverables section after week 14

[[Image: Genialomics-banner.jpg | center | 1055px]]
 
{{Template:GÉNialOMICS}}
 
=Week 10=
*On November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
*On November 5, 2015, a journal detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) titled [http://jb.asm.org/content/191/1/261.short The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients] was found.

 
=Week 11=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete journal club individual assignment
* Create and practice journal club presentation with Brandon
* Find a MOD
* Create project timeline with soft deadlines for each person/milestone
* Complete milestone 0: Working Environment Setup
* Complete milestone 1: Version Control Setup
* Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Reformat Home Page with Dr. Dahlquists recommendations
|
*Perform an initial import/export cycle (with Anu)
*Figure out a file management system (with Anu)
*Characterize regular expression patterns for ID detection
*Further explore the found MOD and review it
*Complete Journal Club presentation on the genome paper
|
''Work with Kevin Wyllie''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|
''Work with Veronica Pacheco''
* Understand experimental design
* Understand sample-data relationship
** raw.zip and .sdrf
** Construct sample-data diagram
* Develop compiled raw data file
|-
!scope="row"|'''Progress'''
|
*Found a possible [http://www.burkholderia.com/ model organism database] (with Brandon Litvak)
*The journal club presentation and outline was prepared; MOD was examined and reviewed
* Completed journal club individual assignment
* Created and practice journal club presentation with Brandon
* Found a MOD
* Created project timeline with soft deadlines for each person/milestone
* Completed milestone 0: Working Environment Setup
* Reformatted Home Page with Dr. Dahlquists recommendations
* Journal Club Presentation File: [[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
|
* Found a possible [http://www.burkholderia.com/ model organism database].
**The more recent [http://beta.burkholderia.com/ version] of the MOD was found
*The regular expression patterns for J2315 were determined
*Preparation was done for the Genome Paper Presentation
**Completed outline of the genome paper
*File management system was determined
|
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper
*[[Vpachec3 Week 11]]
| Created methods diagram ([[media:KWVPMethoddiagram.jpg]]).
*[[File:B. Cenopacia.pptx]]
* we understood the experimental design
* made chart for microarray experiment
*finished powerpoint on microarray paper

|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 11]]
|
*[[Blitvak Week 11]]
|
*[[Vpachec3 Week 11]]
|
*[[Kevin Wyllie Week 11]]
|}

==File Management System==
*Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
*Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
*All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"
==Other Progress==
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.

==Journal Club Presentations==
[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf| Genome Paper Presentation Week 11]] 
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 

=Week 12=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Complete milestone 0: Working Environment Setup
** Set up the development machine (my laptop) with all required software for coding.
* Complete milestone 1: Version Control Setup
** Set up a branch specific to our project and clone necessary code from GitHub onto the development machine.
* Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build
** Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine.
** Set up Eclipse and java project workspace.
** Run initial build.
|
*Complete Milestone 1: Initial Database Export
*Create a Gene Database testing report for the initial export
*Further explore the various ID systems; verify previous findings
*Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases
|
''Work with Kevin Wyllie''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|
''Work with Veronica Pacheco''
*Read the microarray paper to understand the experiment.
*Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
|-
!scope="row"|'''Progress'''
|
* Completed milestone 0: Working Environment Setup
* Completed milestone 1: Version Control Setup
* Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build
* Began milestone 3: Species Profile Creation
** Need to consult with Brandon and/or Dr. Dionisio before continuing.
|
*Completed Milestone 1: Initial Database Export
*Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder)
**Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|
* Compiled data into one Excel spreadsheet.
* Centered data and began statistical analysis (stopped at T statistic).
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 12]]
|
*[[Blitvak Week 12]]
|
*[[Vpachec3 Week 12]]
|
*[[Kevin Wyllie Week 12]]
|-
!scope="row"|'''Files Used/Created'''
|
|
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
*[[Media:ORIG GEN BL12.zip|Starting Files]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|
[[Media:Raw_compiled_data_KW20151119.xlsx]]
|}

==Other Progress==

=Week 14=
==Individual Goals and Progress==
{| class="wikitable" style="margin: auto;"
!colspan="9"|Weekly Goals and Progress
|-
!
![[User:Anuvarsh|'''Anu Varshneya''']]
![[User:Blitvak|'''Brandon Litvak''']]
![[User:Vpachec3|'''Veronica Pacheco''']]
![[User:Kwyllie|'''Kevin Wyllie''']]
|-
!scope="row"|'''Goals'''
|
* Finish second build.
* Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code.
* Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags"
* Start writing README and scientific paper (parts of deliverables).
|
|
''Work with Kevin Wyllie''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|
''Work with Veronica Pacheco''
*Perform the statistical analysis in Excel.
*Format the gene expression data for import into GenMAPP.
*Import data into GenMAPP, create ColorSets, and run MAPPFinder.
*Document and take notes on test runs with GenMAPP.
*Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
*Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
Create a .mapp file showing one pathway that is changed in your data.
|-
!scope="row"|'''Progress'''
|
* Finished second build.
|
|
|
|-
!scope="row"|'''Individual Journal Pages'''
|
*[[Anuvarsh Week 14]]
|
*[[Blitvak Week 14]]
|
*[[Vpachec3 Week 14]]
|
*[[Kevin Wyllie Week 14]]
|-
!scope="row"|'''Files Used/Created'''
|
Build 2 - with customized species profile:
* [[Media: Gmbuilder-genialomics-12012015-build-2.zip| gmbuilder-genialomics-12012015-build-2.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:22, 1 December 2015 (PST) 
 
Build 3 - picking up gene names from ORF instead of ordered locus
* [[Media:Gmbuilder-genialomics-12032015-build-3.zip | gmbuilder-genialomics-12032015-build-3.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 14:58, 3 December 2015 (PST) 
 
Build 4 - customized TallyEngine
* [[Media:Gmbuilder-genialomics-12032015-build-4.zip|gmbuilder-genialomics-12032015-build-4.zip]]
[[User:Anuvarsh|Anuvarsh]] ([[User talk:Anuvarsh|talk]]) 15:18, 3 December 2015 (PST)
|
|
|
|}

==Other Progress==

=Deliverables=

=''Burkholderia cenocepacia'' Genome Paper=
'''Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08'''
* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
* Who owns the rights to the article? '''American Society for Microbiology'''
** Does the journal own the copyright? '''Yes'''
** Do the authors own the copyright? '''No'''
** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
** Is the article available “Open Access”? '''Yes'''
* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
* Is this article available in print or online only? '''It is both available in print and online.'''
* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.'''
* How many articles does this article cite? '''It has 150 cited references.'''
* How many articles cite this article? '''It is cited 128 times.'''
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.'''

 
=Microarray Paper=
'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
* This article is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
**Cannot find HTML format on publisher web site.
* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
* Does the journal own the copyright? Yes.
* Do the authors own the copyright? No.
* Do the authors own the rights under a Creative Commons license? Yes.
* Is the article available “Open Access”? Yes.
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
* Is this article available in print or online only? Available in print and online.
* Has LMU paid a subscription or other fee for your access to this article? No.
* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
* How many articles does this article cite? This article has 34 cited references.
* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
* Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.