LMU BioDB 2015 - User contributions [en]

GENialOMICS Deliverables

2015-12-18T23:33:08Z

Kwyllie: 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'')]]
* [[Media:BioDBFinalReport-Genialomics.pdf | Group Report]]
* [[Media:Genialomics-BioDBFinalPresentation.pdf|Final PowerPoint presentation]]

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

 

{{Template:GÉNialOMICS}}

File:KWreflection.pdf

2015-12-18T23:32:21Z

Kwyllie: PDF for my reflection.

PDF for my reflection.

Kevin Wyllie Week 15

2015-12-15T07:19:40Z

Kwyllie: Finished my reflection.

== Final Presentation ==

[[Media:Genialomics-BioDBFinalPresentation.pdf | GENialOMICS Final Presentation]]

== Electronic Lab Notebook ==

=== MAPPFinder Procedure ===

# MAPPFinder was launched from the GenMAPP window: "Tools" > "MAPPFinder".
# "Calculate New Results" was selected from the MAPPFinder window.
# "Find File" was selected and in the directory, the .gex file (created in the Expression Dataset Manager - see week 14) was selected.
#* This file can be found [[media:KWVP20151205.gex|here]].
# Under the "Select Color Set" field, "KWVP_20151205" was selected (the color set's name in this case is the same as the .gex file's name - and there's only one color set in the .gex file).
# After the color set has been selected, under the "Select Criteria to filter by" field, either increase or decrease was chosen.
# The boxes for "Gene Ontology" and "Click here to calculate p values..." were checked.
# The location to save the resulting .txt file was selected with the "Browse" option toward the bottom of the window. Note that because this protocol was carried out both for increase and decrease, there were two text files generated in MAPPFinder.
# "Run MAPPFinder" was selected to generate the gene ontology tree (and the aforementioned .txt files).
#* The files generated can be found here:
#** [[media:KWVP_MAPPfinder_20151208-decrease-GO.txt|For downregulated GO terms.]]
#** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|For upregulated GO terms.]]

=== Filtered GO List ===

*The GO term files above were opened in Excel, and the following filters were placed on the given columns:
** Z score: greater than 2
** PermuteP: less than 0.05
** Number changed: greater than or equal to 4 AND less than 100
** Percent changed: great than or equal to 15
* Values in the following columns were recorded:
** Number Changed
** Number Measured
** Number in GO
** Percent Changed
** Percent Present
** PermuteP
** AdjustedP
* Some of the above filter criteria had to be adjusted to attain 16 non-redundant GO terms. A list of these terms is shown below. For those terms which did not exactly fit this initial criteria, the altered criteria is apparent in the values on the table.
[[file:KWVP_GOterms.jpg|center|thumb]]

=== Sanity Check ===

[[file:KWVPSanitycheck2.png|center]]

== Reflection ==

=== Statement of Work ===

The goal of this project was to create a gene database for ''Burkholderia cenocepacia'' and to use this database for the purpose of conducting an analysis on microarray data generated by Van Acker et al (2013). This data measured the transcriptomic effects of tobramycin (an antibiotic) on the bacterium. The database was constructed using data from [http://www.burkholderia.com/ Burkholderia Genome Database], [http://www.uniprot.org/ UniProt] and [http://geneontology.org/ Gene Ontology Consortium]. The microarray data was taken from the paper, [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]. Once the gene database (found [[Media:Bc-Std_GEN_20151204.zip|here]]) was created, the processed microarray data (found [[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|here]]) were fed through a software called GenMAPP, which analyzed the data and returned significantly changed cellular processes (gene ontology terms - see above for files and results). We then compared the biological implications of our analysis to that of Van Acker et al (2013).

=== Assessment of Project ===

This project, I think, was a success. I can't speak for the QA and Coder (though the process seemed to go smoothly for them as well), but Veronica and I faced a healthy difficulty curve (substantial, yet reasonable) in processing and analyzing the microarray data. The only thing that "didn't" work for us was initially proceeding further than we should've with statistical analysis, which ended up being a waste of time as we had not properly accounted for the multitude of technical replicates within our data. But retracing our steps wasn't horribly difficult. To be quite honest, if I were to do this project again, the only thing I would change is that I would stress out about it less, because it was much easier than I had expected!

I believe the quality of our work was high. We got slightly ahead of schedule, and thus had more time afterward to carefully examine our methods and verify that we had processed the data correctly. The organization may have been the most difficult part at first, managing between my individual page and the group page. The requirements for the group page initially seemed overwhelming, but it wasn't a problem in the end. We certainly completed all of the "milestones" in this project. Again, this was not an issue because we overestimated the difficult of this project and thus spent ample time on it.

=== Reflection on the Process ===

* What did you learn?
** With your head?
*** I learned a lot about the microbial response to certain antibiotics! But more broadly, this project gave me a deeper understanding of the importance of deeply comprehending the scientific reasons for carrying out each step in the process of analyzing results.
** With your heart?
*** I think this project taught me a lot about how to communicate with people of different skillsets. Although every student in the class did the same assignments before this project, upon beginning this project we each re-familiarized ourselves with the appropriate processes to carry out our specific roles (and, being busy college students, ''only'' those necessary processes). Thus, when communicating with Anu and Brandon, I had to find ways to explain my part of the project to someone who didn't know as much about the data processing protocols (and that's totally ok; it wasn't their responsibility to know these things, and this is mirrored in real workplace settings). Of course, when they communicated with Veronica and I, they had to water down their protocols as well.
** With your hands (technical skills)?
*** Every time I do microarray analysis-related tasks in Excel (whether in this class or with the Dahlquist Lab), it feels like I get a little better at it. And this project was no different. Excel, in general, is a skill that develops through repeated use, so that's certainly a technical skill I developed further. However, in this project we faced the added difficulty of knowing that nobody more experienced than Veronica and I would be checking our work as closely. So there was more pressure, but it just meant that we scrutinized our work more closely, which only added to the learning experience.
* What lesson will you take away from this project that you will still use a year from now?
** A deeper understanding of the scientific principles behind microarray analysis, particularly with respect to how it is processed. While I may not be ''carrying out'' microarray analyses upon graduating from LMU (and thus graduating from the Dahlquist Lab), it seems like this technology will become even more pervasive within the field of biology, so and understanding of its inner-workings will be useful. Who knows? It may even become a standard method in medicinal science!

== Links ==

{{Template:GÉNialOMICS}}
{{Template:KwyllieJournalLinks}}

[[Category:Journal Entry]]

Kevin Wyllie Week 15

2015-12-15T05:59:50Z

Kwyllie: Added the assessment of the project.

== Final Presentation ==

[[Media:Genialomics-BioDBFinalPresentation.pdf | GENialOMICS Final Presentation]]

== Electronic Lab Notebook ==

=== MAPPFinder Procedure ===

# MAPPFinder was launched from the GenMAPP window: "Tools" > "MAPPFinder".
# "Calculate New Results" was selected from the MAPPFinder window.
# "Find File" was selected and in the directory, the .gex file (created in the Expression Dataset Manager - see week 14) was selected.
#* This file can be found [[media:KWVP20151205.gex|here]].
# Under the "Select Color Set" field, "KWVP_20151205" was selected (the color set's name in this case is the same as the .gex file's name - and there's only one color set in the .gex file).
# After the color set has been selected, under the "Select Criteria to filter by" field, either increase or decrease was chosen.
# The boxes for "Gene Ontology" and "Click here to calculate p values..." were checked.
# The location to save the resulting .txt file was selected with the "Browse" option toward the bottom of the window. Note that because this protocol was carried out both for increase and decrease, there were two text files generated in MAPPFinder.
# "Run MAPPFinder" was selected to generate the gene ontology tree (and the aforementioned .txt files).
#* The files generated can be found here:
#** [[media:KWVP_MAPPfinder_20151208-decrease-GO.txt|For downregulated GO terms.]]
#** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|For upregulated GO terms.]]

=== Filtered GO List ===

*The GO term files above were opened in Excel, and the following filters were placed on the given columns:
** Z score: greater than 2
** PermuteP: less than 0.05
** Number changed: greater than or equal to 4 AND less than 100
** Percent changed: great than or equal to 15
* Values in the following columns were recorded:
** Number Changed
** Number Measured
** Number in GO
** Percent Changed
** Percent Present
** PermuteP
** AdjustedP
* Some of the above filter criteria had to be adjusted to attain 16 non-redundant GO terms. A list of these terms is shown below. For those terms which did not exactly fit this initial criteria, the altered criteria is apparent in the values on the table.
[[file:KWVP_GOterms.jpg|center|thumb]]

=== Sanity Check ===

[[file:KWVPSanitycheck2.png|center]]

== Reflection ==

=== Statement of Work ===

The goal of this project was to create a gene database for ''Burkholderia cenocepacia'' and to use this database for the purpose of conducting an analysis on microarray data generated by Van Acker et al (2013). This data measured the transcriptomic effects of tobramycin (an antibiotic) on the bacterium. The database was constructed using data from [http://www.burkholderia.com/ Burkholderia Genome Database], [http://www.uniprot.org/ UniProt] and [http://geneontology.org/ Gene Ontology Consortium]. The microarray data was taken from the paper, [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]. Once the gene database (found [[Media:Bc-Std_GEN_20151204.zip|here]]) was created, the processed microarray data (found [[media:Raw_compiled_data_FINAL_KWVP20151507.xlsx|here]]) were fed through a software called GenMAPP, which analyzed the data and returned significantly changed cellular processes (gene ontology terms - see above for files and results). We then compared the biological implications of our analysis to that of Van Acker et al (2013).

=== Assessment of Project ===

This project, I think, was a success. I can't speak for the QA and Coder (though the process seemed to go smoothly for them as well), but Veronica and I faced a healthy difficulty curve (substantial, yet reasonable) in processing and analyzing the microarray data. The only thing that "didn't" work for us was initially proceeding further than we should've with statistical analysis, which ended up being a waste of time as we had not properly accounted for the multitude of technical replicates within our data. But retracing our steps wasn't horribly difficult. To be quite honest, if I were to do this project again, the only thing I would change is that I would stress out about it less, because it was much easier than I had expected!

I believe the quality of our work was high. We got slightly ahead of schedule, and thus had more time afterward to carefully examine our methods and verify that we had processed the data correctly. The organization may have been the most difficult part at first, managing between my individual page and the group page. The requirements for the group page initially seemed overwhelming, but it wasn't a problem in the end. We certainly completed all of the "milestones" in this project. Again, this was not an issue because we overestimated the difficult of this project and thus spent ample time on it.

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

== Links ==

{{Template:GÉNialOMICS}}
{{Template:KwyllieJournalLinks}}

[[Category:Journal Entry]]

Kevin Wyllie Week 15

2015-12-15T05:32:38Z

Kwyllie: Edited the statement of work.

Kevin Wyllie Week 15

2015-12-15T05:30:44Z

Kwyllie: Added the statement of work.

2015-12-14T20:04:50Z

Kwyllie: Syntax.

GENialOMICS Deliverables

2015-12-13T01:15:19Z

Kwyllie: Syntax fix.

== 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-decrease-GO.txt|Decrease]]
** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|Increase]]
* [[media:KWVP20151205.gmf|''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
** [[media:KWVP_MAPPfinder_20151208-increase-GO.xlsx|Increase]]
** Decrease
* 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)

GENialOMICS Deliverables

2015-12-13T01:14:34Z

Kwyllie: Added a bunch of deliverables.

== 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-decrease-GO.txt|Decrease]]
** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|Increase]]
* [[media:KWVP20151205.gmf|''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
** [[KWVP_MAPPfinder_20151208-increase-GO.xlsx|Increase]]
** Decrease
* 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)

File:KWVP MAPPfinder 20151208-increase-GO.xlsx

2015-12-13T01:14:08Z

Kwyllie: Filtered MAPPFinder results for the increased GO terms.

Filtered MAPPFinder results for the increased GO terms.

File:KWVP20151205.gmf

2015-12-13T01:13:16Z

Kwyllie: Our gmf file.

Our gmf file.

Kevin Wyllie Week 15

2015-12-13T01:05:22Z

Kwyllie: Format fix.

Kevin Wyllie Week 15

2015-12-13T01:04:17Z

Kwyllie: Added sanity check image.

File:KWVPSanitycheck2.png

2015-12-13T01:04:00Z

Kwyllie: Another sanity check table.

Another sanity check table.

2015-12-07T19:58:09Z

Kwyllie: Added more protocol.

Kevin Wyllie Week 14

2015-12-07T05:37:54Z

Kwyllie: Added my good practice links.

Kevin Wyllie Week 14

2015-12-07T01:38:50Z

Kwyllie: Continued the protocol.

GENialOMICS

2015-12-05T21:20:02Z

Kwyllie: Added our first exceptions 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
* 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.
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''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'''
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* Finished second build.
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!scope="row"|'''Individual Journal Pages'''
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*[[Anuvarsh Week 14]]
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*[[Blitvak Week 14]]
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*[[Vpachec3 Week 14]]
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*[[Kevin Wyllie Week 14]]
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!scope="row"|'''Files Used/Created'''
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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)
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*[[Media:Bc-Std_GEN_20151204.zip|Compressed gdb from Build 4]]
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| [[media:For_genMAPP_KWVP20151205.EX.txt|Exceptions file from first export.]]
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==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.

File:For genMAPP KWVP20151205.EX.txt

2015-12-05T21:18:56Z

Kwyllie: The exceptions file for our first export.

The exceptions file for our first export.

Kevin Wyllie Week 14

2015-12-03T23:52:11Z

Kwyllie: Began protocol and sanity check. Very incomplete at this point, though.

Template:KwyllieJournalLinks

2015-12-03T22:38:06Z

Kwyllie: Fixed a missing link!

[[User:kwyllie]]
* [[Kevin Wyllie Week 2]] (See the [[Week 2|original assignment]] and [[Class Journal Week 2|class journal]].)
* [[Kevin Wyllie Week 3]] (See the [[Week 3|original assignment]] and [[Class Journal Week 3|class journal]].)
* [[Kevin Wyllie Week 4]] (See the [[Week 4|original assignment]] and [[Class Journal Week 4|class journal]].)
* [[Kevin Wyllie Week 5]] (See the [[Week 5|original assignment]] and [[Class Journal Week 5|class journal]].)
* [[Kevin Wyllie Week 6]] (See the [[Week 6|original assignment]] and [[Class Journal Week 6|class journal]].)
* [[Kevin Wyllie Week 7]] (See the [[Week 7|original assignment]] and [[Class Journal Week 7|class journal]].)
* [[Kevin Wyllie Week 8]] (See the [[Week 8|original assignment]] and [[Class Journal Week 8|class journal]].)
* [[Kevin Wyllie Week 9]] (See the [[Week 9|original assignment]] and [[Class Journal Week 9|class journal]].)
* [[Kevin Wyllie Week 10]] (See the [[Week 10|original assignment]].)
* [[Kevin Wyllie Week 11]] (See the [[Week 11|original assignment]].)
* [[Kevin Wyllie Week 12]] (See the [[Week 12|original assignment]].)
* [[Kevin Wyllie Week 14]] (See the [[Week 14|original assignment]].)
* [[Kevin Wyllie Week 15]] (See the [[Week 14|original assignment]].)

GENialOMICS

2015-11-24T04:52:01Z

Kwyllie: Added download link for the spreadsheet containing our progress in analyzing the microarray data.

File:Raw compiled data KW20151119.xlsx

2015-11-24T04:50:59Z

Kwyllie: Our progress in compiling and processing the data.

Our progress in compiling and processing the data.

GENialOMICS

2015-11-24T04:49:13Z

Kwyllie: Added progress for this week.