Difference between revisions of "GENialOMICS"

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[[Image: Genialomics-banner.jpg | center | 1055px]]
 
[[Image: Genialomics-banner.jpg | center | 1055px]]
 +
<br>
 +
{{Template:GÉNialOMICS}}
 +
<br>
 +
=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.
  
−
==Group Members==
+
<br>
−
Project Manager and Coder: [[User:Anuvarsh | Anu Varshneya]]<br>
+
=Week 11=
−
Quality Assurance: [[User:Blitvak | Brandon Litvak]]<br>
+
==Individual Goals and Progress==
−
GenMAPP Users: [[User:Vpachec3 | Veronica Pacheco]] & [[User:Kwyllie | Kevin Wyllie]]<br>
+
{| 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'''
 +
|<!--Anu-->
 +
* 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
 +
|<!--Brandon-->
 +
*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
 +
|<!--Veronica-->
 +
''Work with Kevin Wyllie''
 +
* Understand experimental design
 +
* Understand sample-data relationship
 +
** raw.zip and .sdrf
 +
** Construct sample-data diagram
 +
* Develop compiled raw data file
 +
|<!--Kevin-->
 +
''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'''
 +
|<!--Anu-->
 +
*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]]
 +
|<!--Brandon-->
 +
* 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
 +
|<!--Veronica-->
 +
* we understood the experimental design
 +
* made chart for microarray experiment
 +
*finished powerpoint on microarray paper
 +
*[[Vpachec3 Week 11]]
 +
|<!--Kevin--> 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
  
−
==''Burkholderia cenocepacia''==
+
|-
−
*In class on November 3, 2015, GÉNialOMICS chose to create database for ''Burkholderia cenocepacia''.
+
!scope="row"|'''Individual Journal Pages'''
−
*On 11/5/15, a [http://jb.asm.org/content/191/1/261.short] detailing the complete genome of ''Burkholderia cenocepacia'' (strain J2315) was found (The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients)
+
|<!--Anu-->
−
*Possible MOD was found: [http://www.burkholderia.com/]
+
*[[Anuvarsh Week 11]]
 +
|<!--Brandon-->
 +
*[[Blitvak Week 11]]
 +
|<!--Veronica-->
 +
*[[Vpachec3 Week 11]]
 +
|<!--Kevin-->
 +
*[[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]]<br>
 +
[[Media:B._Cenopacia.pptx| Microarray Paper Presentation Week 12]]
 +
<br>
  
 +
=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'''
 +
|<!--Anu-->
 +
* 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.
 +
|<!--Brandon-->
 +
*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
 +
|<!--Veronica-->
 +
''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).
 +
|<!--Kevin-->
 +
''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'''
 +
|<!--Anu-->
 +
* 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.
 +
|<!--Brandon-->
 +
*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)
 +
|<!--Veronica-->
 +
* Compiled data into one Excel spreadsheet.
 +
* Centered data and began statistical analysis (stopped at T statistic).
 +
|<!--Kevin-->
 +
* Compiled data into one Excel spreadsheet.
 +
* Centered data and began statistical analysis (stopped at T statistic).
 +
|-
 +
!scope="row"|'''Individual Journal Pages'''
 +
|<!--Anu-->
 +
*[[Anuvarsh Week 12]]
 +
|<!--Brandon-->
 +
*[[Blitvak Week 12]]
 +
|<!--Veronica-->
 +
*[[Vpachec3 Week 12]]
 +
|<!--Kevin-->
 +
*[[Kevin Wyllie Week 12]]
 +
|-
 +
!scope="row"|'''Files Used/Created'''
 +
|<!--Anu-->
 +
|<!--Brandon-->
 +
*[[Media:WEEK12FILES GEN BL.zip|Week 12 Files]]
 +
*[[Media:ORIG GEN BL12.zip|Starting Files]]
 +
|<!--Veronica-->
 +
[[Media:Raw_compiled_data_KW20151119.xlsx]]
 +
|<!--Kevin-->
 +
[[Media:Raw_compiled_data_KW20151119.xlsx]]
 +
|}
  
−
----
+
==Other Progress==
−
{{Template:GÉNialOMICS}}
+
 
 +
=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'''
 +
|<!--Anu-->
 +
* 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).
 +
|<!--Brandon-->
 +
* 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.
 +
|<!--Veronica-->
 +
''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.
 +
|<!--Kevin-->
 +
''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'''
 +
|<!--Anu-->
 +
* 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.
 +
|<!--Brandon-->
 +
* 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
 +
|<!--Veronica-->
 +
''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
 +
|<!--Kevin-->
 +
''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'''
 +
|<!--Anu-->
 +
*[[Anuvarsh Week 14]]
 +
|<!--Brandon-->
 +
*[[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]]
 +
|<!--Veronica-->
 +
*[[Vpachec3 Week 14]]
 +
|<!--Kevin-->
 +
*[[Kevin Wyllie Week 14]]
 +
|-
 +
!scope="row"|'''Files Used/Created'''
 +
|<!--Anu-->
 +
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) <br>
 +
<br>
 +
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)<br>
 +
<br>
 +
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)
 +
|<!--Brandon-->
 +
*[[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]]
 +
|<!--Veronica--> see Kevin's section -->
 +
|<!--Kevin-->
 +
*[[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'''
 +
|<!--Anu-->
 +
* Fix any problems with the build
 +
* Finish presentation
 +
* Start paper
 +
|<!--Brandon-->
 +
* 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)
 +
|<!--Veronica-->
 +
''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.
 +
|<!--Kevin-->
 +
''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'''
 +
|<!--Anu-->
 +
* 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.
 +
|<!--Brandon-->
 +
* 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)
 +
* Finalized readme
 +
* Helped in finalizing the slides
 +
* Practiced presentation
 +
|<!--Veronica-->
 +
* 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.
 +
|<!--Kevin-->
 +
* 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'''
 +
|<!--Anu-->
 +
*[[Anuvarsh Week 15]]
 +
|<!--Brandon-->
 +
*[[Blitvak Week 15]]
 +
|<!--Veronica-->
 +
*[[Vpachec3 Week 15]]
 +
|<!--Kevin-->
 +
*[[Kevin Wyllie Week 15]]
 +
|-
 +
!scope="row"|'''Files Used/Created'''
 +
|<!--Anu-->
 +
*[[Media:ReadMe_Bc-Std_GEN_Build4_20151204.doc.zip | readMe_Bc-Std_GEN_Build4_20151204.doc.zip]] <br>
 +
*[[Media:gmbuilder-genialomics-20151210-build-5.zip | gmbuilder-genialomics-20151210-build-5.zip]]<br>
 +
*[[Media:Genialomics-DatabaseSchema-20151211.pdf | Genialomics-DatabaseSchema-20151211.pdf]]
 +
*[[Media:BioDB_Final_Presentation_GEN_20151214.pdf| Final Presentation Slides (.pdf)]]
 +
|<!--Brandon-->
 +
*[[Media:ReadMe Bc-Std GEN Build4 20151214 final.pdf| Final Readme]]
 +
*[[Media:GÉNialOMICS Gene Database Testing Report (Build 4 Export) - LMU BioDB 2015.pdf| Final Testing Report, as PDF]]
 +
*[[Media:BioDB_Final_Presentation_GEN_20151214.pdf| Final Presentation Slides (.pdf)]]
 +
|<!--Veronica-->
 +
*[[Media:BioDB_Final_Presentation_GEN_20151214.pdf| Final Presentation Slides (.pdf)]]
 +
*[[Media:Oxphosmappkwvp20151212.mapp| MAPP ]]
 +
|<!--Kevin-->
 +
* Generated sanity check table.
 +
* Upload deliverables.
 +
*[[Media:BioDB_Final_Presentation_GEN_20151214.pdf| Final Presentation Slides (.pdf)]]
 +
*[[Media:Oxphosmappkwvp20151212.mapp| MAPP]]
 +
|}
 +
 
 +
==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.'''
 +
 
 +
<br>
 +
=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.  ''&mdash; [[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.
 +
<!-- #'''Sass, A., Marchbank, A., Tullis, E., LiPuma, J. J., & Mahenthiralingam, E. (2011) Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis. ''BMC genomics'', 12(1), 373. doi:10.1186/1471-2164-12-373'''
 +
#* Transcriptomic analysis was performed using the following strains, after exposure to different antibiotics in the presence of an antibiotic potentiator:
 +
#** Control: the wild-type J2315 strain
 +
#** Treatment: mutant strains which showed antibiotic resistance
 +
#** Treatment: ET12 outbreak isolates, described as "pan-resistant"
 +
#* Three biological replicates were used for each experiment.
 +
#* The raw data does not appear to be directly linked from the article itself. The supplement includes a summary spreadsheet, which only displays values for fold-changes that were statistically significant. However both the raw and processed data files are available on the [https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2747/files/ ArrayExpress entry].
 +
#* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/21781329
 +
#* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155924/
 +
#* Publisher Full Text (HTML): http://www.biomedcentral.com/1471-2164/12/373
 +
#* Publisher Full Text (PDF):  http://www.biomedcentral.com/content/pdf/1471-2164-12-373.pdf
 +
#* Copyright:  2011 Sass et al; licensee BioMed Central Ltd. "This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited."
 +
#* Publisher:  BioMedCentral, respected Open Access organization.
 +
#* Availability:  Article does not initially appear to be available in print, however, BioMedCentral's website mentions that "high quality, bound reprints" can be purchased for any published article.
 +
#* Did LMU pay a fee for this article: No - open access.
 +
#* This article cites 64 other articles.
 +
#* This article has been cited by 29 other articles (across all databases).
 +
#* The scientific community seems to be particularly interested in this organism's antimicrobial resistance, probably because this is a known pathogen, particularly relevant in the context of cystic fibrosis.
 +
# '''Mira, N. P., Madeira, A., Moreira, A. S., Coutinho, C. P., & Sá-Correia, I. (2011). Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to cystic fibrosis patients’ airways and antimicrobial therapy. PLoS One, 6(12), e28831.'''
 +
#* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genomic+Expression+Analysis+Reveals+Strategies+of+Burkholderia+cenocepacia+to+Adapt+to+Cystic+Fibrosis+Patients%27+Airways+and+Antimicrobial+Therapy
 +
#* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244429/
 +
#* 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.0028831
 +
#**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.0028831&representation=PDF
 +
#* Who owns the rights to the article? Authors of the article: Nuno P. Mira, Andreia Madeira, Ana Sílvia Moreira, Carla P. Coutinho, Isabel Sá-Correia
 +
#* 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-MTAB-809/?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 "treatments" strains were collected from a cystic fibrosis patient. The strain "IST439" was collected first, and the strain "IST4113" was collected 3 years later. The control for this experiment is reference data of Burkholderia cenocepacia.
 +
#* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? There were 3 replicates of each of the 2 strains and 6 replicates of the reference strain. It is unclear whether these are biological or technical replicates.
 +
#* How many articles does this article cite? This article has 75 cited references.
 +
#* How many articles cite this article? This article has been cited 22 times in All Databases, and 22 times 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 articles are related to Burkholderia's pathogenesis and antibiotic resistance.
 +
#'''Yoder-Himes, D. R., Konstantinidis, K. T., & Tiedje, J. M. (2010). Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS One, 5(1), e8724.'''
 +
#* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/20090946
 +
#* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806911/
 +
#* Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008724
 +
#* Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0008724&representation=PDF
 +
#* Copyright: '''© 2010 Yoder-Himes et al''' (information found on PDF version of article); the article is open-access and is distributed under a '''Creative Commons license'''
 +
#* Publisher: '''PLOS''' (Public Library of Science); nonprofit open-access publisher/advocate           
 +
#* Availability: '''online only'''
 +
#* Did LMU pay a fee for this article: '''No'''
 +
#* Data Found At: [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15817/ ArrayExpress]
 +
#* Experiment Information: The transcriptome of a clinical and a environmental strain of ''B. cenocepacia'' was analyzed under conditions mimicking soil versus conditions mimicking the sputum resulting from cystic fibrosis. Identification and observation related to putative virulence factors was conducted. "Treatment" conditions were those mimicking CF sputum and "Control" conditions were those mimicking soil.
 +
#* Replicate Information: Replicate experiments of the "treatment" and "control" were conducted (quadruplicates were employed using different cultures). These were biological replicates (total of 8 arrays, '''four biological replicates''').
 +
#* How many articles does this article cite: '''61'''
 +
#* How many articles cite this article: '''14'''
 +
#* The papers that cite this article appear to focus upon the aspects of the J2315 strain and other BCC bacteria that are related to virulence and host-pathogen interactions. A few articles also explored the role of certain genes which are related to the pathogenic character of the strain (which were possibly examined in the paper by Yoder-Himes et al).
 +
#'''Coenye, T., Van Acker, H., Peeters, E., Sass, A., Buroni, S., Riccardi, G., & Mahenthiralingam, E. (2011). Molecular Mechanisms of Chlorhexidine Tolerance in Burkholderia cenocepacia Biofilms. Antimicrobial Agents and Chemotherapy, 55(5), 1912–1919. http://doi.org/10.1128/AAC.01571-10'''
 +
#* State what you used as search terms and what type of search terms they were. '''Used the search bar in Array Express and used the terms Burkholderia cenocepacia J2315. I used the filters RNA assay and Array assay.'''
 +
#* How many results did you get? '''There were 18 experiments that resulted in the search.'''
 +
#* Give an assessment of how relevant the results were. '''A good chunk of the experiments we weren't going to look at because the assay numbers were smaller than 9 which was as low as we were going to test.'''
 +
#* The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/21357299?dopt=Abstract]
 +
#* 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/PMC3088199/]
 +
#* The link to the full text of the article (HTML format) from the publisher web site. [http://aac.asm.org/content/55/5/1912.full]
 +
#* The link to the full PDF version of the article from the publisher web site. [http://aac.asm.org/content/55/5/1912.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? '''Both online and in print.'''
 +
#* Has LMU paid a subscription or other fee for your access to this article? '''No'''
 +
#* How many articles does this article cite? '''It sites 36 other articles.'''
 +
#* How many articles cite this article? '''32 on Google Scholar and 22 on Web of Science'''
 +
#* 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?
 +
#* In addition, you must also link to the web site where the microarray data resides.[ https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2502/?keywords=Burkholderia+cenocepacia+J2315&organism=&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=]
 +
#* For each of the microarray articles/datasets, answer the following:
 +
#* What experiment was performed?  What was the "treatment" and what was the "control" in the experiment? '''B. cenocepacia J2315 cells were treated by exposure to high levels of H2O2, NaOCl or chlorhexidine. In addition differences in gene expression were examined between untreated B. cenocepacia sessile cells and B. cenocepacia planktonic cells.'''
 +
#*  Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each? '''There were 20 assays.Hybridizations for all experimental conditions were performed in 4 replicates.'''
 +
# '''Drevinek, P., Holden, M. T., Ge, Z., Jones, A. M., Ketchell, I., Gill, R. T., & Mahenthiralingam, E. (2008). Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepacia grows in cystic fibrosis sputum. BMC Infectious Diseases, 8, 121. http://doi.org/10.1186/1471-2334-8-121'''
 +
#* The link to the abstract from PubMed: [http://www.ncbi.nlm.nih.gov/pubmed/18801206?dopt=Abstract&holding=f1000,f1000m,isrctn]
 +
#* The link to the full text of the article in PubMedCentral: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559838/]
 +
#* The link to the full text of the article (HTML format) from the publisher web site: [http://www.biomedcentral.com/1471-2334/8/121]
 +
#* The link to the full PDF version of the article from the publisher web site: [http://www.biomedcentral.com/content/pdf/1471-2334-8-121.pdf]
 +
#* Who owns the rights to the article? Authors of the article: '''Copyright © 2008 Drevinek et al; licensee BioMed Central Ltd.'''
 +
#* Does the journal own the copyright? '''No'''
 +
#* Do the authors own the copyright? '''Yes'''
 +
#* 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? '''BMC Infectious Diseases is an open access, peer-reviewed journal'''
 +
#* 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-1261/?keywords=+Burkholderia+cenocepacia+J2315&organism=&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 genome of Burkholderia cenocepacia J2315 and transcriptomics used to identify genes that were differentially regulated when the pathogen was grown in a CF sputum-based infection model. Sputum samples from CF individuals infected with the same B. cenocepacia strain as genome isolate were used, hence, other than a dilution into a minimal growth medium (used as the control condition), no further treatment of the sputum was carried out.'''
 +
#* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? '''A replicate self-hybridization control experiment was performed. There were 8 essays and 4 biological replicates.'''
 +
#* How many articles does this article cite? '''50 references cited.'''
 +
#* How many articles cite this article? '''52 in Google Scholar and 44 in Web of Science.'''
 +
#* 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? '''It has been working on antibiotic resistance in cystic fibrosis patients and how the bacteria had evolves and reacts to different extreme treatments.''' -->
 +
 
 +
 
 +
<br>

Latest revision as of 07:32, 15 December 2015

Genialomics-banner.jpg


Weekly Group Assignments Shared Group Journals Project Links Team Members


Week 10


Week 11

Individual Goals and Progress

Weekly Goals and Progress
Anu Varshneya Brandon Litvak Veronica Pacheco Kevin Wyllie
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
Progress
  • Found a possible 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: Genome Presentation
  • Found a possible model organism database.
    • The more recent 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
Individual Journal Pages

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

Journal Club Presentations

Genome Paper Presentation Week 11
Microarray Paper Presentation Week 12

Week 12

Individual Goals and Progress

Weekly Goals and Progress
Anu Varshneya Brandon Litvak Veronica Pacheco Kevin Wyllie
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).
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).
Individual Journal Pages
Files Used/Created

Media:Raw_compiled_data_KW20151119.xlsx

Media:Raw_compiled_data_KW20151119.xlsx

Other Progress

Week 14

Individual Goals and Progress

Weekly Goals and Progress
Anu Varshneya Brandon Litvak Veronica Pacheco Kevin Wyllie
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.

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
Individual Journal Pages
Files Used/Created

Build 2 - with customized species profile:

Anuvarsh (talk) 15:22, 1 December 2015 (PST)

Build 3 - picking up gene names from ORF instead of ordered locus

Anuvarsh (talk) 14:58, 3 December 2015 (PST)

Build 4 - customized TallyEngine

Anuvarsh (talk) 15:18, 3 December 2015 (PST)

see Kevin's section -->

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

  1. What worked?
    • Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
  2. 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.
  3. 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

  1. 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.
  2. 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.
  3. 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

  1. 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.
  2. 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).
  3. 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

Weekly Goals and Progress
Anu Varshneya Brandon Litvak Veronica Pacheco Kevin Wyllie
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.
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)
  • Finalized readme
  • Helped in finalizing the slides
  • Practiced presentation
  • 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.
Individual Journal Pages
Files Used/Created

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 PubMed. [1]
  • The link to the full text of the article in PubMedCentral. [2]
  • The link to the full text of the article (HTML format) from the publisher web site. [3]
  • The link to the full PDF version of the article from the publisher web site. [4]
  • 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 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 Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (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. — 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.



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