Revision as of 02:52, 24 November 2015

Team Information & Links

GenMAPP Analysis of Bordetella pertussis Microarray Data

Journal Entries

Group Members

• Project Manager & Coder: Brandon Klein
• Quality Assurance: Mahrad Saeedi
• GenMAPP User: Lena Olufson
• Team Page

Team Weekly Assignments

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

Weekly Updates

Week 12

Goals

• Assignment due date: Midnight Tuesday, November 24
• Coder: Set up a GitHub repository clone of the XMLPipeDB project on your development device, the development rig, and the initial as-is build for gmbuilder. Complete an import-export cycle in association with QA.
• Quality Assurance: Complete an import-export cycle for the 1st Bordetella pertussis gene database. Complete a Gene Database Testing Report for this export.
• GenMAPP Users: 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

• Brandon (Quality Assurance and Interim Coder): This week, I focused on completing an import-export cycle for our first Bordetella pertussis gene database- File:Bpertussis-std cw20151119.zip. With my QA hat, I imported the appropriate data, exported the gene database, and discussed the gene database creation & counting protocol here- Gene Database Testing Report- cw20151119. With my Coder hat, I followed the instructions on the Coder Guild Page to setup a GitHub repository clone of the XMLPipdeDB project on my personal laptop, the Eclipse developer rig, and the initial as-is build for gmbuilder. The electronic lab notebook for my QA and Coder work is present on my Week 12 Page. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my Week 12 Page as well.
  • Bklein7 (talk) 18:48, 23 November 2015 (PST)
• Lena (GenMAPP): I worked on downloading the correct data sample files from the provided files on the microarray paper page. The files were unzipped and prepared to be imported into excel. In excel, the data was manipulated to form a spreadsheet that had all of the gene IDs from the different samples with their appropriate columns to be analyzed. The corrections and further manipulations of the data are to be continued to be done in the coming week in order to create the desired dataset to be exported from excel.

Lenaolufson (talk) 17:33, 23 November 2015 (PST)

• Mahrad (GenMAPP):
• Nicole was absent this week as well. Bklein7 (talk) 18:52, 23 November 2015 (PST)

Meetings!

• Monday, November 23: Seaver 120- Brandon and Lena met to work on the GenMAPP testing of the gene IDs from our database.

Week 11

Goals

• For all:
  • Outline your assigned paper on your user page and include a list of 10 defined terms from the paper.
• Nicole & Brandon
  • Prepare Journal Club presentation on the designated genome sequencing article
  • Slides Due: by midnight, Tuesday, November 17
  • Presentation Date: Tuesday, November 24
• Lena & Mahrad
  • Prepare Journal Club presentation on the designated microarray paper
  • Slides Due: by midnight, Tuesday, November 17
  • Presentation Date: Tuesday, November 17

Progress

• Nicole Anguiano (Coder): Nicole was absent this week for a medical emergency and is (hopefully) getting some much deserved rest. Bklein7 (talk) 23:14, 16 November 2015 (PST)
• Brandon Klein (QA): This week I made several edits to the Class Whoopers Team Page in accordance with the Week 11 assignment. These edits included the following: revising the Class Whoopers template, reorganizing the Team Page structure, commenting out unneeded articles in the annotated bibliography, creating the new bibliography entry as requested by Dr. Dahlquist, and writing the naming conventions for our files. Additionally, I outlined our genome sequencing paper for "Bordetella pertussis" and assessed the GeneDB MOD on my Week 11 Individual Journal Entry. A preliminary draft of the genome sequencing paper that I will likely be presenting solo was uploaded there. Finally, I kept tabs on group members as the interim Project Manager. Bklein7 (talk) 23:14, 16 November 2015 (PST)
• Lena Olufson (GennMAPP): This week Mahrad and I met up and analyzed the microarray paper together. We split up the powerpoint into two halves; I did the introduction/significance of the study as well as the methods performed. Mahrad and I created our presentation together and worked through a google doc to edit it simultaneously as we discussed out loud. We also created a flow chart together that demonstrated the experimental design, thus we have the same ones included in our individual assignments. We made sure to check in with the temporary project manager and keep him updated on our progress. Lenaolufson (talk) 23:24, 16 November 2015 (PST)
• Mahrad Saeedi (GennMAPP): This week Lena and I worked on analyzing the microarray paper and creating an outline. We each defined 10 terms separately based upon words we didn't recognize in the article. We then proceeded to producing the powerpoint presentation for journal club.

Msaeedi23 (talk) 23:46, 16 November 2015 (PST)

Meetings!

• 11/15- Lena & Mahrad met to work on outlining article and answering questions
• 11/16- Lena & Mahrad met to prepare powerpoint presentation for journal club

Week 10

Goals

• For all:
  • Create an annotated bibliography including one genome sequencing paper and two microarray experiments for Bordetella pertussis
  • Create/update team page & compile group annotated bibliography
  • Assignment due date: Midnight Tuesday, November 10

Progress

• All group members created annotated bibliographies and compiled them on the newly created group page.

Meetings!

• Monday, November 9, 8pm-9pm, Seaver 120

Deliverables

File Naming Protocol

All file types generated in this project will receive their own unique names composed of two key parts:

1. Description
   • This will contain a brief, file-specific description of what content the file contains.
   • Descriptions for different versions of the same file will remain consistent.
2. Identifier Tag
   • This tag will be listed as a suffix in the following form: "_cwYYYYMMDD"
     • cw- team name abbreviation
     • YYYYMMDD- date the file was created in the form year/month/day

Additionally, the following file naming best practices will be observed when creating descriptions for new files:

• Our species will be referred to consistently as "bpertussis".
• Files including microarray data taken from the paper by Hoo et al. (2014) will begin with "hoo".
• Spaces will be written as underscores.
• No capitalization will be used.
• No special characters will be used.
• If sequential numbering systems are used, leading zeros will be included for clarity.

Sample .xls file name: hoo_analyzed_data_cw20151122.xls

Files

• GenMAPP Gene Database for assigned species (.gdb): bpertussis-std_cwYYYYMMDD.gdb
• ReadMe file to accompany the Gene Database (.pdf): readme_bpertussis-std_external_cwYYYYMMDD.pdf
• Include Gene Database Schema diagram in ReadMe: bpertussis_schema_cwYYYYMMDD.pdf
• Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file): bpertussis_gdb_report_cwYYYYMMDD.pdf
• Processed and analyzed DNA microarray dataset (.xls): hoo_analyzed_data_cwYYYYMMDD.xls
• GenMAPP Expression Dataset file (.gex): hoo_expression_dataset_cwYYYYMMDD.gex
• Filtered MAPPFinder Results (.xls): hoo_mappfinder_results_cwYYYYMMDD.xls
• Sample MAPP file of a relevant biological pathway for your species (.mapp): hoo_sample_mapp_cwYYYYMMDD.mapp
• Group Report describing the creation of the Gene Database and the biological analysis of the data (.doc or .pdf): bpertussis_analysis_methods_cwYYYYMMDD.pdf
• PowerPoint presentation (.ppt, given on Tuesday, December 15): bpertussis_analysis_presentation_cwYYYYMMDD.ppt

Microarray Journal Club Presentation

• File:Microarray Journal Club Presentation.pdf

Annotated Bibliography

Genome Sequencing Paper

Neither of these papers is the first to report the genome sequence of B. pertussis. The paper that you will want to use is this one. I found it by looking at the introduction and references of the Zhang et. al (2011) paper. For your Week 11 assignment, please remove your annotated bibliography entries for the two papers below and create one for this new paper by Parkhill et al. (2003). You will use the Parkhill paper for your project. — Kdahlquist (talk) 09:54, 10 November 2015 (PST)

• Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., et al. (2003). Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nature genetics, 35(1), 32-40. doi:10.1038/ng1227
• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/12910271
• PubMed Central: Not available on PubMed Central.
• Publisher Full Text (HTML): http://www.nature.com/ng/journal/v35/n1/full/ng1227.html
• Publisher Full Text (PDF): http://www.nature.com/ng/journal/v35/n1/pdf/ng1227.pdf
• Copyright: ©2003 Nature Publishing Group (information found on PDF version of article). This article is not Open Access, but it is freely available 6 months after publication.
• Publisher: Nature Publishing Group (for-profit).
• Availability: In print and online.
• Did LMU pay a fee for this article: Yes, LMU pays a subscription fee for access to the journal Nature Genetics.

Microarray Paper

This paper is suitable for your project. — Kdahlquist (talk) 10:04, 10 November 2015 (PST)

Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE, 9(12):e115243. doi: 10.1371/journal.pone.0115243

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25501560
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264864/
• Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243
• Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0115243&representation=PDF
• Copyright: © 2014 Hoo et al. 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 author and source are credited (info found here).
• Publisher: PLOS ONE (respected open access organization).
• Availability: Online only.
• Did LMU pay a fee for this article: No.
• Web site where the data resides: NCBI GEO data