LMU BioDB 2015 - User contributions [en]

Msaeedi23 Week 15

2015-12-21T07:10:44Z

Msaeedi23: /* Gene Database Testing Report */

==TallyEngine Customization (cw20151203)==
In GenMAPP Builder version 3.0.0 Build 5 - cw20151203, the ''Bordetella pertussis'' species profile was customized to import 11 ORF gene IDs that were not exported in previous versions. To account for this change, the TallyEngine was customized for ''Bordetella pertussis'' to count "ORF" gene listings separately from "Ordered Locus Names". To do this, I followed the procedure documented below:

* First, it was determined that we wanted to count the "ordered locus" IDs and "ORF" IDs from the ''gene/name'' tag in the UniProt XML file.
** In the relational database ''bpertussis_cw20151203_gmb3build5'', gene IDs were defined by the type "ordered locus" or "ORF" in the table "genenametype".
* Next, Brandon opened our team's branch of GenMAPP Builder in Eclipse.
* Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', he opened ''gmbuilder.properties''.
* I located the block of text below (it was near the bottom).
#
# wizard.properties
#
* Brandon added the necessary customizations above this block of text. The resulting code was as follows:
# Bordetella pertussis
bordetellapertussis_level_amount=1

bordetellapertussis_element_level0=uniprot/entry/gene/name&type&ORF

bordetellapertussis_query_level0=select count(*) from genenametype where type = 'ORF';

bordetellapertussis_table_name_level0=ORF

#
# wizard.properties
#
* Brandon then committed and pushed the changes in the code to Github and created a new distribution of GenMAPP Builder.
* Using the updated build of GenMAPP Builder present in the distribution folder, the relational database was connected ''bpertussis_cw20151203_gmb3build5'' and TallyEngine was run. The results are pictured below:
**[[File: Tallyenginecustomization_cw20151203.png]]
***The TallyEngine results successfully reflected the customizations we made to the TallyEngine, listing all 11 ORF genes in addition to the 3435 "Ordered Locus Names" gene IDs present in the ''Bordetella pertussis'' gene database.

==Testing the Bordetella Pertussis Gene Database (cw20151203)==
The full Gene Database Testing Report for the .gdb file tagged cw20151203 can be found here: [[Gene Database Testing Report- cw20151203]]. In assessing this gene database with [[User:Bklein7 | Brandon]], we found one gene ID that was not successfully exported into the .gdb file. A summary of this issue and the steps that were taken to detail it is presented below:

*TallyEngine Count
**As described in the "TallyEngine Customization (cw20151203)" section of this page, the expected gene ID count including "Ordered Locus Names" and "ORF" listings was 3446.
**This count was confirmed using the customized TallyEngine.
*XMLPipeDB Match Count
**With the help of [[User:Dondi|Dr. Dionisio]], a new regex was crafted to retrieve all possible "ordered locus" and "ORF" gene ID patterns that we identified. The XMLPipeDB Match query and result are pictured below:
***[[File:Xmlpipedbmatch cw20151203.png]]
****To our surprise, XMLPipeDB Match returned a result of 3447 gene IDs that matched our updated regex.
****Thus, this revealed that one ID matching our regex was not successfully epxorted to the cw20151203 .gdb file. Further investigation was necessary.
*XMLPipeDB Match vs. "Ordered Locus Names" from [[File:Bpertussis-std cw20151203.zip]]
**In order to identify the missing gene ID, we compared the XMLPipeDB Match output to the gene IDs listed in the "Ordered Locus Names" table of the file [[File:Bpertussis-std cw20151203.zip]] (retrieved using Microsoft Access).
** In Excel, the missing gene ID was identified to be ''BP3167A'':
***[[File:Xmlpipedbmatch vs gdb cw20151203.PNG]]
****Interestingly, this gene ID had another unusual variant that we previously documented- BP3167.1.
****Although this gene ID's pattern (BP####A) matched that of the ORF values, it was not present in the list of ORF genes retrieved in PostgreSQL (see [[Bklein7_Week_14]]).
*Identifying "BP3167A" in the Original XML File
**Based on our TallyEngine and PostgreSQL results, it appeared as though the gene ID "BP3167A" was not listed under the type "ordered locus" or "ORF". To determine its gene type, we opened the original XML file ([[File:Uniprot-proteome-UP000002676 cw20151201.zip]]) and searched for "BP3167A":
***[[File:MissedID cw20151203.png]]
****In the XML file, "BP3167A" was listed with the general gene type "gene ID". This specific designation had not been observed as a stand alone gene type before.
****Nevertheless, the manner in which "BP3167A" was listed in the XML file indicated that it was in fact a proper gene ID and not an artifactual finding. This necessitated further research.
*Researching the Different Forms of "BP3167"
**UniProt
***Searching for "BP3167", "BP3167.1", or "BP3167A" all linked to the following gene page: http://www.uniprot.org/uniprot/Q7VUD4
****The above page specifies that the gene ID "BP3167.1" refers to the gene ureE that codes for Urease accessory protein UreE.
**EnsemblBacteria-
***Searching for "BP3167" and "BP3167A" retrieves two different results:
****[[http://bacteria.ensembl.org/Multi/Search/Results?species=all;idx=;q=bp3167;site=ensemblunit BP3167]]- gene ureF is a pseudogene.
****[[http://bacteria.ensembl.org/Multi/Search/Results?species=all;idx=;q=bp3167A;site=ensemblunit BP3167A]]- gene ureE, which codes for urease accessory protein (as in UniProt).
***Therefore, the gene ID "BP3167A" is a valid ID that corresponds to the same ID as "BP3167.1" in the UniProt database.
**Conclusion: "BP3167A" is a reference ID from EnsemblBacteria that is valid and must be exported.

==Gene Database Testing Report 12/10==
The Gene Database Testing Report for this new gene database can be found here: [[Gene Database Testing Report- cw20151210]].

{{template: msaeedi23}}

Msaeedi23 Week 15

2015-12-21T07:10:23Z

Msaeedi23:

==TallyEngine Customization (cw20151203)==
In GenMAPP Builder version 3.0.0 Build 5 - cw20151203, the ''Bordetella pertussis'' species profile was customized to import 11 ORF gene IDs that were not exported in previous versions. To account for this change, the TallyEngine was customized for ''Bordetella pertussis'' to count "ORF" gene listings separately from "Ordered Locus Names". To do this, I followed the procedure documented below:

* First, it was determined that we wanted to count the "ordered locus" IDs and "ORF" IDs from the ''gene/name'' tag in the UniProt XML file.
** In the relational database ''bpertussis_cw20151203_gmb3build5'', gene IDs were defined by the type "ordered locus" or "ORF" in the table "genenametype".
* Next, Brandon opened our team's branch of GenMAPP Builder in Eclipse.
* Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', he opened ''gmbuilder.properties''.
* I located the block of text below (it was near the bottom).
#
# wizard.properties
#
* Brandon added the necessary customizations above this block of text. The resulting code was as follows:
# Bordetella pertussis
bordetellapertussis_level_amount=1

bordetellapertussis_element_level0=uniprot/entry/gene/name&type&ORF

bordetellapertussis_query_level0=select count(*) from genenametype where type = 'ORF';

bordetellapertussis_table_name_level0=ORF

#
# wizard.properties
#
* Brandon then committed and pushed the changes in the code to Github and created a new distribution of GenMAPP Builder.
* Using the updated build of GenMAPP Builder present in the distribution folder, the relational database was connected ''bpertussis_cw20151203_gmb3build5'' and TallyEngine was run. The results are pictured below:
**[[File: Tallyenginecustomization_cw20151203.png]]
***The TallyEngine results successfully reflected the customizations we made to the TallyEngine, listing all 11 ORF genes in addition to the 3435 "Ordered Locus Names" gene IDs present in the ''Bordetella pertussis'' gene database.

==Testing the Bordetella Pertussis Gene Database (cw20151203)==
The full Gene Database Testing Report for the .gdb file tagged cw20151203 can be found here: [[Gene Database Testing Report- cw20151203]]. In assessing this gene database with [[User:Bklein7 | Brandon]], we found one gene ID that was not successfully exported into the .gdb file. A summary of this issue and the steps that were taken to detail it is presented below:

*TallyEngine Count
**As described in the "TallyEngine Customization (cw20151203)" section of this page, the expected gene ID count including "Ordered Locus Names" and "ORF" listings was 3446.
**This count was confirmed using the customized TallyEngine.
*XMLPipeDB Match Count
**With the help of [[User:Dondi|Dr. Dionisio]], a new regex was crafted to retrieve all possible "ordered locus" and "ORF" gene ID patterns that we identified. The XMLPipeDB Match query and result are pictured below:
***[[File:Xmlpipedbmatch cw20151203.png]]
****To our surprise, XMLPipeDB Match returned a result of 3447 gene IDs that matched our updated regex.
****Thus, this revealed that one ID matching our regex was not successfully epxorted to the cw20151203 .gdb file. Further investigation was necessary.
*XMLPipeDB Match vs. "Ordered Locus Names" from [[File:Bpertussis-std cw20151203.zip]]
**In order to identify the missing gene ID, we compared the XMLPipeDB Match output to the gene IDs listed in the "Ordered Locus Names" table of the file [[File:Bpertussis-std cw20151203.zip]] (retrieved using Microsoft Access).
** In Excel, the missing gene ID was identified to be ''BP3167A'':
***[[File:Xmlpipedbmatch vs gdb cw20151203.PNG]]
****Interestingly, this gene ID had another unusual variant that we previously documented- BP3167.1.
****Although this gene ID's pattern (BP####A) matched that of the ORF values, it was not present in the list of ORF genes retrieved in PostgreSQL (see [[Bklein7_Week_14]]).
*Identifying "BP3167A" in the Original XML File
**Based on our TallyEngine and PostgreSQL results, it appeared as though the gene ID "BP3167A" was not listed under the type "ordered locus" or "ORF". To determine its gene type, we opened the original XML file ([[File:Uniprot-proteome-UP000002676 cw20151201.zip]]) and searched for "BP3167A":
***[[File:MissedID cw20151203.png]]
****In the XML file, "BP3167A" was listed with the general gene type "gene ID". This specific designation had not been observed as a stand alone gene type before.
****Nevertheless, the manner in which "BP3167A" was listed in the XML file indicated that it was in fact a proper gene ID and not an artifactual finding. This necessitated further research.
*Researching the Different Forms of "BP3167"
**UniProt
***Searching for "BP3167", "BP3167.1", or "BP3167A" all linked to the following gene page: http://www.uniprot.org/uniprot/Q7VUD4
****The above page specifies that the gene ID "BP3167.1" refers to the gene ureE that codes for Urease accessory protein UreE.
**EnsemblBacteria-
***Searching for "BP3167" and "BP3167A" retrieves two different results:
****[[http://bacteria.ensembl.org/Multi/Search/Results?species=all;idx=;q=bp3167;site=ensemblunit BP3167]]- gene ureF is a pseudogene.
****[[http://bacteria.ensembl.org/Multi/Search/Results?species=all;idx=;q=bp3167A;site=ensemblunit BP3167A]]- gene ureE, which codes for urease accessory protein (as in UniProt).
***Therefore, the gene ID "BP3167A" is a valid ID that corresponds to the same ID as "BP3167.1" in the UniProt database.
**Conclusion: "BP3167A" is a reference ID from EnsemblBacteria that is valid and must be exported.

==Gene Database Testing Report==
The Gene Database Testing Report for this new gene database can be found here: [[Gene Database Testing Report- cw20151210]].

{{template: msaeedi23}}

The Class Whoopers

2015-12-21T07:08:05Z

Msaeedi23: /* Week 14 */

= Team Information & Links =

{{Template:Class Whoopers}}

= Deliverables =
[[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==Presentation Download Links==
*Journal Club
** Genome Paper: [[File:Genomepaper_cw20151116.pdf]]
** Microarray Paper: [[File: Microarray_Journal_Club_Presentation.pdf]]
*'''Final Project'''
**[[File:Bpertussis_findings_powerpoint.pdf]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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".
*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.

=Weekly Updates=
==Week 15==
*'''Goals'''
**'''Assignment due date:''' Midnight Tuesday, December 15
** '''Coder:''' Adjust the GenMAPP Builder code to account for the one EnsemblBacteria reference ID that was missing in our last export; conduct a new import-export cycle to create the (hopefully) final .gdb file; begin characterizing the exported .gdb file in a Gene Database Testing Report; customize the GenMAPP Builder TallyEngine to account for any changes made.
**'''Quality Assurance:''' Reconfigure TallyEngine Configuration with Coder in order to accommodate missing gene IDs that were not exported the previous time. Test the revised database by running TallyEngine count, XmlpipeDB Match, and PostgreSQL. Locate missing gene IDs if any.
**'''GenMAPP User:''' 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. Create a .mapp file showing one pathway that is changed in your data.

*'''Progress'''
**'''Brandon (Coder and Project Manager):''' I began this week by customizing the GenMAPP Builder TallyEngine to report ORF counts for ''Bordetella pertussis'' (see [[Bklein7_Week_15]]). After this, I worked with [[User:Msaeedi23|Mahrad]] to identify the 1 gene ID that was missing in the .gdb file [[File:bpertussis-std_cw20151203.zip]]. I found that this gene was a necessary EnsemblBacteria reference ID and edited the GenMAPP Builder code with the help of [[User:Dondi|Dr. Dionisio]] to include this ID in our next export (see [[Bklein7_Week_15]]). I conducted a complete import-export cycle on 12/10/2015 to create the .gdb file [[File:bpertussis-std_cw20151210.zip]]. I then characterized this export, authoring sections 1-5.2 of its testing report: [[Gene_Database_Testing_Report-_cw20151210]]. During our Sunday meeting, I worked with [[User:Lenaolufson|Lena]] to use this new gene database in GenMAPP. During our Monday meeting, I worked on our PowerPoint presentation: [[File:Bpertussis findings powerpoint.pdf]].
*** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 22:31, 14 December 2015 (PST)
**'''Mahrad (Quality Assurance):''' I worked closely with the coder [[User: Bklein7|Brandon]] in order to re-customize TallyEngine to include the 11 missing ORF genes. The specific customizations and following results are detailed in my [[Msaeedi23 Week 15| Week 15 Journal Entry]] Having located the missing gene IDs, Brandon went into Eclipse to code for them to be included in the export. Following this, we tested out revised gene database to make sure these missing IDs were actually exported. We ran TallyEngine count, which gave a total of 3446 gene IDs, demonstrating that the IDs were now exported. Then we ran XMLpipeDB Match, and this provided a total of 3447 gene IDs exported, one additional. Finally, we ran PostgreSQL and this gave a total of 3446 gene IDs. We came to find that gene "BP3167A" was in the original XML file, but not accounted for in the exported file. With further investigation we concluded that "BP3167A" is a reference ID from EnsemblBacteria and corresponds to the same ID as "BP3167.1" which was exported.
**'''Lena (GenMAPP User):''' I was able to import the data into GenMAPP and then I created color sets in order to run MAPPFinder. I obtained the ontology results and did some background research on what exactly the top results related to from the microarray article. I then used Kegg pathways for my specific organism to create two separate MAPPS, one for ribosome and one for the nitrogen cycle.

*'''Meetings!'''
**This week, our group used class work sessions to coordinate our work:
***Tuesday, December 8, 2:40 - 4:00
***Thursday, December 10, 2:40 - 4:00
**In addition, we scheduled meetings outside of class to work on the final PowerPoint Presentation and deliverables for our project:
***Sunday, December 13, 7:00 PM - 1:00 AM
***Monday, December 14, 2:00 PM - 11:00 PM

==Week 14==

*'''Goals'''
**'''Assignment due date:''' Midnight Tuesday, December 8
**'''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
**'''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
**'''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

*'''Progress'''
**'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
*** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
**'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 Week 14| Week 14 Journal Entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing. Week 14 reflection:
# What worked?
#*We were able to use the various counting systems to detect the total number of gene IDs that were imported into our gdb file. Through our investigation, Brandon and I came to find four specific missing IDs.
# What didn't work?
#*There were four ID inconsistencies detected to be missing in our gdb file. We were able to target the specific IDs that were missing and now the code will have to be changed to incorporate these missing IDs in our database.
# What will I do next to fix what didn't work?
#*Work more closely with Brandon to ensure the Tally Engine is configured properly and that we can properly import and obtain confirmation that all the gene IDs were imported successfully.
**'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

*'''Meetings!'''
**This week, our group used class work sessions to coordinate our work:
***Tuesday, December 1, 2:40 - 4:00
***Thursday, December 3, 2:40 - 4:00
*** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
***[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
***[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
**'''Mahrad (GenMAPP--> Quality Assurance)''': This week I downloaded the six data sample files provided by the microarray paper. The process is detailed in my [[Msaeedi23 Week 12| Week 12 Journal Entry]]. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
** '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
**Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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. The outline and detailed process involved with the experiment can be found in my [[Msaeedi23 Week 11| Week 11 Journal Entry]]. 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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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

= 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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

Msaeedi23 Week 14

2015-12-21T06:56:05Z

Msaeedi23:

Link to completed gene database testing report for most recent created database 12/3: [[Gene Database Testing Report- cw20151203]]

==Bordetella Pertussis Species Profile Customization==

===ID inconsistencies===
To assess the need for further customization of the ''Bordetella pertussis'' species profile, I worked directly with our coder [[User:Bklein7|Brandon]] to compare the gene IDs present in the cw20151201 .gdb file ([[File:Bpertussis-std cw20151201.zip]]) and the original .xml file ([[File:Uniprot-proteome-UP000002676 cw20151201.zip]]). This was done by copying the "OrderedLocusNames" table from the .gdb file into a new Excel document alongside the list of ''Bordetella pertussis'' gene IDs in the original .xml file that was generated using xmlpipedb match. Further details can be found in [[Msaeedi23 Week 14| Mahrad's Week 14 Journal Entry]]. Overall, we found 4 discrepant IDs.
Together we went through and processed each individual gene which had an apparent discrepancy from the original dataset to the exported one.

#'''BP3167.1'''- existed in the .gdb file but not in the the xmlpipedb match result
#*Additionally, we found that the expected variant of this ID, BP3167, existed in the xmlpipedb match result but not in the .gdb file.
#*We hypothesized that the ID existed as BP3167.1 in the original .xml file but was retrieved incompletely in the xmlpipedb match result due to the use of an imprecise regex (BP####).
#**To test this hypothesis, we conducted a new xmlpipedb match query using the updated regex BP####.1:
#**[[File: Bp3167issue_cw20151119.png]]
#***This test confirmed our hypothesis, demonstrating that BP3167.1 is the complete gene ID. Additionally, no other gene IDs in the .xml file exhibited this pattern.
#'''BP0101'''- did not get exported into the .gdb file
#*To investigate why this gene was not exported, we looked up this ID in the original .xml file.
#**We found that the gene ID was actually listed as both BP0101A and BP0101B, which was not retrieved in the xmlpipedb match result due to the use of an imprecise regex (BP####).
#**The gene IDs BP0101A and BP0101B were both listed as open reading frame (ORF) genes in the .xml file as opposed to ordered locus names. This presented a new category of gene IDs that the custom ''Bordetella pertussis'' species profile was not designed to export.
#*ORF investigation
#**To see if there were other ORF genes with the pattern BP####A or BP####B, we ran a query to retrieve such IDs from the original PostgreSQL database: ''bpertussis_cw20151119_gmb3build5''.
#***[[File: ORFissue_cw20151119.png]]
#****This query retrieved a list of 11 ORF genes. Seven of these genes exhibited numerical sequences (####) that were cross-listed as ordered locus names, whereas four of the genes exhibited unique numerical sequences that were only listed as ORF genes. Therefore, only four of the ORF IDs should been discrepant during our comparative analysis between .gdb and .xml IDs. Of these four, two were BP0101A and BP0101B.
#**To evaluate the total number of genes that should be exported into the .gdb file, including both genes listed under the ordered locus names and ORF tables, we queried the original PostgreSQL database once more:
#***[[File: Oln-orfcounts_cw20151119.png]]
#****This demonstrates that 3446 unique genes exist in the original .xml file, all of which need to be exported into our .gdb file. The number 3446 comes from 3435 ordered locus names listings and 11 ORF listings.
#'''BP0970'''- did not get exported into the .gdb file
#*This was the third ORF gene with a unique numerical sequence. The gene was listed as BP0970A in the original .xml file.
#'''BP0684'''- did not get exported into the .gdb file
#*This was the third ORF gene with a unique numerical sequence. The gene was listed as BP0684A in the original .xml file.

'''Conclusion:''' The custom ''Bordetella pertussis'' species profile in GenMAPP Builder needs to be customized to export the 11 ORF genes. The gene BP3167.1 was already being exported and, therefore, does not warrant coding changes. Instead, this unique pattern should be incorporated into the regex used to count ''Bordetella pertussis'' gene IDs when running future gene database testing reports.

===Changes to the Code===
To make changes to the GenMAPP Builder code, Brandon opened the ''gmbuilder'' project within the ''Java perspective'' using the program ''Eclipse''. The details regarding the developer rig, used can be found on Brandon's page. [[Bklein7 Week 12| Week 12 Assignment Page]].

{{template: msaeedi23}}

The Class Whoopers

2015-12-21T06:49:00Z

Msaeedi23: /* Week 15 */

= Team Information & Links =

{{Template:Class Whoopers}}

= Deliverables =
[[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==Presentation Download Links==
*Journal Club
** Genome Paper: [[File:Genomepaper_cw20151116.pdf]]
** Microarray Paper: [[File: Microarray_Journal_Club_Presentation.pdf]]
*'''Final Project'''
**[[File:Bpertussis_findings_powerpoint.pdf]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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".
*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.

=Weekly Updates=
==Week 15==
*'''Goals'''
**'''Assignment due date:''' Midnight Tuesday, December 15
** '''Coder:''' Adjust the GenMAPP Builder code to account for the one EnsemblBacteria reference ID that was missing in our last export; conduct a new import-export cycle to create the (hopefully) final .gdb file; begin characterizing the exported .gdb file in a Gene Database Testing Report; customize the GenMAPP Builder TallyEngine to account for any changes made.
**'''Quality Assurance:''' Reconfigure TallyEngine Configuration with Coder in order to accommodate missing gene IDs that were not exported the previous time. Test the revised database by running TallyEngine count, XmlpipeDB Match, and PostgreSQL. Locate missing gene IDs if any.
**'''GenMAPP User:''' 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. Create a .mapp file showing one pathway that is changed in your data.

*'''Progress'''
**'''Brandon (Coder and Project Manager):''' I began this week by customizing the GenMAPP Builder TallyEngine to report ORF counts for ''Bordetella pertussis'' (see [[Bklein7_Week_15]]). After this, I worked with [[User:Msaeedi23|Mahrad]] to identify the 1 gene ID that was missing in the .gdb file [[File:bpertussis-std_cw20151203.zip]]. I found that this gene was a necessary EnsemblBacteria reference ID and edited the GenMAPP Builder code with the help of [[User:Dondi|Dr. Dionisio]] to include this ID in our next export (see [[Bklein7_Week_15]]). I conducted a complete import-export cycle on 12/10/2015 to create the .gdb file [[File:bpertussis-std_cw20151210.zip]]. I then characterized this export, authoring sections 1-5.2 of its testing report: [[Gene_Database_Testing_Report-_cw20151210]]. During our Sunday meeting, I worked with [[User:Lenaolufson|Lena]] to use this new gene database in GenMAPP. During our Monday meeting, I worked on our PowerPoint presentation: [[File:Bpertussis findings powerpoint.pdf]].
*** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 22:31, 14 December 2015 (PST)
**'''Mahrad (Quality Assurance):''' I worked closely with the coder [[User: Bklein7|Brandon]] in order to re-customize TallyEngine to include the 11 missing ORF genes. The specific customizations and following results are detailed in my [[Msaeedi23 Week 15| Week 15 Journal Entry]] Having located the missing gene IDs, Brandon went into Eclipse to code for them to be included in the export. Following this, we tested out revised gene database to make sure these missing IDs were actually exported. We ran TallyEngine count, which gave a total of 3446 gene IDs, demonstrating that the IDs were now exported. Then we ran XMLpipeDB Match, and this provided a total of 3447 gene IDs exported, one additional. Finally, we ran PostgreSQL and this gave a total of 3446 gene IDs. We came to find that gene "BP3167A" was in the original XML file, but not accounted for in the exported file. With further investigation we concluded that "BP3167A" is a reference ID from EnsemblBacteria and corresponds to the same ID as "BP3167.1" which was exported.
**'''Lena (GenMAPP User):''' I was able to import the data into GenMAPP and then I created color sets in order to run MAPPFinder. I obtained the ontology results and did some background research on what exactly the top results related to from the microarray article. I then used Kegg pathways for my specific organism to create two separate MAPPS, one for ribosome and one for the nitrogen cycle.

*'''Meetings!'''
**This week, our group used class work sessions to coordinate our work:
***Tuesday, December 8, 2:40 - 4:00
***Thursday, December 10, 2:40 - 4:00
**In addition, we scheduled meetings outside of class to work on the final PowerPoint Presentation and deliverables for our project:
***Sunday, December 13, 7:00 PM - 1:00 AM
***Monday, December 14, 2:00 PM - 11:00 PM

==Week 14==

*'''Goals'''
**'''Assignment due date:''' Midnight Tuesday, December 8
**'''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
**'''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
**'''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

*'''Progress'''
**'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
*** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
**'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 Week 14| Week 14 Journal Entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
**'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

*'''Meetings!'''
**This week, our group used class work sessions to coordinate our work:
***Tuesday, December 1, 2:40 - 4:00
***Thursday, December 3, 2:40 - 4:00
*** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
***[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
***[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
**'''Mahrad (GenMAPP--> Quality Assurance)''': This week I downloaded the six data sample files provided by the microarray paper. The process is detailed in my [[Msaeedi23 Week 12| Week 12 Journal Entry]]. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
** '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
**Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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. The outline and detailed process involved with the experiment can be found in my [[Msaeedi23 Week 11| Week 11 Journal Entry]]. 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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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

= 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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-21T06:47:33Z

Msaeedi23: /* Week 12 */

= Team Information & Links =

{{Template:Class Whoopers}}

= Deliverables =
[[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==Presentation Download Links==
*Journal Club
** Genome Paper: [[File:Genomepaper_cw20151116.pdf]]
** Microarray Paper: [[File: Microarray_Journal_Club_Presentation.pdf]]
*'''Final Project'''
**[[File:Bpertussis_findings_powerpoint.pdf]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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".
*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.

=Weekly Updates=
==Week 15==
*'''Goals'''
**'''Assignment due date:''' Midnight Tuesday, December 15
** '''Coder:''' Adjust the GenMAPP Builder code to account for the one EnsemblBacteria reference ID that was missing in our last export; conduct a new import-export cycle to create the (hopefully) final .gdb file; begin characterizing the exported .gdb file in a Gene Database Testing Report; customize the GenMAPP Builder TallyEngine to account for any changes made.
**'''Quality Assurance:''' Reconfigure TallyEngine Configuration with Coder in order to accommodate missing gene IDs that were not exported the previous time. Test the revised database by running TallyEngine count, XmlpipeDB Match, and PostgreSQL. Locate missing gene IDs if any.
**'''GenMAPP User:''' 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. Create a .mapp file showing one pathway that is changed in your data.

*'''Progress'''
**'''Brandon (Coder and Project Manager):''' I began this week by customizing the GenMAPP Builder TallyEngine to report ORF counts for ''Bordetella pertussis'' (see [[Bklein7_Week_15]]). After this, I worked with [[User:Msaeedi23|Mahrad]] to identify the 1 gene ID that was missing in the .gdb file [[File:bpertussis-std_cw20151203.zip]]. I found that this gene was a necessary EnsemblBacteria reference ID and edited the GenMAPP Builder code with the help of [[User:Dondi|Dr. Dionisio]] to include this ID in our next export (see [[Bklein7_Week_15]]). I conducted a complete import-export cycle on 12/10/2015 to create the .gdb file [[File:bpertussis-std_cw20151210.zip]]. I then characterized this export, authoring sections 1-5.2 of its testing report: [[Gene_Database_Testing_Report-_cw20151210]]. During our Sunday meeting, I worked with [[User:Lenaolufson|Lena]] to use this new gene database in GenMAPP. During our Monday meeting, I worked on our PowerPoint presentation: [[File:Bpertussis findings powerpoint.pdf]].
*** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 22:31, 14 December 2015 (PST)
**'''Mahrad (Quality Assurance):''' I worked closely with the coder [[User: Bklein7|Brandon]] in order to re-customize TallyEngine to include the 11 missing ORF genes. Having located the missing gene IDs, Brandon went into Eclipse to code for them to be included in the export. Following this, we tested out revised gene database to make sure these missing IDs were actually exported. We ran TallyEngine count, which gave a total of 3446 gene IDs, demonstrating that the IDs were now exported. Then we ran XMLpipeDB Match, and this provided a total of 3447 gene IDs exported, one additional. Finally, we ran PostgreSQL and this gave a total of 3446 gene IDs. We came to find that gene "BP3167A" was in the original XML file, but not accounted for in the exported file. With further investigation we concluded that "BP3167A" is a reference ID from EnsemblBacteria and corresponds to the same ID as "BP3167.1" which was exported.
**'''Lena (GenMAPP User):''' I was able to import the data into GenMAPP and then I created color sets in order to run MAPPFinder. I obtained the ontology results and did some background research on what exactly the top results related to from the microarray article. I then used Kegg pathways for my specific organism to create two separate MAPPS, one for ribosome and one for the nitrogen cycle.

*'''Meetings!'''
**This week, our group used class work sessions to coordinate our work:
***Tuesday, December 8, 2:40 - 4:00
***Thursday, December 10, 2:40 - 4:00
**In addition, we scheduled meetings outside of class to work on the final PowerPoint Presentation and deliverables for our project:
***Sunday, December 13, 7:00 PM - 1:00 AM
***Monday, December 14, 2:00 PM - 11:00 PM

==Week 14==

*'''Goals'''
**'''Assignment due date:''' Midnight Tuesday, December 8
**'''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
**'''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
**'''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

*'''Progress'''
**'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
*** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
**'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 Week 14| Week 14 Journal Entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
**'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

*'''Meetings!'''
**This week, our group used class work sessions to coordinate our work:
***Tuesday, December 1, 2:40 - 4:00
***Thursday, December 3, 2:40 - 4:00
*** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
***[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
***[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
**'''Mahrad (GenMAPP--> Quality Assurance)''': This week I downloaded the six data sample files provided by the microarray paper. The process is detailed in my [[Msaeedi23 Week 12| Week 12 Journal Entry]]. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
** '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
**Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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. The outline and detailed process involved with the experiment can be found in my [[Msaeedi23 Week 11| Week 11 Journal Entry]]. 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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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

= 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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-21T06:46:43Z

Msaeedi23: /* Week 11 */

= Team Information & Links =

{{Template:Class Whoopers}}

= Deliverables =
[[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==Presentation Download Links==
*Journal Club
** Genome Paper: [[File:Genomepaper_cw20151116.pdf]]
** Microarray Paper: [[File: Microarray_Journal_Club_Presentation.pdf]]
*'''Final Project'''
**[[File:Bpertussis_findings_powerpoint.pdf]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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".
*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.

=Weekly Updates=
==Week 15==
*'''Goals'''
**'''Assignment due date:''' Midnight Tuesday, December 15
** '''Coder:''' Adjust the GenMAPP Builder code to account for the one EnsemblBacteria reference ID that was missing in our last export; conduct a new import-export cycle to create the (hopefully) final .gdb file; begin characterizing the exported .gdb file in a Gene Database Testing Report; customize the GenMAPP Builder TallyEngine to account for any changes made.
**'''Quality Assurance:''' Reconfigure TallyEngine Configuration with Coder in order to accommodate missing gene IDs that were not exported the previous time. Test the revised database by running TallyEngine count, XmlpipeDB Match, and PostgreSQL. Locate missing gene IDs if any.
**'''GenMAPP User:''' 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. Create a .mapp file showing one pathway that is changed in your data.

*'''Progress'''
**'''Brandon (Coder and Project Manager):''' I began this week by customizing the GenMAPP Builder TallyEngine to report ORF counts for ''Bordetella pertussis'' (see [[Bklein7_Week_15]]). After this, I worked with [[User:Msaeedi23|Mahrad]] to identify the 1 gene ID that was missing in the .gdb file [[File:bpertussis-std_cw20151203.zip]]. I found that this gene was a necessary EnsemblBacteria reference ID and edited the GenMAPP Builder code with the help of [[User:Dondi|Dr. Dionisio]] to include this ID in our next export (see [[Bklein7_Week_15]]). I conducted a complete import-export cycle on 12/10/2015 to create the .gdb file [[File:bpertussis-std_cw20151210.zip]]. I then characterized this export, authoring sections 1-5.2 of its testing report: [[Gene_Database_Testing_Report-_cw20151210]]. During our Sunday meeting, I worked with [[User:Lenaolufson|Lena]] to use this new gene database in GenMAPP. During our Monday meeting, I worked on our PowerPoint presentation: [[File:Bpertussis findings powerpoint.pdf]].
*** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 22:31, 14 December 2015 (PST)
**'''Mahrad (Quality Assurance):''' I worked closely with the coder [[User: Bklein7|Brandon]] in order to re-customize TallyEngine to include the 11 missing ORF genes. Having located the missing gene IDs, Brandon went into Eclipse to code for them to be included in the export. Following this, we tested out revised gene database to make sure these missing IDs were actually exported. We ran TallyEngine count, which gave a total of 3446 gene IDs, demonstrating that the IDs were now exported. Then we ran XMLpipeDB Match, and this provided a total of 3447 gene IDs exported, one additional. Finally, we ran PostgreSQL and this gave a total of 3446 gene IDs. We came to find that gene "BP3167A" was in the original XML file, but not accounted for in the exported file. With further investigation we concluded that "BP3167A" is a reference ID from EnsemblBacteria and corresponds to the same ID as "BP3167.1" which was exported.
**'''Lena (GenMAPP User):''' I was able to import the data into GenMAPP and then I created color sets in order to run MAPPFinder. I obtained the ontology results and did some background research on what exactly the top results related to from the microarray article. I then used Kegg pathways for my specific organism to create two separate MAPPS, one for ribosome and one for the nitrogen cycle.

*'''Meetings!'''
**This week, our group used class work sessions to coordinate our work:
***Tuesday, December 8, 2:40 - 4:00
***Thursday, December 10, 2:40 - 4:00
**In addition, we scheduled meetings outside of class to work on the final PowerPoint Presentation and deliverables for our project:
***Sunday, December 13, 7:00 PM - 1:00 AM
***Monday, December 14, 2:00 PM - 11:00 PM

==Week 14==

*'''Goals'''
**'''Assignment due date:''' Midnight Tuesday, December 8
**'''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
**'''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
**'''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

*'''Progress'''
**'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
*** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
**'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 Week 14| Week 14 Journal Entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
**'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

*'''Meetings!'''
**This week, our group used class work sessions to coordinate our work:
***Tuesday, December 1, 2:40 - 4:00
***Thursday, December 3, 2:40 - 4:00
*** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
***[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
***[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
**'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
** '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
**Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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. The outline and detailed process involved with the experiment can be found in my [[Msaeedi23 Week 11| Week 11 Journal Entry]]. 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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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

= 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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

Msaeedi23 Week 11

2015-12-21T06:41:02Z

Msaeedi23: /* DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL. */

==Process for GenMapp analysis==
Microarray paper:
<http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243>
Genome Paper:
<http://www.nature.com/ng/journal/v35/n1/full/ng1227.html>

==Journal Club Presentation==
[[File: Microarray_Journal_Club_Presentation.pdf]]

===Week 11===
* For the microarray paper (GenMAPP Users only), include the following:
* Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.

* Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.

* Construct a flow chart that illustrates the above.

==Unknown Term Definitions==
* Phosphorelay: A multi-stage process, involving the movement of phophoryl groups by histidine kinases in bacterial signal transduction.
< https://en.wiktionary.org/wiki/phosphorelay>
* Putative: Believed or deemed to be the case; accepted by supposition rather than from proof.
< https://en.wiktionary.org/wiki/putative>
* Supernatant: Floating on the surface or over something; the chemistry of a liquid-lying above a sediment or settled precipitate.
< http://dictionary.reference.com/browse/supernatant?s=t>
* Chemiluminescent: The emission of light as the result of a chemical reaction.
< https://en.wikipedia.org/wiki/Chemiluminescence>
* Endogenous: Growing or developing from within; originating within.
< http://dictionary.reference.com/browse/endogenous>
* Non-Permeabilized: Made not permeable, unable to infiltrate a surface.
< https://en.wiktionary.org/wiki/nonpermeabilized>
* Albeit: Although, even if.
< http://dictionary.reference.com/browse/albeit?s=ts>
* Attenuated: To render less virulent, as a strain of pathogenic virus or bacterium.
< http://dictionary.reference.com/browse/attenuated?s=t>
* Modulating: To regulate or adjust to a certain measure or proportion; soften or tone down.
< http://dictionary.reference.com/browse/modulating?s=t>
* Homodimerization: Any reaction which leads to the formation of a homodimer, a molecule composed of paired identical proteins.
< http://dictionary.reference.com/browse/modulating?s=t>

==Article Outline==
Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
What is the importance or significance of this work (i.e., your species)?
===Introduction/Significance===
(Used in accordance with GenMAPP user lolufson)
**The Gram-negative bacterium Bordetella pertussis is the causative agent of pertussis or whooping cough.
***Pertussis is responsible for 300,000-400,000 deaths each year as it is one of the top ten most infectious diseases worldwide.
**B. pertussis creates a lot of different virulence factors that include adhesions, toxins, and multiple others that are regulated by the BvgA/S two-component system when a change in the environment is detected.
***B. pertussis produces an intact PS microcapsule on the surface of its bacteria.
***The B. pertussis capsule does not play a role in the capsule-mediated defense mechanisms, some of which include adherence to mammalian host cell, complement-mediated killing and antimicrobial attack.
**This study characterizes the role of the capsule locus and the expression in pertussis pathogenesis.
**This study showed that a protein, KpsT, located on the membrane is involved via a structural role in the transportation of the PS capsule across the cell envelope, and this protein is necessary for the greatest BvgA/S-mediated signal transduction.

What were the methods used in the study?
(Used in accordance with GenMAPP user lolufson)
===Methods===
**''Bacterial Strains and growth conditions''
***All B. pertussis strains were grown at 37°C on Bordet-Gengou (BG) agar (Difco) supplemented with 10% defibrinated sheep blood with 1% glycerol or in modified Stainer-Scholte (SS) medium containing 2,6-O-dimethyl-β-cyclodextrin (Sigma Chemical) at 1 g/liter supplemented with either 10 μg/ml gentamicin, 100 μg/ml streptomycin or 30 μg/ml chloramphenicol.
***E. coli strains were grown at 37°C overnight in fresh Luria-Bertani broth or on LB agar (Difco) plates, and suitably 100 µg/ml ampicillin, 50 µg/ml kanamycin, 10 µg/ml gentamicin, 30 µg/ml chloramphenicol was added to select for antibiotic-resistant strains.
**''Construction of B. pertussis capsule-deficient mutant strains''
***Non-polar single gene deletion was performed for kpsT, kpsE, and vipC ORFs by using the double homologous recombination method.
***The final products of the vector insertions yielded pJQT1-2, pJQE1-2, and pJQV1-2, and the recombinant pJQ constructs were used for allelic exchange in wild-type BPSM to yield the mutant strains.
**''Construction of recombinant B. pertussis BPSH strain''
***The B. pertussis BPSH strain that expressed a histidine tag at the N-terminal end of BvgS was created by PCR amplification.
***The final products of the vector insertions yielded pJQ-His-BvgS, and this was used to further develop mutant and wild-type BPSH strains.
**''Southern blot analysis''
***Chromosomal DNA was extracted and purified from BPSM and ΔkpsT and ΔkpsE bacteria and the B. pertussis strains were digested using restriction enzymes.
***Detection of hybridization was done using alkaline phosphatase-conjugates anti-DIG antibody, and the membrane was developed using NBT/BCIP AP substrate (Chemicon).
**''Whole cell extract and supernatant concentration preparation''
***Whole cell extract was harvested from bacteria previously grown and then washed to prepare it for incubation with centrifugation proceeding it.
***The bacteria pellet created was solubilized and the cell lysate produced from this was centrifuged to pellet unsolubilized cell and debris.
**''Purification of His-BvgS affinity chromatography''
***Protein lysate was mixed with Qiagen to allow overnight binding to occur, and then the cellular lysate underwent chromatography column for gravity flow purification.
**''SDS-Page and Western blot analysis''
***Ten times concentrated supernatant of B. pertussis and whole cell extract were run on an SDS-PAGE and then the transferred membranes were incubated with mouse anti-FHA monoclonal antibody, mouse anti-PT monoclonal antibody, rabbit anti-BrkA polyclonal antibodies.
***The purified His-BvgS were run on 10% SDS-PAGE and were then either stained or transferred onto PVDF membranes and incubated with other antibodies.
**''RNA extraction from in vitro B. pertussis culture''
***B. pertussis bacteria in virulent phase were harvested and then incubated with an RNA bacteria reagent designed to stabilize the RNA.
***After the pelleted bacteria were resuspended, RNA extraction was performed and the purified RNA were treated to remove contaminant DNA and finally reverse transcription was performed on 10 ng of bacterial RNA.
**''RNA extraction from B. pertussis infected mice lungs.''
***B. pertussis-infected mice were euthanized so their lungs could be removed to be drowned in RNAprotect Bacteria Reagent for 1 hour.
***The lung homogenates from the individual mice lungs were filtered and then centrifuged to pellet the remaining cell debris.
***Bacterial RNA was extracted using lysozyme and then in-solution DNA digestion was performed, finally ending with the elution of total RNA in DPEC water.
**''Real-time polymerase chain reaction''
***PCR was performed in a 96 well-plate with each well containing 2 µl of cDNA mix, 0.5 µl of forward and reverse primers (0.5 µM final), and 25 µl SYBR-Green Supermix with ROX (Bio-Rad) to a final volume of 50 µl.
***Samples were run in triplicate.
***Expression of each target gene was based on relative quantification using the comparative critical threshold value method.
***Relative quantification of a specific gene was measure in each reaction by normalization to the Ct value obtained for the endogenous control gene, recA.
***Control reactions without cDNA were used as negative controls.
**''Microarray production and analysis''
***Oligonucleotides were synthesized and spotted on slides in a buffer.
***For each of the samples done, 15 µg of total RNA was reverse transcribed in the presence of either 100 µM Cy3-dCTP or Cy5-dCTP (GE).
***The newly labeled cDNA was treated with NaOH to degrade RNA and then purified to allow hybridization to occur.
***Hybridization was then performed and the slides were washed and then scanned using an Innoscan microarray scanner to be analyzed.
***The LIMMA package was used for the differential expression and normalization, while moderated t-statistic was used to identify statistically significant regulation.
***Due to multiple testing, obtained P-values were corrected using Benjamini & Hochberg method to control the false discovery rate.
***Microarray data were deposited in the GEO online database.
**''Reverse Transcribed (RT)-PCR''
***RNA was purified from exponentially grown B. pertussis bacteria in virulent phase, and the cDNA was obtained as described previously.
***PCR was performed using recA primers (endogenous control) or using primers mapping to the respective downstream region of the deleted ORFs.
**''FACS''
***In order to make an accurate estimation of the surface polysaccharide capsule expression, fluorescence-activated cell sorting (FACS) analysis was done on the B. pertussis strains grown in a medium containing MgSO4 by using the anti-Vi polyclonal mouse immune serum.
***Each assay was performed 3 times independently.
**''Intranasal infection''
***Female adult mice were selected for their specific pathogen free qualities and then infected intranasally with B. pertussis strains for lung colonization, as well as BPSM for bacterial RNA extraction.
***Using an interval, four mice were killed using CO2 in order to allow their lungs to be removed and homogenized.
***The serial dilutions of the individual lung homogenates were plated and then counted for CFU quantities after 4 days of incubation.
***Each experiment was performed at least twice independently.

===Briefly state the result shown in each of the figures and tables===
*Table 1: Lists all of the B. Pertussis strains used in the study along with their genotypes/relevant features, and the source where the strain was obtained.
*Table 2: A complete list of all of the forward and reverse primers used in cloning are provided with their sequences, 5'-3', and their indicated mode of amplification (forward or reverse).
*Table 3: Lists specific reverse and forward primers used in the real-time PCR analysis.
*Figure 1: Two biological replicates were performed and the expression of the capsule locus was monitored using real-time PCR and observed to be significantly up-regulated in the mouse lungs compared to its in vitro Bvg+ expression level, with a peak of expression at day 3 p.i. A similar trend of expression was seen for another bvg-repressed gene, vrg6. Concurrently, the expression of vags including bvgA, fhaB and ptx were all up regulated at day 3 and day 7 p.i. compared to Day 0 and to the in vitro Bvg+ expression level.
*Figure 2: Outlines the construction of the kpsT, kpsE, vipC, and BPSM B. pertussis mutants. Goes on to portray the Southern blot analysis and the transcription efficacy of the downstream gene. Finally it looked at the growth kinetic profiles of each mutant. "The ΔkpsT, ΔkpsE and ΔvipC mutant strains displayed hemolytic and domed colony morphology on blood agar plates (data not shown) and in vitro growth kinetics comparable to the parental BPSM strain (Fig. 2 D), implying that these single gene deletions within the capsule locus did not affect the in vitro fitness of the bacteria." <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243#pone-0115243-g002>
*Figure 3: Depicts phenotypic characterization of the kpsT, kpsE, and vipC mutants. It was observed that ΔkpsT, ΔkpsE and ΔvipC cells consistently displayed levels of fluorescence shift comparable to that measured with KOcaps, corresponding to nonspecific background shift. "The FACS data supports that in-frame deletion of the single ORF kpsT, kpsE or vipC within the capsule locus is sufficient to prevent the presence of the PS capsule at the bacterial surface."
*Figure 4:Compared to BPSM, the band signal intensity for FHA in ΔkpsT 10x concentrated culture supernatant was about 30% down-regulated (Fig. 4 A). In contrast, signal intensities for FHA in the whole cell lysates appeared comparable between mutant strains (Fig. 4A), indicating that secretion into the culture supernatant may be compromised in ΔkpsT. Similarly, secretion but not production of PT appeared to be impaired in ΔkpsT (Fig. 4C). "In contrast, both production and secretion of BrkA in ΔkpsT were visibly reduced (Fig. 4 B). Production/secretion levels of FHA, PT and BrkA were partially restored to parental level in ΔkpsTcom strain (Fig. 4 A, B and C)."
*Figure 5: Consistent with the Real-time PCR analysis, expression of the bvgAS locus and fhaB was not found to be down-regulated in the ΔkpsT mutant (S1 Table).In addition to further support this analysis, the microarray data revealed that the absence of KpsT affects negatively the expression of a large number of bvg-regulated genes. "Such overall down-regulation is likely to be responsible for the attenuated phenotype observed with the ΔkpsT mutant in mice."
*Figure 6: "Higher amounts of BrkA, PT and to a lesser extent FHA were detected with the BvgS-VFT2- ΔkpsT double mutant compared to ΔkpsT single mutant, with band signal intensities comparable to those observed for wild type BPSM and BvgS-VFT2 strain (Fig. 6A). Also, real-time PCR analysis showed that down-regulation of the brkA, ptx and sphB1 genes observed with the ΔkpsT single mutant was not seen with the BvgS-VFT2- ΔkpsT double mutant (Fig. 6B). These data thus indicated that deletion of kpsT in a Bvg+-phase locked mutant did not affect the virulence genes expression therefore suggesting that VFT2 mutation in the BvgS sensor is dominant over kpsT deletion. Consistently, a parental in vivo virulent phenotype was observed with BvgS-VFT2- ΔkpsT double mutant in mice (Fig. 6C). Altogether, these results indicate that deletion of kpsT ORF in a constitutive bvgS background had no effect on the expression of bvg-regulated genes."
*Figure 7: "Western blot analysis using anti-His and anti-BvgS antibodies confirmed the identity of the 140 kDa eluted protein as His-BvgS monomers in E2 and E3 from BPSH but not from BPSM extracts (Fig. 7B). A band at 50 kDa MW was also observed in E3 and E4 from both BPSM and BPSH, suggesting that this unknown protein bound to the Ni-NTA beads likely due to high His content (Fig. 7A). A stronger signal intensity of the 140 kDa band was observed under reducing/heat treatment conditions (Fig. 7C). Altogether these data supported that KpsT is necessary for BvgS oligomerization although no direct physical interaction seems to occur between both proteins."
*Figure 8: The results portrayed in this figure support that neither KpsT alone nor the KpsMT complex is enough to restore fully a parental colonization profile in KOcaps. "Therefore, instead of KpsT alone, the entire capsule transport machinery may play a role in the BvgS-mediated signal transduction and indirectly in the overall bacterial virulence."

===How do the results of this study compare to the results of previous studies?===
* Previous research showed that B. pertussis PS capsule is not involved in the classical capsule-defense mechanisms including phagocytosis, complement-mediated killing and antimicrobial peptides attack. This new study provides evidence that the PS capsule transport proteins, in particular the membrane associated KpsT protein, are necessary for B. pertussis virulence in an indirect mode-of-action. The data suggest a structural role for the entire PS capsule transport machinery in the cell envelope and a consequential impact on the BvgA/S-mediated signal transduction and virulence gene expression. The work presented in this paper demonstrates for the first time that a vrg locus (the PS capsule locus) plays a role in pertussis pathogenesis. Therefore, it is demonstrated for the first time that a vrg locus (specifically the capsule locus) i) is expressed and modulated during in vivo infection, and ii) plays an indirect role in B. pertussis in vivo virulence. This finding apparently contradicts a previous study which claimed that the Bvg- phase is dispensable for bacterial in vivo virulence based on a Bvg+ phase locked mutant. This new observation thus suggests that in vivo, dynamic gene regulation occurs thereby implying that over time the micro-environmental conditions encountered by the bacteria vary. The PS capsule locus in B. pertussis is physically distinct from the bps locus which encodes proteins involved in biofilm formation. The data indicates that absence of the membrane-associated protein KpsT (and to a lesser extent KpsE) affects significantly pertussis pathogenesis. "In conclusion, this research portrays that the B. pertussis PS capsule transporter-export machinery and in particular KpsT are necessary for optimal expression of virulence genes and therefore play an important role in pertussis pathogenesis."
<http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243#pone-0115243-g006>

==For the microarray paper (GenMAPP Users only)==
**Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
This paper identified polysaccharide (PS) capsules as important virulence determinants for bacterial pathogens and and KpsT as a membrane protein involved in the transport of PS polymers across the cellular envelope in ''Bordetella pertussis''. To determine the impact of PS capsules on the virulence of ''B. pertussis'', a microarray experiment was run testing a ∆KpsT mutant against the wild-type.
*Treatment Group: ∆KpsT Mutant
*Control Group: Wild-type (BPSM)
Biological replicates: 3 replicates of both the control and treatment groups; Technical replicates: 2 per biological replicate (dye-swapped)
*Replicate Listings (taken from [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]):
**GSM1519507 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 1
**GSM1519509 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 1 by dye-swap color
**GSM1519511 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 2
**GSM1519514 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 2 by dye-swap color
**GSM1519516 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 3
**GSM1519519 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 3 by dye-swap color

* Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
*[[Media: GSM1519507_1-A3_vs_dA5.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 1.
*[[Media: GSM1519509_2-A5_vs_dA3.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 1 by dye-swap color.
*[[Media: GSM1519511_3-B3_vs_dB5.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 2.
*[[Media: GSM1519514_4-B5_vs_dB3.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 2 by dye-swap color.
*[[Media: GSM1519516_5-C3_vs_dC5.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 3.
*[[Media: GSM1519519_6-C5_vs_dC3.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 3 by dye-swap color.

* Construct a flow chart that illustrates the above.
[[Media: Flow_chart_db_project.docx]]

==DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL.==

1. Experimental design-what is the treatment and what is the control
* Biological vs technical replicants- for vibrio control was the untreated strain, technical replicates = splitting a sample, different from biological replicates. Biological replicates are derived from the original strain. *note how many replicates of each. # of chips(microarrays) (for vibrio it was 9, total number of samples)
#** Dye swaps, cy3 green dye and cy5 red. note how many swaps. Swaps done to avoid dye playing an effect in replication.
#***Draw a diagram to help of how chips were obtained. [[File: Microarray_flow_chart.docx]]

2. Sample + data relationship. In raw data there should be one file to each chip. Match file name to sample. raw.zip on arrayexpress has one file for each chip. Sdrf.txt open in excel to show whats in the samples-should tell you all of the samples, their matches, and dye swaps.

3. Compiled raw data file. Include columns for: ID, Sample log2FC, sample log2FC. Compiling raw data files into one spreadsheet to prepare for statistical analysis.

4. Normalization + statistical analysis. Customized for each dataset due to different treatments. Either t-test or one way anova. Also due sanity check, which will be a result in the paper. Compare it to what was written in the paper, corresponding to specific genes. Comparing log-fold changes of specific genes between our data and the paper's.

5. GenMAPP + mappfinder. Run data through database created by groupmates.

6. Deliverables-describing methods, production of tables including the sanity check, etc.
*In discussion compare what we found vs to what they found.

[[User:Msaeedi23|Msaeedi23]] ([[User talk:Msaeedi23|talk]]) 23:42, 16 November 2015 (PST)

{{Template: msaeedi23}}

File:Microarray flow chart.docx

2015-12-21T06:39:25Z

Msaeedi23:

File:Flow chart db project.docx

2015-12-21T06:38:33Z

Msaeedi23: Msaeedi23 uploaded a new version of File:Flow chart db project.docx

Template:Msaeedi23

2015-12-18T20:45:23Z

Msaeedi23: /* Shared Journals */

The Class Whoopers

2015-12-15T06:17:50Z

Msaeedi23: /* Progress */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 15==
===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 15
* '''Coder:''' Adjust the GenMAPP Builder code to account for the one EnsemblBacteria reference ID that was missing in our last export; conduct a new import-export cycle to create the (hopefully) final .gdb file; begin characterizing the exported .gdb file in a Gene Database Testing Report; customize the GenMAPP Builder TallyEngine to account for any changes made.
* '''Quality Assurance:''' Reconfigure TallyEngine Configuration with Coder in order to accommodate missing gene IDs that were not exported the previous time. Test the revised database by running TallyEngine count, XmlpipeDB Match, and PostgreSQL. Locate missing gene IDs if any.
* '''GenMAPP User:''' 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. Create a .mapp file showing one pathway that is changed in your data.

===Progress===
*'''Brandon (Coder and Project Manager):'''
*'''Mahrad (Quality Assurance):''' I worked closely with the coder [[User: Bklein7|Brandon]] in order to re-customize TallyEngine to include the 11 missing ORF genes. Having located the missing gene IDs, Brandon went into Eclipse to code for them to be included in the export. Following this, we tested out revised gene database to make sure these missing IDs were actually exported. We ran TallyEngine count, which gave a total of 3446 gene IDs, demonstrating that the IDs were now exported. Then we ran XMLpipeDB Match, and this provided a total of 3447 gene IDs exported, one additional. Finally, we ran PostgreSQL and this gave a total of 3446 gene IDs. We came to find that gene "BP3167A" was in the original XML file, but not accounted for in the exported file. With further investigation we concluded that "BP3167A" is a reference ID from EnsemblBacteria and corresponds to the same ID as "BP3167.1" which was exported.
*'''Lena (GenMAPP User):''' I was able to import the data into GenMAPP and then I created color sets in order to run MAPPFinder. I obtained the ontology results and did some background research on what exactly the top results related to from the microarray article. I then used Kegg pathways for my specific organism to create two separate MAPPS, one for ribosome and one for the nitrogen cycle.

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 8, 2:40 - 4:00
**Thursday, December 10, 2:40 - 4:00
*In addition, we scheduled meetings outside of class to work on the final PowerPoint Presentation and deliverables for our project:
**Sunday, December 13, 7:00 PM - 1:00 AM
**Monday, December 14, 2:00 PM - _______

==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 Week 14| Week 14 Journal Entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00
** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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 =
Download links to the deliverables for this project can be found here: [[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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

==File Names==
*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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-15T06:17:16Z

Msaeedi23: /* Progress */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 15==
===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 15
* '''Coder:''' Adjust the GenMAPP Builder code to account for the one EnsemblBacteria reference ID that was missing in our last export; conduct a new import-export cycle to create the (hopefully) final .gdb file; begin characterizing the exported .gdb file in a Gene Database Testing Report; customize the GenMAPP Builder TallyEngine to account for any changes made.
* '''Quality Assurance:''' Reconfigure TallyEngine Configuration with Coder in order to accommodate missing gene IDs that were not exported the previous time. Test the revised database by running TallyEngine count, XmlpipeDB Match, and PostgreSQL. Locate missing gene IDs if any.
* '''GenMAPP User:''' 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. Create a .mapp file showing one pathway that is changed in your data.

===Progress===
*'''Brandon (Coder and Project Manager):'''
*'''Mahrad (Quality Assurance):''' I worked closely with the coder [[user: Bklein7:Brandon]] in order to re-customize TallyEngine to include the 11 missing ORF genes. Having located the missing gene IDs, Brandon went into Eclipse to code for them to be included in the export. Following this, we tested out revised gene database to make sure these missing IDs were actually exported. We ran TallyEngine count, which gave a total of 3446 gene IDs, demonstrating that the IDs were now exported. Then we ran XMLpipeDB Match, and this provided a total of 3447 gene IDs exported, one additional. Finally, we ran PostgreSQL and this gave a total of 3446 gene IDs. We came to find that gene "BP3167A" was in the original XML file, but not accounted for in the exported file. With further investigation we concluded that "BP3167A" is a reference ID from EnsemblBacteria and corresponds to the same ID as "BP3167.1" which was exported.
*'''Lena (GenMAPP User):''' I was able to import the data into GenMAPP and then I created color sets in order to run MAPPFinder. I obtained the ontology results and did some background research on what exactly the top results related to from the microarray article. I then used Kegg pathways for my specific organism to create two separate MAPPS, one for ribosome and one for the nitrogen cycle.

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 8, 2:40 - 4:00
**Thursday, December 10, 2:40 - 4:00
*In addition, we scheduled meetings outside of class to work on the final PowerPoint Presentation and deliverables for our project:
**Sunday, December 13, 7:00 PM - 1:00 AM
**Monday, December 14, 2:00 PM - _______

==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 Week 14| Week 14 Journal Entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00
** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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 =
Download links to the deliverables for this project can be found here: [[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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

==File Names==
*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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-15T06:06:48Z

Msaeedi23: /* Goals */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 15==
===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 15
* '''Coder:''' Adjust the GenMAPP Builder code to account for the one EnsemblBacteria reference ID that was missing in our last export; conduct a new import-export cycle to create the (hopefully) final .gdb file; begin characterizing the exported .gdb file in a Gene Database Testing Report; customize the GenMAPP Builder TallyEngine to account for any changes made.
* '''Quality Assurance:''' Reconfigure TallyEngine Configuration with Coder in order to accommodate missing gene IDs that were not exported the previous time. Test the revised database by running TallyEngine count, XmlpipeDB Match, and PostgreSQL. Locate missing gene IDs if any.
* '''GenMAPP User:''' 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. Create a .mapp file showing one pathway that is changed in your data.

===Progress===
*'''Brandon (Coder and Project Manager):'''
*'''Mahrad (Quality Assurance):'''
*'''Lena (GenMAPP User):''' I was able to import the data into GenMAPP and then I created color sets in order to run MAPPFinder. I obtained the ontology results and did some background research on what exactly the top results related to from the microarray article. I then used Kegg pathways for my specific organism to create two separate MAPPS, one for ribosome and one for the nitrogen cycle.

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 8, 2:40 - 4:00
**Thursday, December 10, 2:40 - 4:00
*In addition, we scheduled meetings outside of class to work on the final PowerPoint Presentation and deliverables for our project:
**Sunday, December 13, 7:00 PM - 1:00 AM
**Monday, December 14, 2:00 PM - _______

==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 Week 14| Week 14 Journal Entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00
** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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 =
Download links to the deliverables for this project can be found here: [[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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

==File Names==
*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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

Msaeedi23 Week 15

2015-12-14T07:37:21Z

Msaeedi23:

The Class Whoopers

2015-12-14T04:30:38Z

Msaeedi23: /* Progress */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 15==
===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 15
* '''Coder:'''
* '''Quality Assurance:'''
* '''GenMAPP User:'''

===Progress===
*'''Brandon (Coder and Project Manager):'''
*'''Mahrad (Quality Assurance):'''
*'''Lena (GenMAPP User):''' [[File:Errors in genmapp.png]]

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 8, 2:40 - 4:00
**Thursday, December 10, 2:40 - 4:00

==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 Week 14| Week 14 Journal Entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00
** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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 =
Download links to the deliverables for this project can be found here: [[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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

==File Names==
*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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-14T04:29:09Z

Msaeedi23: /* Progress */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 15==
===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 15
* '''Coder:'''
* '''Quality Assurance:'''
* '''GenMAPP User:'''

===Progress===
*'''Brandon (Coder and Project Manager):'''
*'''Mahrad (Quality Assurance):'''
*'''Lena (GenMAPP User):''' [[File:Errors in genmapp.png]]

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 8, 2:40 - 4:00
**Thursday, December 10, 2:40 - 4:00

==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 week 14| week 14 journal entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00
** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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 =
Download links to the deliverables for this project can be found here: [[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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

==File Names==
*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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-14T04:28:48Z

Msaeedi23: /* Progress */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 15==
===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 15
* '''Coder:'''
* '''Quality Assurance:'''
* '''GenMAPP User:'''

===Progress===
*'''Brandon (Coder and Project Manager):'''
*'''Mahrad (Quality Assurance):'''
*'''Lena (GenMAPP User):''' [[File:Errors in genmapp.png]]

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 8, 2:40 - 4:00
**Thursday, December 10, 2:40 - 4:00

==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. The work can be summarized here: [[Msaeedi23 week 15| week 15 journal entry]]. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00
** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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 =
Download links to the deliverables for this project can be found here: [[Bordetella Pertussis GenMAPP Analysis Deliverables]]

==File Naming Protocol==
All file types generated in this project will receive their own unique names composed of two key parts:
#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.
#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

==File Names==
*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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

Msaeedi23 Week 15

2015-12-14T04:26:34Z

Msaeedi23:

==12/8/15==

Msaeedi23 Week 15

2015-12-14T04:26:23Z

Msaeedi23: Created page with "12/8/15"

12/8/15

Msaeedi23 Week 14

2015-12-10T23:49:57Z

Msaeedi23:

Link to completed gene database testing report for most recent created database 1203: [[Gene Database Testing Report- cw20151203]]

==Bordetella Pertussis Species Profile Customization==

===ID inconsistencies===
To assess the need for further customization of the ''Bordetella pertussis'' species profile, I worked directly with our coder [[User:Bklein7|Brandon]] to compare the gene IDs present in the cw20151201 .gdb file ([[File:Bpertussis-std cw20151201.zip]]) and the original .xml file ([[File:Uniprot-proteome-UP000002676 cw20151201.zip]]). This was done by copying the "OrderedLocusNames" table from the .gdb file into a new Excel document alongside the list of ''Bordetella pertussis'' gene IDs in the original .xml file that was generated using xmlpipedb match. Further details can be found in [[Msaeedi23 Week 14| Mahrad's Week 14 Journal Entry]]. Overall, we found 4 discrepant IDs.
Together we went through and processed each individual gene which had an apparent discrepancy from the original dataset to the exported one.

#'''BP3167.1'''- existed in the .gdb file but not in the the xmlpipedb match result
#*Additionally, we found that the expected variant of this ID, BP3167, existed in the xmlpipedb match result but not in the .gdb file.
#*We hypothesized that the ID existed as BP3167.1 in the original .xml file but was retrieved incompletely in the xmlpipedb match result due to the use of an imprecise regex (BP####).
#**To test this hypothesis, we conducted a new xmlpipedb match query using the updated regex BP####.1:
#**[[File: Bp3167issue_cw20151119.png]]
#***This test confirmed our hypothesis, demonstrating that BP3167.1 is the complete gene ID. Additionally, no other gene IDs in the .xml file exhibited this pattern.
#'''BP0101'''- did not get exported into the .gdb file
#*To investigate why this gene was not exported, we looked up this ID in the original .xml file.
#**We found that the gene ID was actually listed as both BP0101A and BP0101B, which was not retrieved in the xmlpipedb match result due to the use of an imprecise regex (BP####).
#**The gene IDs BP0101A and BP0101B were both listed as open reading frame (ORF) genes in the .xml file as opposed to ordered locus names. This presented a new category of gene IDs that the custom ''Bordetella pertussis'' species profile was not designed to export.
#*ORF investigation
#**To see if there were other ORF genes with the pattern BP####A or BP####B, we ran a query to retrieve such IDs from the original PostgreSQL database: ''bpertussis_cw20151119_gmb3build5''.
#***[[File: ORFissue_cw20151119.png]]
#****This query retrieved a list of 11 ORF genes. Seven of these genes exhibited numerical sequences (####) that were cross-listed as ordered locus names, whereas four of the genes exhibited unique numerical sequences that were only listed as ORF genes. Therefore, only four of the ORF IDs should been discrepant during our comparative analysis between .gdb and .xml IDs. Of these four, two were BP0101A and BP0101B.
#**To evaluate the total number of genes that should be exported into the .gdb file, including both genes listed under the ordered locus names and ORF tables, we queried the original PostgreSQL database once more:
#***[[File: Oln-orfcounts_cw20151119.png]]
#****This demonstrates that 3446 unique genes exist in the original .xml file, all of which need to be exported into our .gdb file. The number 3446 comes from 3435 ordered locus names listings and 11 ORF listings.
#'''BP0970'''- did not get exported into the .gdb file
#*This was the third ORF gene with a unique numerical sequence. The gene was listed as BP0970A in the original .xml file.
#'''BP0684'''- did not get exported into the .gdb file
#*This was the third ORF gene with a unique numerical sequence. The gene was listed as BP0684A in the original .xml file.

'''Conclusion:''' The custom ''Bordetella pertussis'' species profile in GenMAPP Builder needs to be customized to export the 11 ORF genes. The gene BP3167.1 was already being exported and, therefore, does not warrant coding changes. Instead, this unique pattern should be incorporated into the regex used to count ''Bordetella pertussis'' gene IDs when running future gene database testing reports.

===Changes to the Code===
To make changes to the GenMAPP Builder code, Brandon opened the ''gmbuilder'' project within the ''Java perspective'' using the program ''Eclipse''. The details regarding the developer rig, used can be found on Brandon's page. [[Bklein7 Week 12| Week 12 Assignment Page]].

{{template: msaeedi23}}

Msaeedi23 Week 14

2015-12-08T08:30:19Z

Msaeedi23:

Gene Database Testing Report- cw20151203

2015-12-08T08:27:15Z

Msaeedi23: /* OriginalRowCounts Comparison */

==Files Asked for in the Gene Database Testing Report==
For convenience, all of the files explicitly asked for in the sections below were compressed together in this file: [[]]

==Pre-requisites==
The following set of software was used in the creation and testing of the ''Bordetella pertussis'' gene database:

# [http://www.7-zip.org/ 7-zip]tool that for unpacking .gz and .zip files
# [http://www.postgresql.org PostgreSQL] on Windows (version 9.4.x)
# [https://sourceforge.net/projects/xmlpipedb/files/ GenMAPP Builder]
# Java JDK 1.8 64-bit
# [https://github.com/GenMAPPCS/genmapp GenMAPP 2]
# [https://sourceforge.net/projects/xmlpipedb/files/ XMLPipeDB match utility] for counting IDs in XML files
# Microsoft Access for reading .mdb files

==Gene Database Creation==
===Downloading Data Source Files and GenMAPP Builder===

*I download the UniProt XML, GOA, and GO OBO-XML files for ''Bordetella Pertussis'' along with the GenMAPP Builder program.
**All files were saved to the folder ''Bklein7_CW\bpertussis_cw20151203'' on my computer's ThawSpace.
**Files that required extraction were unzipped using [http://www.7-zip.org/ 7-zip].
**Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.

====UniProt XML====

* I went to the [http://www.uniprot.org/taxonomy/complete-proteomes UniProt Complete Proteomes] page.
**From there, I navigated to the complete proteome download page for [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)].
** I clicked on the "Download" button at the top of the page above and selected the following options:
***"Download all"
***"XML" from the "Format" drop-down menu
***"Compressed" format
**I extracted the file using [http://www.7-zip.org/ 7-zip].

====GOA====

* UniProt-GOA files can be downloaded from the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/ UniProt-GOA ftp site].
*Within the above site, I navigated to the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I].
**This text file was automatically opened by my browser. Therefore, I had to manually download the file.

====GO OBO-XML====

* I downloaded the GO OBO-XML formatted file from the [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page].
*I extracted the file using [http://www.7-zip.org/ 7-zip].

====Downloaded GenMAPP Builder====

# I downloaded the custom version of GenMAPP Builder including the ''Bordetella pertussis'' custom class expanded to include ORF listings in exports (Version 3.0.0 Build 5 - cw20151203): [[File:Dist cw20151203.zip]].
# I extracted the GenMAPP Builder folder using [http://www.7-zip.org/ 7-zip].

===Creating the New Database in PostgreSQL===

* I launched ''pgAdmin III'' and connected to the PostgreSQL 9.4 server (localhost:5432).
** On this server, I created a new database: ''bpertussis_cw20151201_gmb3build5''.
** I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
*** I clicked on the Open File icon and selected the file ''gmbuilder.sql''. This imported a series of SQL commands into the editor tab.
*** I clicked on the Execute Query icon to run this command.
***In viewing the schema for this database, I confirmed that there were 167 tables after running the above command.

===Configuring GenMAPP Builder to Connect to the PostgreSQL Database===

* To begin, I launched gmbuilder.bat.
* I selected the "Configure Database" option and entered the following information into the fields below:
** Host or address: localhost
** Port number: 5432
** Database name: bpertussis_cw20151201_gmb3build5
** Username: postgres
** Password: Welcome1

===Importing Data into the PostgreSQL Database===

*The downloaded data files for ''Bordetella pertussis'' were specified and imported into the database by clicking on the following buttons:
** Selected File > Import UniProt XML...
** Selected File > Import GO OBO-XML...
** Clicked OK to the message asking to process the GO data.
** Selected File > Import GOA...

===Exporting a GenMAPP Gene Database (.gdb)===

* I selected File > Export to GenMAPP Gene Database... to begin the export process.
* I typed my name in the owner field (Brandon Klein).
* I selected "Bordetella pertussis (strain Tohama I/ATCC BAA-589/NCTC 13251), Taxon ID 257313" as the gene database species and then clicked ''Next''.
* The database was saved as ''bpertussis-std_cw20151203''.
* I checked the boxes for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms.
* Finally, I clicked the "Next" button to begin the export process.

==Gene Database Testing Report==
===Export Information===

Version of GenMAPP Builder: Version 3.0.0 Build 5 - cw20151203

Computer on which export was run: Seaver 120- Last computer on the right in the row farthest from the front of the room

Postgres Database name: bpertussis_cw20151201_gmb3build5

UniProt XML filename: [[File:Uniprot-proteome-UP000002676 cw20151201.zip]]
* UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_11
* UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)]
* Time taken to import: 2.59 minutes
** Note: The import time was nearly equivalent to that when creating the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (2.60 minute). No interruptions occurred during this process.

GO OBO-XML filename: [[File:Go daily-termdb cw20151201.zip]]
* GO OBO-XML version (The version information was found in the file properties): Last Modified- ‎‎December ‎01, ‎2015, ‏‎2:21:31 AM
* GO OBO-XML download link: [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page]
* Time taken to import: 7.08 minutes
* Time taken to process: 4.42 minutes
** Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (6.99 minutes and 4.48 minutes respectively). No interruptions occurred during these processes.

GOA filename: [[File:145.B pertussis ATCC BAA-589 cw20151201.zip]]
* GOA version (found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): Last Modified- 11/10/15 1:39:00 PM
* GOA download link: [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I]
* Time taken to import: 0.04 minutes
** Note: The import time was equal to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb. No interruptions occurred during this process.

Name of .gdb file: [[File:Bpertussis-std cw20151203.zip]]
* Time taken to export:
** Start time: 4:02 PM
** End time: 4:56 PM
** Elapsed time: 54 minutes
Note: No interruptions occurred during the export process.

===TallyEngine===

* I ran the TallyEngine in GenMAPP Builder and specified the following files:
**XML- [[File:Uniprot-proteome-UP000002676 cw20151201.zip]]
**GO- [[File:Go daily-termdb cw20151201.zip]]
*Results:
**[[File: Tallyenginecustomization_cw20151203.png]]
**All tally results were consistent across both files.
=== Using XMLPipeDB match to Validate the XML Results from the TallyEngine===
The following functions were performed using the Windows command line (cmd).
*I entered my project folder using the following command:
cd /d T:\Bklein7_CW
*I used XMLPipeDB match to identify matches of any ordered locus name following the pattern "BP####" in the UniProt XML file. The command sequence used is as follows:\
java -jar xmlpipedb-match-1.1.1.jar "BP[0-9][0-9][0-9][0-9]" < "uniprot-proteome%3AUP000002676_cw20151201.xml"
*Match Results:
----------
*make note to ask dondi specific code to use to obtain 3446 match results

=== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine===
I ran a SQL query designed to match the pattern BP####:

select count (*) from genenametype where type = 'ordered locus' and value ~ 'BP[0-9][0-9][0-9][0-9]';

Results:
*[[File:Sqlcount_cw20151203.png]]
* The number of unique matches yielded by this SQL query, 3446.

===OriginalRowCounts Comparison===

I opened the gene database file [[File:Bpertussis-std_cw20151203.zip]] in Microsoft Access and assessed the "OriginalRowCounts" table to see if the expected tables were listed with the expected number of records. The contents of this table were compared to the ''OriginalRowCounts'' table of an existing .gdb file created during Week 9.

Benchmark .gdb file: ''Vc-Std_20151027_TR''

"OriginalRowCounts" table from the benchmark and new gdb:

*All 52 tables present in the 2015 ''Vibrio cholerae'' database were also present in the ''B. pertussis'' database tagged _cw20151203. This confirmed that all expected tables were successfully created.
*Further, the "OrderedLocusNames" count produced by Tally Engine should hopefully represent this number.
Here is a screenshot comparing the two:
[[File: Access_orderedlocusnamescomparison_20151203.png]]

Note: The "OriginalRowCounts" tables were too large to screenshot. To circumvent this problem and facilitate the comparison, I copied the "OriginalRowCounts" tables from both gene databases into an Excel file and zoomed out. The above screenshot was taken from this Excel file. The "OrderedLocusNames" row counts are highlighted in yellow.

===Visual Inspection===
I visually inspected individual tables within [[File:Bpertussis-std_cw20151203.zip]] using Microsoft Access.
*Systems Table
**35 gene ID systems were listed, 11 of which listed the appropriate import date (12/03/2015)
***All gene ID systems relevant to ''B. pertussis'' were listed. This includes: EMBL, EnsemblBacteria, GeneID, GeneOntology, InterPro, OrderedLocusNames, Pfam, RefSeq, and UniProt.
***This result corresponded with that of the benchmark .gdb file listed in the "OriginalRowCounts Comparison" section.
*UniProt Table
**This table contained 3258 entries with 6 character IDs.
**All ID's in the UniProt table conform to the following pattern: [[File:UniProt Ascension Number info.PNG]]

*RefSeq Table
**This table contained 6627 entries. All IDs began with one of three prefixes: "NP_", "YP_", or "WP_". The meanings of these prefixes can be found in the RefSeq documentation found [http://www.ncbi.nlm.nih.gov/books/NBK50679/ here].
***"NP_" and "YP_" Prefixes
****Refer to proteins. There are 3410 "NP_" IDs and 7 "YP_" IDs.
***"WP_" Prefixes
****Refer to "autonomous non-redundant proteins that are not yet directly annotated on a genome". There were 3210 IDs with the "WP_" prefixes.
***Overall, every entry in the ID column was an expected value.
*OrderedLocusNames Table
**This table contained 3446 entries (consistent with & SQL counts).
**The IDs were copied into an Excel document for analysis:
***3434 IDs conformed to the pattern "BP####"
***1 ID was unique: "BP3167.1"
***The other 11 IDs showed up as ORF

===.gdb Use in GenMAPP===


*By following the instructions in [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols Part 2 of the ''Vibrio cholerae'' Microarray Data Analysis] and looking at Brandon's Week 9 individual journal assignment, I was able to verify that our Gene Database works in GenMAPP.
*I was able to open the GenMAPP program on the computer, and then I went to Data -> Choose Gene Database -> and selected the cw20151119 gdb file.
**There were no problems thus far as our database was able to load into the program.

====Putting a gene on the MAPP using the GeneFinder window====

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I went through each of the five inconsistent Gene IDs in GeneFinder.

**I typed in the gene Id BP3167.1 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

*I typed in the gene Id BP1252 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system. This served as a "control" to look up a consistent Gene ID to compare to.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

***I typed in the gene Id BP0101A into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0101B into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0684A into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**When the gene was found this is the back page that popped up:

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0970A into the Gene ID field and selected "GeneID" for the Gene ID system.

**All of the expected cross-referenced IDs were present.

*Screenshot of all of the sample ID's on a MAPP:
*[[File: Genesonmap_cw20151203.png]]

====Expression Dataset and MAPPFinder Analysis====
*We do not have the expression dataset yet that is to be created by the GenMAPP Builders; they are still working on performing the corrections to the data that has been compiled into an excel spreadsheet.
*Once the file is complete, we will proceed with the data analysis using the desired programs.

=== Compare Gene Database to Outside Resource===
*We will complete this step after progressing further into the project.
The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.

[[Category: Class Whoopers]]

File:Access orderedlocusnamescomparison 20151203.png

2015-12-08T08:26:46Z

Msaeedi23:

Gene Database Testing Report- cw20151203

2015-12-08T08:18:44Z

Msaeedi23: /* Putting a gene on the MAPP using the GeneFinder window */

==Files Asked for in the Gene Database Testing Report==
For convenience, all of the files explicitly asked for in the sections below were compressed together in this file: [[]]

==Pre-requisites==
The following set of software was used in the creation and testing of the ''Bordetella pertussis'' gene database:

# [http://www.7-zip.org/ 7-zip]tool that for unpacking .gz and .zip files
# [http://www.postgresql.org PostgreSQL] on Windows (version 9.4.x)
# [https://sourceforge.net/projects/xmlpipedb/files/ GenMAPP Builder]
# Java JDK 1.8 64-bit
# [https://github.com/GenMAPPCS/genmapp GenMAPP 2]
# [https://sourceforge.net/projects/xmlpipedb/files/ XMLPipeDB match utility] for counting IDs in XML files
# Microsoft Access for reading .mdb files

==Gene Database Creation==
===Downloading Data Source Files and GenMAPP Builder===

*I download the UniProt XML, GOA, and GO OBO-XML files for ''Bordetella Pertussis'' along with the GenMAPP Builder program.
**All files were saved to the folder ''Bklein7_CW\bpertussis_cw20151203'' on my computer's ThawSpace.
**Files that required extraction were unzipped using [http://www.7-zip.org/ 7-zip].
**Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.

====UniProt XML====

* I went to the [http://www.uniprot.org/taxonomy/complete-proteomes UniProt Complete Proteomes] page.
**From there, I navigated to the complete proteome download page for [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)].
** I clicked on the "Download" button at the top of the page above and selected the following options:
***"Download all"
***"XML" from the "Format" drop-down menu
***"Compressed" format
**I extracted the file using [http://www.7-zip.org/ 7-zip].

====GOA====

* UniProt-GOA files can be downloaded from the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/ UniProt-GOA ftp site].
*Within the above site, I navigated to the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I].
**This text file was automatically opened by my browser. Therefore, I had to manually download the file.

====GO OBO-XML====

* I downloaded the GO OBO-XML formatted file from the [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page].
*I extracted the file using [http://www.7-zip.org/ 7-zip].

====Downloaded GenMAPP Builder====

# I downloaded the custom version of GenMAPP Builder including the ''Bordetella pertussis'' custom class expanded to include ORF listings in exports (Version 3.0.0 Build 5 - cw20151203): [[File:Dist cw20151203.zip]].
# I extracted the GenMAPP Builder folder using [http://www.7-zip.org/ 7-zip].

===Creating the New Database in PostgreSQL===

* I launched ''pgAdmin III'' and connected to the PostgreSQL 9.4 server (localhost:5432).
** On this server, I created a new database: ''bpertussis_cw20151201_gmb3build5''.
** I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
*** I clicked on the Open File icon and selected the file ''gmbuilder.sql''. This imported a series of SQL commands into the editor tab.
*** I clicked on the Execute Query icon to run this command.
***In viewing the schema for this database, I confirmed that there were 167 tables after running the above command.

===Configuring GenMAPP Builder to Connect to the PostgreSQL Database===

* To begin, I launched gmbuilder.bat.
* I selected the "Configure Database" option and entered the following information into the fields below:
** Host or address: localhost
** Port number: 5432
** Database name: bpertussis_cw20151201_gmb3build5
** Username: postgres
** Password: Welcome1

===Importing Data into the PostgreSQL Database===

*The downloaded data files for ''Bordetella pertussis'' were specified and imported into the database by clicking on the following buttons:
** Selected File > Import UniProt XML...
** Selected File > Import GO OBO-XML...
** Clicked OK to the message asking to process the GO data.
** Selected File > Import GOA...

===Exporting a GenMAPP Gene Database (.gdb)===

* I selected File > Export to GenMAPP Gene Database... to begin the export process.
* I typed my name in the owner field (Brandon Klein).
* I selected "Bordetella pertussis (strain Tohama I/ATCC BAA-589/NCTC 13251), Taxon ID 257313" as the gene database species and then clicked ''Next''.
* The database was saved as ''bpertussis-std_cw20151203''.
* I checked the boxes for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms.
* Finally, I clicked the "Next" button to begin the export process.

==Gene Database Testing Report==
===Export Information===

Version of GenMAPP Builder: Version 3.0.0 Build 5 - cw20151203

Computer on which export was run: Seaver 120- Last computer on the right in the row farthest from the front of the room

Postgres Database name: bpertussis_cw20151201_gmb3build5

UniProt XML filename: [[File:Uniprot-proteome-UP000002676 cw20151201.zip]]
* UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_11
* UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)]
* Time taken to import: 2.59 minutes
** Note: The import time was nearly equivalent to that when creating the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (2.60 minute). No interruptions occurred during this process.

GO OBO-XML filename: [[File:Go daily-termdb cw20151201.zip]]
* GO OBO-XML version (The version information was found in the file properties): Last Modified- ‎‎December ‎01, ‎2015, ‏‎2:21:31 AM
* GO OBO-XML download link: [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page]
* Time taken to import: 7.08 minutes
* Time taken to process: 4.42 minutes
** Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (6.99 minutes and 4.48 minutes respectively). No interruptions occurred during these processes.

GOA filename: [[File:145.B pertussis ATCC BAA-589 cw20151201.zip]]
* GOA version (found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): Last Modified- 11/10/15 1:39:00 PM
* GOA download link: [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I]
* Time taken to import: 0.04 minutes
** Note: The import time was equal to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb. No interruptions occurred during this process.

Name of .gdb file: [[File:Bpertussis-std cw20151203.zip]]
* Time taken to export:
** Start time: 4:02 PM
** End time: 4:56 PM
** Elapsed time: 54 minutes
Note: No interruptions occurred during the export process.

===TallyEngine===

* I ran the TallyEngine in GenMAPP Builder and specified the following files:
**XML- [[File:Uniprot-proteome-UP000002676 cw20151201.zip]]
**GO- [[File:Go daily-termdb cw20151201.zip]]
*Results:
**[[File: Tallyenginecustomization_cw20151203.png]]
**All tally results were consistent across both files.
=== Using XMLPipeDB match to Validate the XML Results from the TallyEngine===
The following functions were performed using the Windows command line (cmd).
*I entered my project folder using the following command:
cd /d T:\Bklein7_CW
*I used XMLPipeDB match to identify matches of any ordered locus name following the pattern "BP####" in the UniProt XML file. The command sequence used is as follows:\
java -jar xmlpipedb-match-1.1.1.jar "BP[0-9][0-9][0-9][0-9]" < "uniprot-proteome%3AUP000002676_cw20151201.xml"
*Match Results:
----------
*make note to ask dondi specific code to use to obtain 3446 match results

=== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine===
I ran a SQL query designed to match the pattern BP####:

select count (*) from genenametype where type = 'ordered locus' and value ~ 'BP[0-9][0-9][0-9][0-9]';

Results:
*[[File:Sqlcount_cw20151203.png]]
* The number of unique matches yielded by this SQL query, 3446.

===OriginalRowCounts Comparison===

I opened the gene database file [[File:Bpertussis-std_cw20151203.zip]] in Microsoft Access and assessed the "OriginalRowCounts" table to see if the expected tables were listed with the expected number of records. The contents of this table were compared to the ''OriginalRowCounts'' table of an existing .gdb file created during Week 9.

Benchmark .gdb file: ''Vc-Std_20151027_TR''

"OriginalRowCounts" table from the benchmark and new gdb:

*All 52 tables present in the 2015 ''Vibrio cholerae'' database were also present in the ''B. pertussis'' database tagged _cw20151203. This confirmed that all expected tables were successfully created.
*Further, the "OrderedLocusNames" count produced by Tally Engine should hopefully represent this number.

Note: The "OriginalRowCounts" tables were too large to screenshot. To circumvent this problem and facilitate the comparison, I copied the "OriginalRowCounts" tables from both gene databases into an Excel file and zoomed out. The above screenshot was taken from this Excel file. The "OrderedLocusNames" row counts are highlighted in yellow.

===Visual Inspection===
I visually inspected individual tables within [[File:Bpertussis-std_cw20151203.zip]] using Microsoft Access.
*Systems Table
**35 gene ID systems were listed, 11 of which listed the appropriate import date (12/03/2015)
***All gene ID systems relevant to ''B. pertussis'' were listed. This includes: EMBL, EnsemblBacteria, GeneID, GeneOntology, InterPro, OrderedLocusNames, Pfam, RefSeq, and UniProt.
***This result corresponded with that of the benchmark .gdb file listed in the "OriginalRowCounts Comparison" section.
*UniProt Table
**This table contained 3258 entries with 6 character IDs.
**All ID's in the UniProt table conform to the following pattern: [[File:UniProt Ascension Number info.PNG]]

*RefSeq Table
**This table contained 6627 entries. All IDs began with one of three prefixes: "NP_", "YP_", or "WP_". The meanings of these prefixes can be found in the RefSeq documentation found [http://www.ncbi.nlm.nih.gov/books/NBK50679/ here].
***"NP_" and "YP_" Prefixes
****Refer to proteins. There are 3410 "NP_" IDs and 7 "YP_" IDs.
***"WP_" Prefixes
****Refer to "autonomous non-redundant proteins that are not yet directly annotated on a genome". There were 3210 IDs with the "WP_" prefixes.
***Overall, every entry in the ID column was an expected value.
*OrderedLocusNames Table
**This table contained 3446 entries (consistent with & SQL counts).
**The IDs were copied into an Excel document for analysis:
***3434 IDs conformed to the pattern "BP####"
***1 ID was unique: "BP3167.1"
***The other 11 IDs showed up as ORF

===.gdb Use in GenMAPP===


*By following the instructions in [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols Part 2 of the ''Vibrio cholerae'' Microarray Data Analysis] and looking at Brandon's Week 9 individual journal assignment, I was able to verify that our Gene Database works in GenMAPP.
*I was able to open the GenMAPP program on the computer, and then I went to Data -> Choose Gene Database -> and selected the cw20151119 gdb file.
**There were no problems thus far as our database was able to load into the program.

====Putting a gene on the MAPP using the GeneFinder window====

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I went through each of the five inconsistent Gene IDs in GeneFinder.

**I typed in the gene Id BP3167.1 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

*I typed in the gene Id BP1252 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system. This served as a "control" to look up a consistent Gene ID to compare to.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

***I typed in the gene Id BP0101A into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0101B into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0684A into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**When the gene was found this is the back page that popped up:

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0970A into the Gene ID field and selected "GeneID" for the Gene ID system.

**All of the expected cross-referenced IDs were present.

*Screenshot of all of the sample ID's on a MAPP:
*[[File: Genesonmap_cw20151203.png]]

====Expression Dataset and MAPPFinder Analysis====
*We do not have the expression dataset yet that is to be created by the GenMAPP Builders; they are still working on performing the corrections to the data that has been compiled into an excel spreadsheet.
*Once the file is complete, we will proceed with the data analysis using the desired programs.

=== Compare Gene Database to Outside Resource===
*We will complete this step after progressing further into the project.
The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.

[[Category: Class Whoopers]]

Gene Database Testing Report- cw20151203

2015-12-08T08:17:53Z

Msaeedi23: /* OriginalRowCounts Comparison */

==Files Asked for in the Gene Database Testing Report==
For convenience, all of the files explicitly asked for in the sections below were compressed together in this file: [[]]

==Pre-requisites==
The following set of software was used in the creation and testing of the ''Bordetella pertussis'' gene database:

# [http://www.7-zip.org/ 7-zip]tool that for unpacking .gz and .zip files
# [http://www.postgresql.org PostgreSQL] on Windows (version 9.4.x)
# [https://sourceforge.net/projects/xmlpipedb/files/ GenMAPP Builder]
# Java JDK 1.8 64-bit
# [https://github.com/GenMAPPCS/genmapp GenMAPP 2]
# [https://sourceforge.net/projects/xmlpipedb/files/ XMLPipeDB match utility] for counting IDs in XML files
# Microsoft Access for reading .mdb files

==Gene Database Creation==
===Downloading Data Source Files and GenMAPP Builder===

*I download the UniProt XML, GOA, and GO OBO-XML files for ''Bordetella Pertussis'' along with the GenMAPP Builder program.
**All files were saved to the folder ''Bklein7_CW\bpertussis_cw20151203'' on my computer's ThawSpace.
**Files that required extraction were unzipped using [http://www.7-zip.org/ 7-zip].
**Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.

====UniProt XML====

* I went to the [http://www.uniprot.org/taxonomy/complete-proteomes UniProt Complete Proteomes] page.
**From there, I navigated to the complete proteome download page for [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)].
** I clicked on the "Download" button at the top of the page above and selected the following options:
***"Download all"
***"XML" from the "Format" drop-down menu
***"Compressed" format
**I extracted the file using [http://www.7-zip.org/ 7-zip].

====GOA====

* UniProt-GOA files can be downloaded from the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/ UniProt-GOA ftp site].
*Within the above site, I navigated to the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I].
**This text file was automatically opened by my browser. Therefore, I had to manually download the file.

====GO OBO-XML====

* I downloaded the GO OBO-XML formatted file from the [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page].
*I extracted the file using [http://www.7-zip.org/ 7-zip].

====Downloaded GenMAPP Builder====

# I downloaded the custom version of GenMAPP Builder including the ''Bordetella pertussis'' custom class expanded to include ORF listings in exports (Version 3.0.0 Build 5 - cw20151203): [[File:Dist cw20151203.zip]].
# I extracted the GenMAPP Builder folder using [http://www.7-zip.org/ 7-zip].

===Creating the New Database in PostgreSQL===

* I launched ''pgAdmin III'' and connected to the PostgreSQL 9.4 server (localhost:5432).
** On this server, I created a new database: ''bpertussis_cw20151201_gmb3build5''.
** I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
*** I clicked on the Open File icon and selected the file ''gmbuilder.sql''. This imported a series of SQL commands into the editor tab.
*** I clicked on the Execute Query icon to run this command.
***In viewing the schema for this database, I confirmed that there were 167 tables after running the above command.

===Configuring GenMAPP Builder to Connect to the PostgreSQL Database===

* To begin, I launched gmbuilder.bat.
* I selected the "Configure Database" option and entered the following information into the fields below:
** Host or address: localhost
** Port number: 5432
** Database name: bpertussis_cw20151201_gmb3build5
** Username: postgres
** Password: Welcome1

===Importing Data into the PostgreSQL Database===

*The downloaded data files for ''Bordetella pertussis'' were specified and imported into the database by clicking on the following buttons:
** Selected File > Import UniProt XML...
** Selected File > Import GO OBO-XML...
** Clicked OK to the message asking to process the GO data.
** Selected File > Import GOA...

===Exporting a GenMAPP Gene Database (.gdb)===

* I selected File > Export to GenMAPP Gene Database... to begin the export process.
* I typed my name in the owner field (Brandon Klein).
* I selected "Bordetella pertussis (strain Tohama I/ATCC BAA-589/NCTC 13251), Taxon ID 257313" as the gene database species and then clicked ''Next''.
* The database was saved as ''bpertussis-std_cw20151203''.
* I checked the boxes for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms.
* Finally, I clicked the "Next" button to begin the export process.

==Gene Database Testing Report==
===Export Information===

Version of GenMAPP Builder: Version 3.0.0 Build 5 - cw20151203

Computer on which export was run: Seaver 120- Last computer on the right in the row farthest from the front of the room

Postgres Database name: bpertussis_cw20151201_gmb3build5

UniProt XML filename: [[File:Uniprot-proteome-UP000002676 cw20151201.zip]]
* UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_11
* UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)]
* Time taken to import: 2.59 minutes
** Note: The import time was nearly equivalent to that when creating the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (2.60 minute). No interruptions occurred during this process.

GO OBO-XML filename: [[File:Go daily-termdb cw20151201.zip]]
* GO OBO-XML version (The version information was found in the file properties): Last Modified- ‎‎December ‎01, ‎2015, ‏‎2:21:31 AM
* GO OBO-XML download link: [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page]
* Time taken to import: 7.08 minutes
* Time taken to process: 4.42 minutes
** Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (6.99 minutes and 4.48 minutes respectively). No interruptions occurred during these processes.

GOA filename: [[File:145.B pertussis ATCC BAA-589 cw20151201.zip]]
* GOA version (found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): Last Modified- 11/10/15 1:39:00 PM
* GOA download link: [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I]
* Time taken to import: 0.04 minutes
** Note: The import time was equal to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb. No interruptions occurred during this process.

Name of .gdb file: [[File:Bpertussis-std cw20151203.zip]]
* Time taken to export:
** Start time: 4:02 PM
** End time: 4:56 PM
** Elapsed time: 54 minutes
Note: No interruptions occurred during the export process.

===TallyEngine===

* I ran the TallyEngine in GenMAPP Builder and specified the following files:
**XML- [[File:Uniprot-proteome-UP000002676 cw20151201.zip]]
**GO- [[File:Go daily-termdb cw20151201.zip]]
*Results:
**[[File: Tallyenginecustomization_cw20151203.png]]
**All tally results were consistent across both files.
=== Using XMLPipeDB match to Validate the XML Results from the TallyEngine===
The following functions were performed using the Windows command line (cmd).
*I entered my project folder using the following command:
cd /d T:\Bklein7_CW
*I used XMLPipeDB match to identify matches of any ordered locus name following the pattern "BP####" in the UniProt XML file. The command sequence used is as follows:\
java -jar xmlpipedb-match-1.1.1.jar "BP[0-9][0-9][0-9][0-9]" < "uniprot-proteome%3AUP000002676_cw20151201.xml"
*Match Results:
----------
*make note to ask dondi specific code to use to obtain 3446 match results

=== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine===
I ran a SQL query designed to match the pattern BP####:

select count (*) from genenametype where type = 'ordered locus' and value ~ 'BP[0-9][0-9][0-9][0-9]';

Results:
*[[File:Sqlcount_cw20151203.png]]
* The number of unique matches yielded by this SQL query, 3446.

===OriginalRowCounts Comparison===

I opened the gene database file [[File:Bpertussis-std_cw20151203.zip]] in Microsoft Access and assessed the "OriginalRowCounts" table to see if the expected tables were listed with the expected number of records. The contents of this table were compared to the ''OriginalRowCounts'' table of an existing .gdb file created during Week 9.

Benchmark .gdb file: ''Vc-Std_20151027_TR''

"OriginalRowCounts" table from the benchmark and new gdb:

*All 52 tables present in the 2015 ''Vibrio cholerae'' database were also present in the ''B. pertussis'' database tagged _cw20151203. This confirmed that all expected tables were successfully created.
*Further, the "OrderedLocusNames" count produced by Tally Engine should hopefully represent this number.

Note: The "OriginalRowCounts" tables were too large to screenshot. To circumvent this problem and facilitate the comparison, I copied the "OriginalRowCounts" tables from both gene databases into an Excel file and zoomed out. The above screenshot was taken from this Excel file. The "OrderedLocusNames" row counts are highlighted in yellow.

===Visual Inspection===
I visually inspected individual tables within [[File:Bpertussis-std_cw20151203.zip]] using Microsoft Access.
*Systems Table
**35 gene ID systems were listed, 11 of which listed the appropriate import date (12/03/2015)
***All gene ID systems relevant to ''B. pertussis'' were listed. This includes: EMBL, EnsemblBacteria, GeneID, GeneOntology, InterPro, OrderedLocusNames, Pfam, RefSeq, and UniProt.
***This result corresponded with that of the benchmark .gdb file listed in the "OriginalRowCounts Comparison" section.
*UniProt Table
**This table contained 3258 entries with 6 character IDs.
**All ID's in the UniProt table conform to the following pattern: [[File:UniProt Ascension Number info.PNG]]

*RefSeq Table
**This table contained 6627 entries. All IDs began with one of three prefixes: "NP_", "YP_", or "WP_". The meanings of these prefixes can be found in the RefSeq documentation found [http://www.ncbi.nlm.nih.gov/books/NBK50679/ here].
***"NP_" and "YP_" Prefixes
****Refer to proteins. There are 3410 "NP_" IDs and 7 "YP_" IDs.
***"WP_" Prefixes
****Refer to "autonomous non-redundant proteins that are not yet directly annotated on a genome". There were 3210 IDs with the "WP_" prefixes.
***Overall, every entry in the ID column was an expected value.
*OrderedLocusNames Table
**This table contained 3446 entries (consistent with & SQL counts).
**The IDs were copied into an Excel document for analysis:
***3434 IDs conformed to the pattern "BP####"
***1 ID was unique: "BP3167.1"
***The other 11 IDs showed up as ORF

===.gdb Use in GenMAPP===


*By following the instructions in [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols Part 2 of the ''Vibrio cholerae'' Microarray Data Analysis] and looking at Brandon's Week 9 individual journal assignment, I was able to verify that our Gene Database works in GenMAPP.
*I was able to open the GenMAPP program on the computer, and then I went to Data -> Choose Gene Database -> and selected the cw20151119 gdb file.
**There were no problems thus far as our database was able to load into the program.

====Putting a gene on the MAPP using the GeneFinder window====

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I went through each of the five inconsistent Gene IDs in GeneFinder.

**I typed in the gene Id BP3167.1 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

*I typed in the gene Id BP1252 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system. This served as a "control" to look up a consistent Gene ID to compare to.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

***I typed in the gene Id BP0101A into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0101B into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0684A into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**When the gene was found this is the back page that popped up:

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0970A into the Gene ID field and selected "GeneID" for the Gene ID system.

**All of the expected cross-referenced IDs were present.

*Screenshot of all of the sample ID's on a MAPP:
*[[Genesonmap_cw20151203.png]]

====Expression Dataset and MAPPFinder Analysis====
*We do not have the expression dataset yet that is to be created by the GenMAPP Builders; they are still working on performing the corrections to the data that has been compiled into an excel spreadsheet.
*Once the file is complete, we will proceed with the data analysis using the desired programs.

=== Compare Gene Database to Outside Resource===
*We will complete this step after progressing further into the project.
The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.

[[Category: Class Whoopers]]

Gene Database Testing Report- cw20151203

2015-12-08T08:16:41Z

Msaeedi23: gene database testing report cw20151203

==Files Asked for in the Gene Database Testing Report==
For convenience, all of the files explicitly asked for in the sections below were compressed together in this file: [[]]

==Pre-requisites==
The following set of software was used in the creation and testing of the ''Bordetella pertussis'' gene database:

# [http://www.7-zip.org/ 7-zip]tool that for unpacking .gz and .zip files
# [http://www.postgresql.org PostgreSQL] on Windows (version 9.4.x)
# [https://sourceforge.net/projects/xmlpipedb/files/ GenMAPP Builder]
# Java JDK 1.8 64-bit
# [https://github.com/GenMAPPCS/genmapp GenMAPP 2]
# [https://sourceforge.net/projects/xmlpipedb/files/ XMLPipeDB match utility] for counting IDs in XML files
# Microsoft Access for reading .mdb files

==Gene Database Creation==
===Downloading Data Source Files and GenMAPP Builder===

*I download the UniProt XML, GOA, and GO OBO-XML files for ''Bordetella Pertussis'' along with the GenMAPP Builder program.
**All files were saved to the folder ''Bklein7_CW\bpertussis_cw20151203'' on my computer's ThawSpace.
**Files that required extraction were unzipped using [http://www.7-zip.org/ 7-zip].
**Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.

====UniProt XML====

* I went to the [http://www.uniprot.org/taxonomy/complete-proteomes UniProt Complete Proteomes] page.
**From there, I navigated to the complete proteome download page for [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)].
** I clicked on the "Download" button at the top of the page above and selected the following options:
***"Download all"
***"XML" from the "Format" drop-down menu
***"Compressed" format
**I extracted the file using [http://www.7-zip.org/ 7-zip].

====GOA====

* UniProt-GOA files can be downloaded from the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/ UniProt-GOA ftp site].
*Within the above site, I navigated to the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I].
**This text file was automatically opened by my browser. Therefore, I had to manually download the file.

====GO OBO-XML====

* I downloaded the GO OBO-XML formatted file from the [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page].
*I extracted the file using [http://www.7-zip.org/ 7-zip].

====Downloaded GenMAPP Builder====

# I downloaded the custom version of GenMAPP Builder including the ''Bordetella pertussis'' custom class expanded to include ORF listings in exports (Version 3.0.0 Build 5 - cw20151203): [[File:Dist cw20151203.zip]].
# I extracted the GenMAPP Builder folder using [http://www.7-zip.org/ 7-zip].

===Creating the New Database in PostgreSQL===

* I launched ''pgAdmin III'' and connected to the PostgreSQL 9.4 server (localhost:5432).
** On this server, I created a new database: ''bpertussis_cw20151201_gmb3build5''.
** I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
*** I clicked on the Open File icon and selected the file ''gmbuilder.sql''. This imported a series of SQL commands into the editor tab.
*** I clicked on the Execute Query icon to run this command.
***In viewing the schema for this database, I confirmed that there were 167 tables after running the above command.

===Configuring GenMAPP Builder to Connect to the PostgreSQL Database===

* To begin, I launched gmbuilder.bat.
* I selected the "Configure Database" option and entered the following information into the fields below:
** Host or address: localhost
** Port number: 5432
** Database name: bpertussis_cw20151201_gmb3build5
** Username: postgres
** Password: Welcome1

===Importing Data into the PostgreSQL Database===

*The downloaded data files for ''Bordetella pertussis'' were specified and imported into the database by clicking on the following buttons:
** Selected File > Import UniProt XML...
** Selected File > Import GO OBO-XML...
** Clicked OK to the message asking to process the GO data.
** Selected File > Import GOA...

===Exporting a GenMAPP Gene Database (.gdb)===

* I selected File > Export to GenMAPP Gene Database... to begin the export process.
* I typed my name in the owner field (Brandon Klein).
* I selected "Bordetella pertussis (strain Tohama I/ATCC BAA-589/NCTC 13251), Taxon ID 257313" as the gene database species and then clicked ''Next''.
* The database was saved as ''bpertussis-std_cw20151203''.
* I checked the boxes for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms.
* Finally, I clicked the "Next" button to begin the export process.

==Gene Database Testing Report==
===Export Information===

Version of GenMAPP Builder: Version 3.0.0 Build 5 - cw20151203

Computer on which export was run: Seaver 120- Last computer on the right in the row farthest from the front of the room

Postgres Database name: bpertussis_cw20151201_gmb3build5

UniProt XML filename: [[File:Uniprot-proteome-UP000002676 cw20151201.zip]]
* UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_11
* UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)]
* Time taken to import: 2.59 minutes
** Note: The import time was nearly equivalent to that when creating the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (2.60 minute). No interruptions occurred during this process.

GO OBO-XML filename: [[File:Go daily-termdb cw20151201.zip]]
* GO OBO-XML version (The version information was found in the file properties): Last Modified- ‎‎December ‎01, ‎2015, ‏‎2:21:31 AM
* GO OBO-XML download link: [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page]
* Time taken to import: 7.08 minutes
* Time taken to process: 4.42 minutes
** Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (6.99 minutes and 4.48 minutes respectively). No interruptions occurred during these processes.

GOA filename: [[File:145.B pertussis ATCC BAA-589 cw20151201.zip]]
* GOA version (found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): Last Modified- 11/10/15 1:39:00 PM
* GOA download link: [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I]
* Time taken to import: 0.04 minutes
** Note: The import time was equal to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb. No interruptions occurred during this process.

Name of .gdb file: [[File:Bpertussis-std cw20151203.zip]]
* Time taken to export:
** Start time: 4:02 PM
** End time: 4:56 PM
** Elapsed time: 54 minutes
Note: No interruptions occurred during the export process.

===TallyEngine===

* I ran the TallyEngine in GenMAPP Builder and specified the following files:
**XML- [[File:Uniprot-proteome-UP000002676 cw20151201.zip]]
**GO- [[File:Go daily-termdb cw20151201.zip]]
*Results:
**[[File: Tallyenginecustomization_cw20151203.png]]
**All tally results were consistent across both files.
=== Using XMLPipeDB match to Validate the XML Results from the TallyEngine===
The following functions were performed using the Windows command line (cmd).
*I entered my project folder using the following command:
cd /d T:\Bklein7_CW
*I used XMLPipeDB match to identify matches of any ordered locus name following the pattern "BP####" in the UniProt XML file. The command sequence used is as follows:\
java -jar xmlpipedb-match-1.1.1.jar "BP[0-9][0-9][0-9][0-9]" < "uniprot-proteome%3AUP000002676_cw20151201.xml"
*Match Results:
----------
*make note to ask dondi specific code to use to obtain 3446 match results

=== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine===
I ran a SQL query designed to match the pattern BP####:

select count (*) from genenametype where type = 'ordered locus' and value ~ 'BP[0-9][0-9][0-9][0-9]';

Results:
*[[File:Sqlcount_cw20151203.png]]
* The number of unique matches yielded by this SQL query, 3446.

===OriginalRowCounts Comparison===

I opened the gene database file [[File:Bpertussis-std_cw20151203.zip]] in Microsoft Access and assessed the "OriginalRowCounts" table to see if the expected tables were listed with the expected number of records. The contents of this table were compared to the ''OriginalRowCounts'' table of an existing .gdb file created during Week 9.

Benchmark .gdb file: ''Vc-Std_20151027_TR''

"OriginalRowCounts" table from the benchmark and new gdb:
*[[File:OriginalRowCountsComparison cw20151119.PNG]]
*All 52 tables present in the 2015 ''Vibrio cholerae'' database were also present in the ''B. pertussis'' database tagged _cw20151203. This confirmed that all expected tables were successfully created.
*Further, the "OrderedLocusNames" count produced by Tally Engine should hopefully represent this number.

Note: The "OriginalRowCounts" tables were too large to screenshot. To circumvent this problem and facilitate the comparison, I copied the "OriginalRowCounts" tables from both gene databases into an Excel file and zoomed out. The above screenshot was taken from this Excel file. The "OrderedLocusNames" row counts are highlighted in yellow.

===Visual Inspection===
I visually inspected individual tables within [[File:Bpertussis-std_cw20151203.zip]] using Microsoft Access.
*Systems Table
**35 gene ID systems were listed, 11 of which listed the appropriate import date (12/03/2015)
***All gene ID systems relevant to ''B. pertussis'' were listed. This includes: EMBL, EnsemblBacteria, GeneID, GeneOntology, InterPro, OrderedLocusNames, Pfam, RefSeq, and UniProt.
***This result corresponded with that of the benchmark .gdb file listed in the "OriginalRowCounts Comparison" section.
*UniProt Table
**This table contained 3258 entries with 6 character IDs.
**All ID's in the UniProt table conform to the following pattern: [[File:UniProt Ascension Number info.PNG]]

*RefSeq Table
**This table contained 6627 entries. All IDs began with one of three prefixes: "NP_", "YP_", or "WP_". The meanings of these prefixes can be found in the RefSeq documentation found [http://www.ncbi.nlm.nih.gov/books/NBK50679/ here].
***"NP_" and "YP_" Prefixes
****Refer to proteins. There are 3410 "NP_" IDs and 7 "YP_" IDs.
***"WP_" Prefixes
****Refer to "autonomous non-redundant proteins that are not yet directly annotated on a genome". There were 3210 IDs with the "WP_" prefixes.
***Overall, every entry in the ID column was an expected value.
*OrderedLocusNames Table
**This table contained 3446 entries (consistent with & SQL counts).
**The IDs were copied into an Excel document for analysis:
***3434 IDs conformed to the pattern "BP####"
***1 ID was unique: "BP3167.1"
***The other 11 IDs showed up as ORF

===.gdb Use in GenMAPP===


*By following the instructions in [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols Part 2 of the ''Vibrio cholerae'' Microarray Data Analysis] and looking at Brandon's Week 9 individual journal assignment, I was able to verify that our Gene Database works in GenMAPP.
*I was able to open the GenMAPP program on the computer, and then I went to Data -> Choose Gene Database -> and selected the cw20151119 gdb file.
**There were no problems thus far as our database was able to load into the program.

====Putting a gene on the MAPP using the GeneFinder window====

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I went through each of the five inconsistent Gene IDs in GeneFinder.

**I typed in the gene Id BP3167.1 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

*I typed in the gene Id BP1252 into the Gene ID field and selected "OrderedLocusName" for the Gene ID system. This served as a "control" to look up a consistent Gene ID to compare to.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

***I typed in the gene Id BP0101A into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
***I clicked on the Drafting Board to place the Gene on the MAPP.
***Then I right-clicked on the gene to access the GeneFinder window.

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0101B into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0684A into the Gene ID field and selected "OrderedLocusName" for the Gene ID system.
**When the gene was found this is the back page that popped up:

*In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.
**I clicked on the Drafting Board to place the Gene on the MAPP.
**Then I right-clicked on the gene to access the GeneFinder window.
**I typed in the gene Id BP0970A into the Gene ID field and selected "GeneID" for the Gene ID system.

**All of the expected cross-referenced IDs were present.

*Screenshot of all of the sample ID's on a MAPP:
*[[Genesonmap_cw20151203.png]]

====Expression Dataset and MAPPFinder Analysis====
*We do not have the expression dataset yet that is to be created by the GenMAPP Builders; they are still working on performing the corrections to the data that has been compiled into an excel spreadsheet.
*Once the file is complete, we will proceed with the data analysis using the desired programs.

=== Compare Gene Database to Outside Resource===
*We will complete this step after progressing further into the project.
The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.

[[Category: Class Whoopers]]

File:Genesonmap cw20151203.png

2015-12-08T08:16:11Z

Msaeedi23:

File:Bpertussis-std cw20151203.zip

2015-12-08T07:50:22Z

Msaeedi23: Msaeedi23 uploaded a new version of File:Bpertussis-std cw20151203.zip

.gdb file made using gmbuilder build cw20151203

File:Sqlcount cw20151203.png

2015-12-08T07:48:08Z

Msaeedi23:

File:Tallyenginecustomization cw20151203.png

2015-12-08T07:31:57Z

Msaeedi23:

Msaeedi23 Week 14

2015-12-08T07:00:43Z

Msaeedi23:

==Bordetella Pertussis Species Profile Customization==

===ID inconsistencies===

{{template: msaeedi23}}

Msaeedi23 Week 14

2015-12-08T06:59:25Z

Msaeedi23: Created page with "==Bordetella Pertussis Species Profile Customization== ===ID inconsistencies==="

==Bordetella Pertussis Species Profile Customization==

===ID inconsistencies===

The Class Whoopers

2015-12-08T06:53:15Z

Msaeedi23: /* Meetings! */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00
** Monday, December 7, 10:30 - 12 am

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-08T06:51:42Z

Msaeedi23: /* Week 14 */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week as Q and A I worked directly with Brandon to do the initial data exports. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species. Now I will focus on the tally configuration which may take some time and coding assistance from Brandon. Once the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-08T06:50:40Z

Msaeedi23: /* Progress */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week I focused on doing the tally configuration which took some time and assistance from Brandon. Now that the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance to accommodate the absence of Nicole.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-08T06:49:27Z

Msaeedi23: /* Progress */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):''' This week I focused on doing the tally configuration which took some time and assistance from Brandon. Now that the Tally Engine has been configured to our specific species, Lena can proceed with with GenMAPP processing.
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance. As Q and A I worked directly with Brandon to do the initial data exports. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-08T06:48:00Z

Msaeedi23: /* Progress */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==

===Goals===
* '''Assignment due date:''' Midnight Tuesday, December 8
* '''Coder:''' Create the custom species profile for ''Bordetella pertussis'', run an export using the customized version of GenMAPP Builder, add further customizations to the custom species profile as appear necessary, and run a second export using the further customized version of GenMAPP Builder.
* '''Quality Assurance:''' Identify gene IDs that are missing in the first custom export, work with the coder to classify these IDs, configure the Tally Engine, and complete a gene database testing report for the second custom export.
* '''GenMAPP User:''' Complete the statistical analysis of the data, format the data for import into GenMAPP, and coordinate with the coder/QA to import this data into GenMAPP using the custom gene database.

===Progress===
*'''Brandon (Coder and Project Manager):''' This week, I focused on creating and customizing the species profile for ''Bordetella pertussis'' in GenMAPP Builder, the details of which can be found in my [[Bklein7 Week 14| Week 14 Journal Entry]]. I documented the first export I conducted using a custom ''Bordetella pertussis'' species profile here: [[Gene Database Testing Report- cw20151201]]. I demonstrated that the custom species information implemented in this export worked as intended, but Mahrad and I identified 11 ORF genes that failed to export. I updated the ''Bordetella pertussis'' species profile to account for these ORF genes and conducted a new export, detailed here: [[Gene Database Testing Report- cw20151203]]. Mahrad analyzed the exported .gdb file. In addition to this, I kept tabs on my fellow group members to keep us on track to accomplish our long-term project goals in a timely manner.
** [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 13:39, 7 December 2015 (PST)
*'''Mahrad (Quality Assurance):'''
*'''Lena (GenMAPP User):''' This week, I made progress on performing the statistical analysis of the data to prepare it for GenMAPP. I was able to post my progress for each of the class working sessions on my [[Lenaolufson Week 14| Week 14 Journal Entry]] as I updated the excel data sheets after each session. Dr. Dahlquist helped me figure out a problem with the original raw data that was causing the values to be very skewed. I then sent her my updated data sheet and she was able to use a program to separate the duplicates of the chips. After she sent me back the data with the sorted values, I performed the statistical analysis on the data, the most updated version of the file can be found on my Week 14 journal entry linked previously.
[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 19:54, 7 December 2015 (PST)

===Meetings!===
*This week, our group used class work sessions to coordinate our work:
**Tuesday, December 1, 2:40 - 4:00
**Thursday, December 3, 2:40 - 4:00

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP--> Quality Assurance)''': Downloaded the six data sample files provided by the microarray paper. Files were unzipped, imported into excel, and manipulated to form a single spreadsheet containing all gene IDs from the different samples. Each sample was placed in its respective column to be further analyzed and manipulated in the upcoming week. Following this, I assumed the position of quality assurance. As Q and A I worked directly with Brandon to do the initial data exports. Next we meticulously characterized regular expression patterns to detect discrepancies in extracting the data from the original samples. In the following week I will work to do the tally configuration to customize it according to our specific species.
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-03T23:41:37Z

Msaeedi23:

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==
===Screenshots===
[[File: ORFissue_cw20151119.png]]
[[File: Systemstable_cw20151201.png]]
[[File: Oln-orfcounts_cw20151119.png]]
[[File: Bp3167issue_cw20151119.png]]
===Goals===
===Progress===
===Meetings!===

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP)''':
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

File:Bp3167issue cw20151119.png

2015-12-03T23:40:51Z

Msaeedi23:

The Class Whoopers

2015-12-03T23:40:36Z

Msaeedi23:

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==
===Screenshots===
[[File: ORFissue_cw20151119.png]]
[[File: Systemstable_cw20151201.png]]
[[File: Oln-orfcounts_cw20151119.png]]
===Goals===
===Progress===
===Meetings!===

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP)''':
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

File:Oln-orfcounts cw20151119.png

2015-12-03T23:39:51Z

Msaeedi23: Msaeedi23 uploaded a new version of File:Oln-orfcounts cw20151119.png

The Class Whoopers

2015-12-03T23:39:40Z

Msaeedi23:

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==
===Screenshots===
[[File: ORFissue_cw20151119.png]]
[[File: Systemstable_cw20151201.png]]
===Goals===
===Progress===
===Meetings!===

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP)''':
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

File:Systemstable cw20151201.png

2015-12-03T23:39:21Z

Msaeedi23: Msaeedi23 uploaded a new version of File:Systemstable cw20151201.png

cw20151201- systems table listing in microsoft access

The Class Whoopers

2015-12-03T23:38:55Z

Msaeedi23: /* Screenshots */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==
===Screenshots===
[[File: ORFissue_cw20151119.png]]

===Goals===
===Progress===
===Meetings!===

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP)''':
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

The Class Whoopers

2015-12-03T23:38:55Z

Msaeedi23: /* Screenshots */

File:ORFissue cw20151119.png

2015-12-03T23:38:32Z

Msaeedi23:

The Class Whoopers

2015-12-03T23:38:16Z

Msaeedi23: /* Week 14 */

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 14==
===Screenshots===
[[File: ORFissue_cw20151119.png]]
===Goals===
===Progress===
===Meetings!===

==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| 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 [[Bklein7 Week 12| Week 12 Page]]. Finally, I wrote a PowerPoint presentation on our genome sequencing paper, which is linked to on my [[Bklein7 Week 12| Week 12 Page]] as well.
**[[User:Bklein7|Bklein7]] ([[User talk: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. [[File:Bpertussis CompiledRawData MS2015.xlsx]]
**[[User:Lenaolufson|Lenaolufson]] ([[User talk:Lenaolufson|talk]]) 17:33, 23 November 2015 (PST)
*'''Mahrad (GenMAPP)''':
* '''Nicole''' was absent this week. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Bklein7|Bklein7]] ([[User talk:Bklein7|talk]]) 23:14, 16 November 2015 (PST)
*Brandon Klein (QA): This week I made several edits to the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers Class Whoopers Team Page] in accordance with the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Week_11 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 [http://www.genedb.org/Homepage/Bpertussis GeneDB MOD] on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Bklein7_Week_11#Identifying_the_Bordetella_Pertussis_MOD 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. [[User:Bklein7|Bklein7]] ([[User talk: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. [[User:Lenaolufson|Lenaolufson]] ([[User talk: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.
[[User:Msaeedi23|Msaeedi23]] ([[User talk: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:
#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.
#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 [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html 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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 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: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

File:Oln-orfcounts cw20151119.png

2015-12-03T23:36:46Z

Msaeedi23:

Msaeedi23 Week 12

2015-12-03T22:33:22Z

Msaeedi23:

*Link to team page: https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers
=Week 12=
*This week there were no specific tasks that were required to be completed; we kept working on the team projects and what each specific role should be doing.
*After analyzing the microarray paper last week, Lena and I were then started analyzing the data.
==GenMAPP User==
===Locating the Sample Data===
*The first step in the data retrieval was to locate the sample files that needed to be downloaded from the microarray paper site, found at: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088].
**Dr. Dahlquist assisted us in choosing which files to download as well as how to prepare them for Excel.
**All of the six sample files were downloaded and saved to the computer.
*Each of the files were unzipped once, and then unzipped again in order to access them in a suitable manner for the assignment, to be opened in Exel.
**Once all six of the files were unzipped, I opened each of them in Excel in order to get the data in the column spreadsheet form.
===Working in Excel===
*I created a new workbook that would contain the final compressed data that is to be eventually exported as one file.
**After opening each of the sample files in Excel, I copied the list of Gene IDs from one of the samples and pasted it into the new workbook I started.
**Now that the Gene ID column was formed, I was then started pasting the desired data columns in from each of the different samples.
**From each of the six samples, I copied and pasted the "Log Ratio" column into my new workbook and titled each of the columns so that they represented the appropriate samples in an orderly fashion.
*Our next task is to perform the correct data manipulations and corrections in order to make the data file ready to be exported for testing and analysis.
**Lena and I completed these construction steps side-by-side and we plan on continuing the Excel work together in order to check our work.
*The current Excel data worksheet we have constructed: [[File:Bpertussis CompiledRawData MS2015.xlsx]]

==Change of Duties==
As of now I am no longer a GenMAPP user and will take over the roll of Quality Assurance and work directly with Brandon. I will still be assisting Lena with data configuration as she needs help.

{{msaeedi23}}
[[Category:Assignment]]
[[Category:Group Projects]]