The Class Whoopers - Revision history

Lenaolufson: /* Week 14 */ added my week 14 answers to the questions

2015-12-22T18:03:01Z

‎Week 14: added my week 14 answers to the questions

Bklein7: added specific reflection questions and responses that we overlooked

2015-12-21T18:59:51Z

added specific reflection questions and responses that we overlooked

Msaeedi23: /* Week 14 */

2015-12-21T07:08:05Z

‎Week 14

Msaeedi23: /* Week 15 */

2015-12-21T06:49:00Z

‎Week 15

Msaeedi23: /* Week 12 */

2015-12-21T06:47:33Z

‎Week 12

Msaeedi23: /* Week 11 */

2015-12-21T06:46:43Z

‎Week 11

Bklein7: made change to invoke new template

2015-12-18T19:30:23Z

made change to invoke new template

@@ Line 77: / Line 77: @@
 #*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)

@@ Line 60: / Line 60: @@
 **'''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'''
+*'''Progress & Reflection'''
 **'''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:

@@ Line 63: / Line 63: @@
 **'''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.
+**'''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:
 **'''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)

@@ Line 41: / Line 41: @@
 **'''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.
+**'''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.

@@ Line 85: / Line 85: @@
 **'''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.
+**'''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)

@@ Line 108: / Line 108: @@
 **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.
+**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)

@@ Line 32: / Line 32: @@
 =Weekly Updates=
 ==Week 15==
 *'''Goals'''
 **'''Assignment due date:''' Midnight Tuesday, December 15