Team H(oo)KD Week 15 Status Report - Revision history

Dwilliams: /* Reflection */ Formatting

2013-12-06T08:41:51Z

‎Reflection: Formatting

2013-12-06T08:41:14Z

‎Reflection

2013-12-06T08:40:55Z

‎GenMAPP User Status Report: Added GenMAPP

2013-12-06T08:05:50Z

‎Quality Assurance Status Report

2013-12-06T08:05:36Z

‎Quality Assurance Status Report: updating the status report for week 15

2013-12-06T07:02:04Z

‎Reflection: Finished reflection

2013-12-06T06:56:14Z

‎Coder Status Report: Started reflection

2013-12-06T06:42:23Z

Added statement regarding where to find the milestones

2013-12-06T06:41:54Z

‎Coder Status Report: Finished status report

2013-12-06T06:40:22Z

‎Coder Status Report: Began status report

@@ Line 45: / Line 45: @@
 #) There wasn't anything that didn't work per se, although we did not get as much done as we were hoping for, we are going to continue working on the project over the course of the weekend.
 #) Next week we will really be focusing our time and energy into ensuring that everything is done correctly and that the paper is done as well as possible. I personally, will also contribute time to cleaning up my electronic lab notebook, streamlining some of the steps and making the page itself more readable (I have already begun to improve some of the formatting on my page). Ultimately, next week will consist of tying off any loose ends and ensuring that everything is running how it should be running.
--[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 00:41, 6 December 2013 (PST)
+-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 22:07, 5 December 2013 (PST)

@@ Line 45: / Line 45: @@
 #) There wasn't anything that didn't work per se, although we did not get as much done as we were hoping for, we are going to continue working on the project over the course of the weekend.
 #) Next week we will really be focusing our time and energy into ensuring that everything is done correctly and that the paper is done as well as possible. I personally, will also contribute time to cleaning up my electronic lab notebook, streamlining some of the steps and making the page itself more readable (I have already begun to improve some of the formatting on my page). Ultimately, next week will consist of tying off any loose ends and ensuring that everything is running how it should be running.
--[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]])
+-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 00:41, 6 December 2013 (PST)

@@ Line 35: / Line 35: @@
 ==GenMAPP User Status Report==
+This week, after fixing the initial issues that we had with running the statistics on the C. trachomatis raw data, I was able to create the final excel spreadsheet that was to be used in GenMAPP. With the help of the coder and QA in formatting the gene ID's for the "for GenMAPP" sheet in the excel master spreadhseet, I was able to create a sheet with all of the information necessary to run the data in GenMAPP.
 ===Reflection===

@@ Line 31: / Line 31: @@
 #What will I do next to fix what didn't work?
 #:We have resolved the problems we faced, so we will make sure to begin the paper as soon as possible (by Saturday) and if there are any questions we will contact Dr. Dionisio and Dr. Dahlquist immediately.
 ==GenMAPP User Status Report==
 ===Reflection===

@@ Line 22: / Line 22: @@
 ==Quality Assurance Status Report==
 ===Reflection===
 ==GenMAPP User Status Report==
 ===Reflection===

@@ Line 17: / Line 17: @@
 #The Quality Assurance person (Hilda) and I were able to finish working on the gene database and figuring out how to separate the gene IDs from the Affymetrix IDs appened to the gene IDs in the microarray data. This allowed as to devote the rest of our time to working with Dillon to perform the GenMAPP and MAPPFinder analysis. Lucky for us, no exceptions file was generated when running GenMAPP with the microarray data with the modified IDs and the gene database for ''C. trachomatis''.
 #When we originally set the milestones, we had planned to start working on both the paper and the presentation this week. Unfortunately, we had not advanced far enough in finalizing the database and performing GenMAPP analysis at the beginning of the week to be able to do this.
 ==Quality Assurance Status Report==

← Older revision		Revision as of 06:56, 6 December 2013
Line 14:		Line 14:

	===Reflection===		===Reflection===
		+
		+	#The Quality Assurance person (Hilda) and I were able to finish working on the gene database and figuring out how to separate the gene IDs from the Affymetrix IDs appened to the gene IDs in the microarray data. This allowed as to devote the rest of our time to working with Dillon to perform the GenMAPP and MAPPFinder analysis. Lucky for us, no exceptions file was generated when running GenMAPP with the microarray data with the modified IDs and the gene database for ''C. trachomatis''.
		+	#When we originally set the milestones, we had planned to start working on both the paper and the presentation this week. Unfortunately, we had not advanced far enough in finalizing the database and performing GenMAPP analysis at the beginning of the week to be able to do this.

	==Quality Assurance Status Report==		==Quality Assurance Status Report==

← Older revision		Revision as of 06:42, 6 December 2013
Line 1:		Line 1:
	{{Team H(oo)KD}}		{{Team H(oo)KD}}
		+
		+	'''Refer to the calendar on the team home page to see the milestones for this week.'''

	==Coder Status Report==		==Coder Status Report==

@@ Line 3: / Line 3: @@
 ==Coder Status Report==
-*Determined why TallyEngine counted 917 genes in the gene database for ''C.trachomatis'' while the count was 919 when viewing the gene database in Access.
+The following was accomplished during Weeks 14-15:
 :*Apparently, one ordered locus ID (CTA_0406/CTA_0407/CTA_0408) is actually a combination of three ordered locus IDs each of which were predicted to correspond to a different gene before it was found that all three IDs actually correspond to the same gene. TallyEngine does not separate the ordered locus IDs while Access does.
 :*In consulting with Dr. Dahlquist and Dr. Dionisio, we decided to leave this as is and describe the discrepancy in the final testing report, which is recorded in my [[Ksherbina Project Notebook|project journal]] under November 27-28, 2013.
 ===Reflection===

← Older revision		Revision as of 06:40, 6 December 2013
Line 2:		Line 2:

	==Coder Status Report==		==Coder Status Report==
		+
		+	*Determined why TallyEngine counted 917 genes in the gene database for ''C.trachomatis'' while the count was 919 when viewing the gene database in Access.
		+	:*Apparently, one ordered locus ID (CTA_0406/CTA_0407/CTA_0408) is actually a combination of three ordered locus IDs each of which were predicted to correspond to a different gene before it was found that all three IDs actually correspond to the same gene. TallyEngine does not separate the ordered locus IDs while Access does.
		+	:*In consulting with Dr. Dahlquist and Dr. Dionisio, we decided to leave this as is and describe the discrepancy in the final testing report, which is recorded in my [[Ksherbina Project Notebook\|project journal]] under November 27-28, 2013.

	===Reflection===		===Reflection===