Team H(oo)KD Week 13 Status Report - Revision history

Ksherbina: /* Reflection */ Added signature

2013-11-22T08:00:24Z

‎Reflection: Added signature

HDelgadi: /* Quality Assurance Status Update */ adding bullet points

2013-11-22T08:00:12Z

‎Quality Assurance Status Update: adding bullet points

Ksherbina: /* Reflection */ Finished questions

2013-11-22T08:00:12Z

‎Reflection: Finished questions

HDelgadi: /* Quality Assurance Status Update */ updating the status report

2013-11-22T07:59:37Z

‎Quality Assurance Status Update: updating the status report

Ksherbina: /* Reflection */ Answered reflection question 1-2

2013-11-22T07:56:19Z

‎Reflection: Answered reflection question 1-2

Ksherbina: /* Reflection */ Copied the list of reflection questions.

2013-11-22T07:47:50Z

‎Reflection: Copied the list of reflection questions.

Ksherbina: /* Coder Status Update */ Added signature

2013-11-22T07:44:28Z

‎Coder Status Update: Added signature

Ksherbina: Added a description of where to find the milestones. Italicized all occurrences of C. trachomatis.

2013-11-22T07:44:07Z

Added a description of where to find the milestones. Italicized all occurrences of C. trachomatis.

Ksherbina: /* Coder Status Update */ Recorded a summary of some of the major accomplishments this week on the coding front

2013-11-22T07:42:35Z

‎Coder Status Update: Recorded a summary of some of the major accomplishments this week on the coding front

HDelgadi: /* Reflection */ added signature

2013-11-22T07:40:18Z

‎Reflection: added signature

@@ Line 31: / Line 31: @@
 #What team weaknesses were seen this week?
 #*Unlike last week, we were not able to meet as a whole group this week outside of class time to check up on our progress and work out some of the difficulties that we were having with some tasks.
 ==Quality Assurance Status Update==

@@ Line 33: / Line 33: @@
 ==Quality Assurance Status Update==
-:The coder, Katrina, and I have completed a full import and export cycle. We were able to look at the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access in order to check our gene ID counts on Katrina's laptop. Fortunately, our numbers matched for the Tally Engine which assured us that our export of our database was essentially successful. The XMLPipeDB Match gave us 911 total unique matches, while in the SQL query the count was 917 and in ACCESS there were 919 unique gene ID matches. Therefore, there is certainly a discrepancy with the SQL query and the Tally Engine in which 917 gene IDs are being found, but are not adding up with the amount found in ACCESS and XMLPipeDB Match. We will look into the discrepancies next week.
+*The coder, Katrina, and I have completed a full import and export cycle. We were able to look at the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access in order to check our gene ID counts on Katrina's laptop. Fortunately, our numbers matched for the Tally Engine which assured us that our export of our database was essentially successful. The XMLPipeDB Match gave us 911 total unique matches, while in the SQL query the count was 917 and in ACCESS there were 919 unique gene ID matches. Therefore, there is certainly a discrepancy with the SQL query and the Tally Engine in which 917 gene IDs are being found, but are not adding up with the amount found in ACCESS and XMLPipeDB Match. We will look into the discrepancies next week.
 ===Reflection===
 #What were the week’s key accomplishments?

@@ Line 27: / Line 27: @@
 #*In addition, we want to try running GenMAPP using the microarray data (or at least a dummy fie with the gene IDs from the data and some fake values) with the latest version of the gene database.
 #What team strengths were seen this week?
 #What team weaknesses were seen this week?
 ==Quality Assurance Status Update==

@@ Line 30: / Line 30: @@
 ==Quality Assurance Status Update==
-:The coder, Katrina, and I have completed a full import and export cycle.
+:The coder, Katrina, and I have completed a full import and export cycle. We were able to look at the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access in order to check our gene ID counts on Katrina's laptop. Fortunately, our numbers matched for the Tally Engine which assured us that our export of our database was essentially successful. The XMLPipeDB Match gave us 911 total unique matches, while in the SQL query the count was 917 and in ACCESS there were 919 unique gene ID matches. Therefore, there is certainly a discrepancy with the SQL query and the Tally Engine in which 917 gene IDs are being found, but are not adding up with the amount found in ACCESS and XMLPipeDB Match. We will look into the discrepancies next week.
 ===Reflection===
 #What were the week’s key accomplishments?

@@ Line 21: / Line 21: @@
 #What were the week’s key accomplishments?
 #What are next week’s target accomplishments?
 #What team strengths were seen this week?
 #What team weaknesses were seen this week?

← Older revision		Revision as of 07:47, 22 November 2013
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	===Reflection===		===Reflection===
		+
		+	#What were the week’s key accomplishments?
		+	#What are next week’s target accomplishments?
		+	#What team strengths were seen this week?
		+	#What team weaknesses were seen this week?

	==Quality Assurance Status Update==		==Quality Assurance Status Update==

@@ Line 15: / Line 15: @@
 :*Next week, we may need to consult with Dr. Dahlquist regarding what may be causing this discrepancy in the gene counts.
 :*The plan then for next week is to try to run GenMAPP with the microarray data (or at least a dummy file with the gene IDs from the data and some fake numbers) and the new gene database.
 ===Reflection===

@@ Line 1: / Line 1: @@
 {{Team H(oo)KD}}
 ==Coder Status Update==
@@ Line 7: / Line 9: @@
 *Tally Engine did not produce the same counts for the UniProt file and the OBO-XML file for this first exported database. We believe that this is a result of duplicate entries being formed when I imported the UniProt, OBO-XML, and GOA files multiple times when I was working out the heap space error.
 *A new database was created in pgAdminIII and a new import/export cycle in 32-bit gmbuilder was performed with this new database.
-*Hilda and I were able to find the gene link pattern, which I was able to add to the custom species profile for C. trachomatis. With this final edit, I was able to build a new version of gmbuilder.
+*Hilda and I were able to find the gene link pattern, which I was able to add to the custom species profile for ''C. trachomatis''. With this final edit, I was able to build a new version of gmbuilder.
 *Using the new build, I exported a new gene database.
-*Hilda and I then performed quality assurance testing with the newest version of the C. trachomatis gene database. In so doing, we found that two genes were counted in Access and xmlpipedb match that were not counted by TallyEngine and pgAdminIII.
+*Hilda and I then performed quality assurance testing with the newest version of the ''C. trachomatis'' gene database. In so doing, we found that two genes were counted in Access and xmlpipedb match that were not counted by TallyEngine and pgAdminIII.
 :*In addition, Hilda and I also found in using xmlpipedb match that some of the genes have the gene ID pCTA_#### rather than CTA_####.
 :*Next week, we may need to consult with Dr. Dahlquist regarding what may be causing this discrepancy in the gene counts.

← Older revision		Revision as of 07:42, 22 November 2013
Line 2:		Line 2:

	==Coder Status Update==		==Coder Status Update==
		+
		+	*When first performing an import/export cycle for the gene database, I ran into Java heap space errors, which I tried to reconcile by manually increasing the maximum heap space allocated for gmbuilder. Through this process, I found that 32-bit gmbuilder has a limit for what the maximum heap space can be set to.
		+	*For the first import/export cycle, I imported the files into the database created in pgAdminIII using 64-bit gmbuilder with increased maximum heap space and performed the export in 32-bit gmbuilder without changing the heap space.
		+	*Tally Engine did not produce the same counts for the UniProt file and the OBO-XML file for this first exported database. We believe that this is a result of duplicate entries being formed when I imported the UniProt, OBO-XML, and GOA files multiple times when I was working out the heap space error.
		+	*A new database was created in pgAdminIII and a new import/export cycle in 32-bit gmbuilder was performed with this new database.
		+	*Hilda and I were able to find the gene link pattern, which I was able to add to the custom species profile for C. trachomatis. With this final edit, I was able to build a new version of gmbuilder.
		+	*Using the new build, I exported a new gene database.
		+	*Hilda and I then performed quality assurance testing with the newest version of the C. trachomatis gene database. In so doing, we found that two genes were counted in Access and xmlpipedb match that were not counted by TallyEngine and pgAdminIII.
		+	:*In addition, Hilda and I also found in using xmlpipedb match that some of the genes have the gene ID pCTA_#### rather than CTA_####.
		+	:*Next week, we may need to consult with Dr. Dahlquist regarding what may be causing this discrepancy in the gene counts.
		+	:*The plan then for next week is to try to run GenMAPP with the microarray data (or at least a dummy file with the gene IDs from the data and some fake numbers) and the new gene database.

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

@@ Line 16: / Line 16: @@
 #What team weaknesses were seen this week?
 #*The team did not really meet all together in a group due to our conflicting class schedule, but Katrina was able to meet with both Dillon and I independently and fill us in as to what was discussed in the previous meeting.
 ==GenMAPP User Status Update==