LMU BioDB 2013 - User contributions [en]

Template:HDelgadi

2013-12-06T08:11:04Z

HDelgadi:

[[Class Journal Week 1]]

[[Week 1]]

[[Class Journal Week 2]]

[[Week 2]]

[[HDelgadi Week 2]]

[[Class Journal Week 3]]

[[HDelgadi Week 3]]

[[Week 4]]

[[Class Journal Week 4]]

[[HDelgadi Week 4]]

[[Week 5]]

[[HDelgadi Week 5]]

[[Class Journal Week 5]]

* Link: [[http://www.violinet.org/protegen/ Protegen]]

* [[Protegen]]

[[Week 6]]

[[HDelgadi Week 6]]

[[Class Journal Week 6]]

[[Week 7]]

[[HDelgadi Week 7]]

[[Class Journal Week 7]]

[[Week 8]]

[[HDelgadi Week 8]]

[[Class Journal Week 8]]

[[Week 9]]

[[HDelgadi Week 9]]

[[Class Journal Week 9]]

[[Week 10]]

[[HDelgadi Week 10]]

[[Week 11]]

[[Chlamydia trachomatis | Team H(oo)KD]]

[[HDelgadi Week 11]]

*[[Media: Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf]]

[[HDelgadi Project Notebook]]

[[Team H(oo)KD Week 12 Status Report| Week 12 Status Report]]

[[Team H(oo)KD Week 13 Status Report| Week 13 Status Report]]

[[Team H(oo)KD Week 15 Status Report| Week 15 Status Report]]

[[Category:Journal Entry]]

[[Category:Shared]]

[[Category: Group Projects]]

[[Category: Team H(oo)KD]]

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

Template:HDelgadi

2013-12-06T08:10:52Z

HDelgadi: adding week 12, 13, and 15 week status report under revised name that will actually link the pages to template

[[Class Journal Week 1]]

[[Week 1]]

[[Class Journal Week 2]]

[[Week 2]]

[[HDelgadi Week 2]]

[[Class Journal Week 3]]

[[HDelgadi Week 3]]

[[Week 4]]

[[Class Journal Week 4]]

[[HDelgadi Week 4]]

[[Week 5]]

[[HDelgadi Week 5]]

[[Class Journal Week 5]]

* Link: [[http://www.violinet.org/protegen/ Protegen]]

* [[Protegen]]

[[Week 6]]

[[HDelgadi Week 6]]

[[Class Journal Week 6]]

[[Week 7]]

[[HDelgadi Week 7]]

[[Class Journal Week 7]]

[[Week 8]]

[[HDelgadi Week 8]]

[[Class Journal Week 8]]

[[Week 9]]

[[HDelgadi Week 9]]

[[Class Journal Week 9]]

[[Week 10]]

[[HDelgadi Week 10]]

[[Week 11]]

[[Chlamydia trachomatis | Team H(oo)KD]]

[[HDelgadi Week 11]]

*[[Media: Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf]]

[[HDelgadi Project Notebook]]

[[Team H(oo)KD Week 12 Status Report| Week 12 Status Report]]

[[Team H(oo)KD Week 13 Status Report| Week 13 Status Report]]

[[Team H(oo)KD Week 15 Status Report| Week 15 Status Report

[[Category:Journal Entry]]

[[Category:Shared]]

[[Category: Group Projects]]

[[Category: Team H(oo)KD]]

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

HDelgadi Project Notebook

2013-12-06T08:07:21Z

HDelgadi: added signature

===HDelgadi Weeks 12,13,14===
'''''Week 12'''''
*GO OBO-XML file for C. trachomatis serovar A.
:I clicked on [[Week 9]] and secondly clicked on the link [[Running_GenMAPP_Builder | Perform an export of the ''Vibrio cholerae'' GenMAPP Gene Database following the instructions on this page.]] which is below the subheading '''Exporting a Vibrio cholerae Gene Database'''. I then clicked on 'obo-xml.gz' and the downloading box popped up, so I clicked on Save File and OK. I then opened the file, dragged it to the Desktop, and used the 7-Zip File Manager to unzip the file. I was able to extract the file 'go_daily-termdb_v1_HD_20131107.obo-xml', but I was only able to post the zipped file,[[Media: Go daily-termdb.obo-xml v1 HD 20131107.gz]], on the [[Chlamydia trachomatis | Team H(oo)KD]] page.

'''Reflection'''
#What were the week’s key accomplishments?
#*This week's key accomplishments included uploading the respective files such as GO OBO-XML file, UniProt XML, and GOA file for C. trachomatis serovar A. We also focused on how to acquire our micro-array data and how to download the particular software to help with identifying our micro-array data from our particularly different micro-array chip.
#What are next week’s target accomplishments?
#*We are targeting our completion in formatting our micro-array information and focusing on starting our statistical analysis.
#What team strengths were seen this week?
#*We were able to assign our individual tasks efficiently.
#What team weaknesses were seen this week?
#*Some of our schedules didn't coincide too well, but we still managed to meet and work effectively.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:18, 14 November 2013 (PST)

'''''Week 13'''''
*'''bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Gene/Summary?g=~ (Gene Database Link Pattern)'''
:I went to the Model Organism Database, EnsemblGenome which can be found through this link, http://bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Info/Index. I then clicked on the Chromosome:592980-593522 which takes me to the genes of the
:Chlamydia trachomatis A/HAR-13. I clicked on the gene ID CTA_0588 which brought me to this webpage http://bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Gene/Summary?g=CTA_0588;r=Chromosome:608460-608543;t=CTA_0588, with further description of this gene. :I replaced the gene ID in bold within this URL, http://bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Gene/Summary?g='''CTA_0588''';r=Chromosome:608460-608543;t=CTA_0588, with CTA_0578. This new URL was able to take me to the webpage particularly for this new gene CTA_0588. Hence, this URL serves as the gene database link pattern.
:'''NOTE'''- I tried the import and export cycle, but unfortunately, the tally engine results did not match and were completely off. I will attempt a second import and export cycle in the coming week, but with the new gmbuilder that Dr. Dionisio and Katrina have created. I hope to get accurate results in my second attempt of the import and export cycle.

'''Reflection'''
#What were the week’s key accomplishments?
#*Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
#What are next week’s target accomplishments?
#*We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
#What team strengths were seen this week?
#*The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
#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.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:45, 19 November 2013 (PST)

'''''Week 14'''''
*I did the import and export cycle with the updated version of gmbuilder-32bit.bat that Dr. Dionisio and Katrina worked on. This new import and export cycle was successful since the Tally Engine gave me the same numbers for both the XML and Database Count.
==Export Information==
Version of GenMAPP Builder:
2.0b71
Computer on which export was run:
Personal Laptop
Postgres Database name:
Chlamydiaimport2
UniProt XML filename:
uniprot-organism%3A315277+keyword%3A181_v1_HD_20131120
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]):
* Time taken to import:
1.24 Minutes
GO OBO-XML filename: go_daily-termdb_v1_HD_20131107.obo-xml
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped):
* Time taken to import: 16.41
* Time taken to process: 16.05
GOA filename: 22183.C_trachomatis_A_v1_HD_20131120.goa
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]):
* Time taken to import: 0.05 minutes
<nowiki>Insert non-formatted text here</nowiki>
Name of .gdb file: C-Std_20131124_HD_24112013
* Time taken to export .gdb: About 1 hour and 20 minutes
* Upload your file and link to it here.
[[Media:C-Std 20131124 HD 24112013.gdb]]

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 23:15, 5 December 2013 (PST)

'''''Week 15'''''

*I looked at separating the IDs, so that we may use them to provide a statistical analysis of the microarray data. I was able to work on separating these genes with Katrina's advice. Hence, in Excel, I made sure to add two columns (Columns B and C). Then, I made sure to highlight the gene IDs (CTA_####... AND pCTA_####...) from the first column. I clicked on 'Data' at the top and "Fixed width", pressed 'Next', moved the cursor to where it was necessary (before the second underscore). I erased what was next to the 'Destination' box and clicked on the arrow next to the empty box so that I may highlight the gene IDs (CTA_####... AND pCTA_####...) from the first column. Then, I would make sure to highlight the second portion of the gene ID that I wanted to separate from the first main portion (from the second underscore to the very end of the gene ID). I went to the 'Destination' box and erased what was on there. I then pressed on the arrow and highlighted the second column (column B) next to the original gene IDs. I clicked the arrow again next to the 'Destination' box and pressed 'Finish'. This process resulted in the separation of the gene IDs. from CTA_###_RRMH#####_... to CTA_#### AND _RRMH#####_... in separate columns. This information is of course useful to begin the statistical analysis of the microarray data to further input this data into GenMAPP.

*Katrina and I were able to look at the relational database schema that I need to make sure to create and were able to find a free trial of adobe illustrator, so that I may have access to "Access" and create the schema. I will work on this by Saturday.

'''Reflection'''
#What worked?
#:Our schedules were able to match much better this week, so we were all able to meet without any problems.
#What didn't work?
#:We had hoped to start on the paper this week, but unfortunately we faced difficulties with the microarray data and gmbuilder, so we were not able to get far enough in the process to run GenMAPP earlier in the week.
#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.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 00:07, 6 December 2013 (PST)

{{HDelgadi}}

Team H(oo)KD Week 15 Status Report

2013-12-06T08:05:50Z

HDelgadi: /* Quality Assurance Status Report */

{{Team H(oo)KD}}

'''Refer to the calendar on the team home page to see the milestones for this week.'''

==Coder Status Report==

The following was accomplished during Weeks 14-15:
*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.
*Customized the Tally Engine for ''C. trachomatis'' and committed the changes to SourceForge.

[[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 22:41, 5 December 2013 (PST)

===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.
#With next week being finals week, we will have several meetings leading up to the final presentation in order to work on the paper, the presentation, and deliverables to make sure we meet the final deadline.

[[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:02, 5 December 2013 (PST)

==Quality Assurance Status Report==
Katrina, the Coder, and I were able to work on separating the gene IDs so that statistical analysis could be performed by Dillon, the GenMAPP User, along with including this information into GenMAPP. The process of separating the IDs were tricky, but with Katrina's advice and some google searches I was able to manage separating the IDs, although I must admit it took Katrina 5 minutes to separate the IDs whereas it took me about close to an hour to figure out how to maneuver my way into figuring out how to go about this process. In any case, once this was done, Dillon (GenMAPP User) was able to generate the statistical analysis and the three of us proceeded to applying the data into GenMAPP. Luckily, we did not receive any errors throughout this transition to GenMAPP, so an exceptions file did not need to be generated. Moreover, we are now able to proceed with the project, so we will meet and start on our paper by Saturday. I will also proceed to complete the relational database schema for the gene database by Saturday. Katrina and I looked at the schema today and asked Dr. Dionisio questions about the schema to make sure we understood its format.

===Reflection===
#What worked?
#:Our schedules were able to match much better this week, so we were all able to meet without any problems.
#What didn't work?
#:We had hoped to start on the paper this week, but unfortunately we faced difficulties with the microarray data and gmbuilder, so we were not able to get far enough in the process to run GenMAPP earlier in the week.
#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.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 00:05, 6 December 2013 (PST)

==GenMAPP User Status Report==

===Reflection===

Team H(oo)KD Week 15 Status Report

2013-12-06T08:05:36Z

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

HDelgadi Project Notebook

2013-12-06T07:54:03Z

HDelgadi: added weekly update

HDelgadi Project Notebook

2013-12-06T07:15:34Z

HDelgadi: finished reflection portion

===HDelgadi Weeks 12,13,14===
'''''Week 12'''''
*GO OBO-XML file for C. trachomatis serovar A.
:I clicked on [[Week 9]] and secondly clicked on the link [[Running_GenMAPP_Builder | Perform an export of the ''Vibrio cholerae'' GenMAPP Gene Database following the instructions on this page.]] which is below the subheading '''Exporting a Vibrio cholerae Gene Database'''. I then clicked on 'obo-xml.gz' and the downloading box popped up, so I clicked on Save File and OK. I then opened the file, dragged it to the Desktop, and used the 7-Zip File Manager to unzip the file. I was able to extract the file 'go_daily-termdb_v1_HD_20131107.obo-xml', but I was only able to post the zipped file,[[Media: Go daily-termdb.obo-xml v1 HD 20131107.gz]], on the [[Chlamydia trachomatis | Team H(oo)KD]] page.

'''Reflection'''
#What were the week’s key accomplishments?
#*This week's key accomplishments included uploading the respective files such as GO OBO-XML file, UniProt XML, and GOA file for C. trachomatis serovar A. We also focused on how to acquire our micro-array data and how to download the particular software to help with identifying our micro-array data from our particularly different micro-array chip.
#What are next week’s target accomplishments?
#*We are targeting our completion in formatting our micro-array information and focusing on starting our statistical analysis.
#What team strengths were seen this week?
#*We were able to assign our individual tasks efficiently.
#What team weaknesses were seen this week?
#*Some of our schedules didn't coincide too well, but we still managed to meet and work effectively.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:18, 14 November 2013 (PST)

'''''Week 13'''''
*'''bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Gene/Summary?g=~ (Gene Database Link Pattern)'''
:I went to the Model Organism Database, EnsemblGenome which can be found through this link, http://bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Info/Index. I then clicked on the Chromosome:592980-593522 which takes me to the genes of the
:Chlamydia trachomatis A/HAR-13. I clicked on the gene ID CTA_0588 which brought me to this webpage http://bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Gene/Summary?g=CTA_0588;r=Chromosome:608460-608543;t=CTA_0588, with further description of this gene. :I replaced the gene ID in bold within this URL, http://bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Gene/Summary?g='''CTA_0588''';r=Chromosome:608460-608543;t=CTA_0588, with CTA_0578. This new URL was able to take me to the webpage particularly for this new gene CTA_0588. Hence, this URL serves as the gene database link pattern.
:'''NOTE'''- I tried the import and export cycle, but unfortunately, the tally engine results did not match and were completely off. I will attempt a second import and export cycle in the coming week, but with the new gmbuilder that Dr. Dionisio and Katrina have created. I hope to get accurate results in my second attempt of the import and export cycle.

'''Reflection'''
#What were the week’s key accomplishments?
#*Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
#What are next week’s target accomplishments?
#*We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
#What team strengths were seen this week?
#*The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
#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.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:45, 19 November 2013 (PST)

'''''Week 14'''''
*I did the import and export cycle with the updated version of gmbuilder-32bit.bat that Dr. Dionisio and Katrina worked on. This new import and export cycle was successful since the Tally Engine gave me the same numbers for both the XML and Database Count.
==Export Information==
Version of GenMAPP Builder:
2.0b71
Computer on which export was run:
Personal Laptop
Postgres Database name:
Chlamydiaimport2
UniProt XML filename:
uniprot-organism%3A315277+keyword%3A181_v1_HD_20131120
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]):
* Time taken to import:
1.24 Minutes
GO OBO-XML filename: go_daily-termdb_v1_HD_20131107.obo-xml
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped):
* Time taken to import: 16.41
* Time taken to process: 16.05
GOA filename: 22183.C_trachomatis_A_v1_HD_20131120.goa
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]):
* Time taken to import: 0.05 minutes

Name of .gdb file: C-Std_20131124_HD_24112013
* Time taken to export .gdb: About 1 hour and 20 minutes
* Upload your file and link to it here.
[[Media:C-Std 20131124 HD 24112013.gdb]]

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 23:15, 5 December 2013 (PST)

'''''Week 15'''''

'''Reflection'''
#What worked?
#:Our schedules were able to match much better this week, so we were all able to meet without any problems.
#What didn't work?
#:We had hoped to start on the paper this week, but unfortunately we faced difficulties with the microarray data and gmbuilder, so we were not able to get far enough in the process to run GenMAPP earlier in the week.
#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.

{{HDelgadi}}

HDelgadi Project Notebook

2013-12-05T18:46:19Z

HDelgadi: Updated information of second import and export cycle of database (This was done as QA for the database Katrina created)

===HDelgadi Weeks 12,13,14===
'''''Week 12'''''
*GO OBO-XML file for C. trachomatis serovar A.
:I clicked on [[Week 9]] and secondly clicked on the link [[Running_GenMAPP_Builder | Perform an export of the ''Vibrio cholerae'' GenMAPP Gene Database following the instructions on this page.]] which is below the subheading '''Exporting a Vibrio cholerae Gene Database'''. I then clicked on 'obo-xml.gz' and the downloading box popped up, so I clicked on Save File and OK. I then opened the file, dragged it to the Desktop, and used the 7-Zip File Manager to unzip the file. I was able to extract the file 'go_daily-termdb_v1_HD_20131107.obo-xml', but I was only able to post the zipped file,[[Media: Go daily-termdb.obo-xml v1 HD 20131107.gz]], on the [[Chlamydia trachomatis | Team H(oo)KD]] page.

'''Reflection'''
#What were the week’s key accomplishments?
#*This week's key accomplishments included uploading the respective files such as GO OBO-XML file, UniProt XML, and GOA file for C. trachomatis serovar A. We also focused on how to acquire our micro-array data and how to download the particular software to help with identifying our micro-array data from our particularly different micro-array chip.
#What are next week’s target accomplishments?
#*We are targeting our completion in formatting our micro-array information and focusing on starting our statistical analysis.
#What team strengths were seen this week?
#*We were able to assign our individual tasks efficiently.
#What team weaknesses were seen this week?
#*Some of our schedules didn't coincide too well, but we still managed to meet and work effectively.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:18, 14 November 2013 (PST)

'''''Week 13'''''
*'''bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Gene/Summary?g=~ (Gene Database Link Pattern)'''
:I went to the Model Organism Database, EnsemblGenome which can be found through this link, http://bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Info/Index. I then clicked on the Chromosome:592980-593522 which takes me to the genes of the
:Chlamydia trachomatis A/HAR-13. I clicked on the gene ID CTA_0588 which brought me to this webpage http://bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Gene/Summary?g=CTA_0588;r=Chromosome:608460-608543;t=CTA_0588, with further description of this gene. :I replaced the gene ID in bold within this URL, http://bacteria.ensembl.org/chlamydia_trachomatis_a_har_13/Gene/Summary?g='''CTA_0588''';r=Chromosome:608460-608543;t=CTA_0588, with CTA_0578. This new URL was able to take me to the webpage particularly for this new gene CTA_0588. Hence, this URL serves as the gene database link pattern.
:'''NOTE'''- I tried the import and export cycle, but unfortunately, the tally engine results did not match and were completely off. I will attempt a second import and export cycle in the coming week, but with the new gmbuilder that Dr. Dionisio and Katrina have created. I hope to get accurate results in my second attempt of the import and export cycle.

'''Reflection'''
#What were the week’s key accomplishments?
#*Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
#What are next week’s target accomplishments?
#*We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
#What team strengths were seen this week?
#*The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
#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.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:45, 19 November 2013 (PST)

'''''Week 14'''''
*I did the import and export cycle with the updated version of gmbuilder-32bit.bat that Dr. Dionisio and Katrina worked on. This new import and export cycle was successful since the Tally Engine gave me the same numbers for both the XML and Database Count.
==Export Information==
Version of GenMAPP Builder:
2.0b71
Computer on which export was run:
Personal Laptop
Postgres Database name:
Chlamydiaimport2
UniProt XML filename:
uniprot-organism%3A315277+keyword%3A181_v1_HD_20131120
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]):
* Time taken to import:
1.24 Minutes
GO OBO-XML filename: go_daily-termdb_v1_HD_20131107.obo-xml
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped):
* Time taken to import: 16.41
* Time taken to process: 16.05
GOA filename: 22183.C_trachomatis_A_v1_HD_20131120.goa
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]):
* Time taken to import: 0.05 minutes

Name of .gdb file: C-Std_20131124_HD_24112013
* Time taken to export .gdb: About 1 hour and 20 minutes
* Upload your file and link to it here.
[[Media:C-Std 20131124 HD 24112013.gdb]]

{{HDelgadi}}

File:C-Std 20131124 HD 24112013.gdb

2013-12-05T18:43:20Z

HDelgadi:

Chlamydia trachomatis

2013-12-03T17:56:38Z

HDelgadi: /* Important Files */ microarray data description

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Work on the final paper outline '''DW'''
*Document the relational database schema '''HD'''
*Commit changes to GenMAPP '''KS'''
| style="vertical-align: top; background: #eee" | 12/04
| style="vertical-align: top; background: #eee" | 12/05
*Begin writing the paper '''DW/KS/HD'''
*Begin working on the presentation '''DW/KS/HD'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
| style="vertical-align: top; background: #eee" | 12/10
*Continue writing the paper '''HD/KS/DW'''
*Continue working on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
** version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
**finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]
**Microarray data with separated IDs CTA_#### from _RRMH#####_...

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

Chlamydia trachomatis

2013-12-03T17:53:44Z

HDelgadi: /* Important Files */ Updated new microarray data with separation of IDs

{{Team_H(oo)KD}}

==Deadlines and Intermediate Milestones==

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 8em; background: #ddd" | Monday
! style="width: 8em; background: #ddd" | Tuesday
! style="width: 8em; background: #ddd" | Wednesday
! style="width: 8em; background: #ddd" | Thursday
! style="width: 8em; background: #ddd" | Friday
|-
| style="vertical-align: top" | 11/11
| style="vertical-align: top" | 11/12
| style="vertical-align: top" | 11/13
| style="vertical-align: top" | 11/14
*Run an export/import of gene database cycle '''KS/HD'''
*Create species profile '''KS'''
*Obtain and format raw microarray data '''DW'''
| style="vertical-align: top" | 11/15
*Rerun export/import of gene database cycle '''KS'''
|-
| style="vertical-align: top; background: #eee" | 11/18
| style="vertical-align: top; background: #eee" | 11/19
*Vet the gene database exported last week '''KS/HD/DW'''
*Format the raw microarray data '''DW'''
| style="vertical-align: top; background: #eee" | 11/20
| style="vertical-align: top; background: #eee" | 11/21
*Perform microarray statistical analysis '''DW'''
*Work on custom species profile '''KS/HD'''
| style="vertical-align: top; background: #eee" | 11/22
|-
| style="vertical-align: top" | 11/25
| style="vertical-align: top" | 11/26
*Build and commit species profile '''KS'''
*Customize Tally Engine '''KS/HD'''
*Perform GenMAPP and MAPPFinder Analysis '''DW'''
| style="vertical-align: top" | 11/27
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/28
'''THANKSGIVING BREAK'''
| style="vertical-align: top" | 11/29
'''THANKSGIVING BREAK'''
|-
| style="vertical-align: top; background: #eee" | 12/02
| style="vertical-align: top; background: #eee" | 12/03
*Work on the final paper outline '''DW'''
*Document the relational database schema '''HD'''
*Commit changes to GenMAPP '''KS'''
| style="vertical-align: top; background: #eee" | 12/04
| style="vertical-align: top; background: #eee" | 12/05
*Begin writing the paper '''DW/KS/HD'''
*Begin working on the presentation '''DW/KS/HD'''
| style="vertical-align: top; background: #eee" | 12/06
|-
| style="vertical-align: top; background: #eee" | 12/09
| style="vertical-align: top; background: #eee" | 12/10
*Continue writing the paper '''HD/KS/DW'''
*Continue working on the presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/11
*Practice the final presentation '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/12
*'''Final Presentation'''
*Proofread the final paper '''HD/KS/DW'''
| style="vertical-align: top; background: #eee" | 12/13
|}

==Annotated Bibliography of Genomics Papers for ''C. trachomatis''==

===Whole genome sequencing of ''C. trachomatis''===

#Journal article describing results of whole genome sequencing:
#*Database: PubMed
#*Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
#*There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of ''C. trachomatis'' to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
#*Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. ''Science'' '''282''': 754-759. 10.1126/science.282.5389.754.
#*The article can be viewed as an [http://www.sciencemag.org/content/282/5389/754.long HTML].
#*The article can be viewed as a [[Media: Science-1998-Stephens-754-9.pdf | PDF]].
#*This article includes [http://www.sciencemag.org/site/feature/data/982604.xhtml Supplementary Material].
#Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
#*How many results did you get?: 872
#*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

===Microarray articles===
The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

#Omsland, A., Sager, J., Nair, V., Sturdevant, D.E., Hackstadt, T. (2012) [http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]. ''PNAS'' '''109''': 19781-19785. doi: 10.1073/pnas.1212831109.
#*[[Media: PNAS-2012-Omsland-19781-5.pdf|PDF Version of Paper]]
#*[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]
#*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
#*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
#*4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".


==Journal Club Presentation on ''C. trachomatis'' Genome Sequencing Paper==

[[Media:Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf|Here]] is the PDF version of the presentation given on November 12, 2013 on the Stephens ''et al.'' (1998) paper.


==Important Files==

*[[Media: Go_daily-termdb_v2_HD_20131107.obo-xml.gz|Go_daily-termdb_v2_HD_20131107.obo-xml.gz]]
:GO OBO-XML file for ''C. trachomatis'' serovar A.
*[[Media: Uniprot XML C.trachomatis serovar A KS 20131114.xml|Uniprot XML C.trachomatis serovar A KS 20131114.xml]]
:UniProt XML file for ''C. trachomatis'' serovar A.
*[[Media: 22183.C trachomatis A KS 20131114.goa|22183.C trachomatis A KS 20131114.goa]]
:GOA file for ''C. trachomatis'' serovar A.
*[[Media: Ct-Std v1 KS 20131119.gdb|Ct-Std v1 KS 20131119.gdb]]
:First iteration of the export/import gene database cycle.
*[[Media: Ct-Std KS 20131121.gdb|Ct-Std KS 20131121.gdb]]
:Updated gene database.
*[[Media: Ct-Std v2 KS 20131121.gdb|Ct-Std v2 KS 20131121.gdb]]
:New gene database created with the new version of gmbuilder built on 11/21/2013 using the custom species profile for ''C. trachomatis.''

'''Array Express Article Raw Files'''

*[[Media:Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt|Raw_Data_DW_V1_12112013_A-GEOD-4692.adf.txt]]
:Microarray raw ADF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.idf.txt]]
:Microarray raw IDF file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.processed.1.zip]]
:Microarray raw processed zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip|Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip]]
:Microarray raw zip file for ''C. trachomatis''.
*[[Media:Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt|Raw_Data_DW_V1_12112013_E-GEOD-39530.sdrf.txt]]
:Microarray SDRF text file for ''C. trachomatis''.
*[[Media:Sdrf information excel.xls|Sdrf information excel.xls]]
:sdrf information in excel spreadsheet format.

'''Excel Master Spreadsheet'''

*[[Media:Master Spreadsheet.xls|master spreadsheet work in progress]]
:Initial Microarray raw data formatted and opened in Microsoft Excel.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.xls]]
:Sample C. trachomatis microarray data that was used to run GenMAPP with the latest ''C. trachomatis'' database.
*[[Media: C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt|C.trachomatis_Sample_Microarray_Data_for_GenMAPP_KS_20131124.txt]]
:Tab-delimited version of the file above.
*[[Media: Final Master Spreadsheet.xls|Final Master Spreadsheet]]
:Microarray data with identified Gene ID's and Log base data.
*[[Media: Master_Spreadsheet_Chlamydia_20131125_KD.xls | Master_Spreadsheet_Chlamydia_20131125_KD.xls]]
** version edited during office hours by Dr. Dahlquist to demonstrate statistics
*[[Media: Master Spreadsheet Chlamydia V1 20131125 DW.xls]]
**finished version of version edited during office hours by Dr. Dahlquist to demonstrate statistics -- finished by Dillon Williams
*[[Media: Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls]]

==Wiki Formatting==

Template: [[Template:Team_H(oo)KD]]

[[Category: Group Projects]]
[[Category: Team H(oo)KD]]

File:Copy of Master Spreadsheet Chlamydia V2 20131203 HD.xls

2013-12-03T17:52:59Z

HDelgadi:

HDelgadi Project Notebook

2013-11-26T18:14:33Z

HDelgadi: updating import export information

HDelgadi Project Notebook

2013-11-22T08:04:24Z

HDelgadi: adding reflection to individual journal

Team H(oo)KD Week 13 Status Report

2013-11-22T08:00:12Z

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

{{Team H(oo)KD}}

'''Refer to the calendar on the team home page to see the milestones for this week.'''

==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.

[[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:44, 21 November 2013 (PST)

===Reflection===

#What were the week’s key accomplishments?
#*This week's key accomplishments included finishing the custom species profile and then creating a new build of gmbuilder. With this new build, we were able to produce a gene database for ''C. trachomatis'' and run through the quality assurance testing for the database.
#*In addition, we were able to access the microarray data as well as normalize it using a software from Affymetrix.
#What are next week’s target accomplishments?
#*For next week, the plan is to finish formatting the microarray data so that we know what chip corresponds to which experimental conditions that were tested by Omsland '''et al.'''
#*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?
#*I think our biggest strength was catching up to where the professors expected us to be in our project at this time.
#*We also were able to help each other with different tasks to make sure that we were all on the same page.
#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==
*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?
#*Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
#What are next week’s target accomplishments?
#*We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
#What team strengths were seen this week?
#*The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
#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.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 23:40, 21 November 2013 (PST)

==GenMAPP User Status Update==

===Status Report===
Milestone 2
Read the microarray paper to understand the experiment.
*Read Microarray Paper to understand experiment and find relations between raw data and article.
Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Downloaded sdrf file and opened in excel to determine list that shows correspondence between samples in experiment and raw data file downloaded.
Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Determined 4 replicates based on article and data.
Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Created [[Media: Master Spreadsheet.xls|Master Spreadsheet]] and uploaded it to team wiki.
Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
*Consulted with Dr. Dahlquist on how to process data and recorded steps in [[Dwilliams Project Notebook|Project Notebook]].

===Reflection===
# What were the week’s key accomplishments?
#*The key accomplishments (for my position in the group) were understanding how to run the dChip software and convert and collect the raw data used into a workable format.
# What are next week’s target accomplishments?
#*By next week we would like to perform GenMAPP and MAPPFinder analysis of the data.
# What team strengths were seen this week?
#*Every member on our team accomplishes their role in an efficient and effective manner. If one member needs help with their role, the others are more than willing to help.
# What team weaknesses were seen this week?
#*The Affymetrix data and use of the dChip software were confusing at first, but easily resolved once Dr. Dahlquist was consulted.
-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 21:27, 21 November 2013 (PST)

[[Category:Journal Entry]]
[[Category:Team H(oo)KD]]

Team H(oo)KD Week 13 Status Report

2013-11-22T07:59:37Z

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

{{Team H(oo)KD}}

'''Refer to the calendar on the team home page to see the milestones for this week.'''

==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.

[[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:44, 21 November 2013 (PST)

===Reflection===

#What were the week’s key accomplishments?
#*This week's key accomplishments included finishing the custom species profile and then creating a new build of gmbuilder. With this new build, we were able to produce a gene database for ''C. trachomatis'' and run through the quality assurance testing for the database.
#*In addition, we were able to access the microarray data as well as normalize it using a software from Affymetrix.
#What are next week’s target accomplishments?
#*For next week, the plan is to finish formatting the microarray data so that we know what chip corresponds to which experimental conditions that were tested by Omsland '''et al.'''
#*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==
: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?
#*Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
#What are next week’s target accomplishments?
#*We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
#What team strengths were seen this week?
#*The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
#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.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 23:40, 21 November 2013 (PST)

==GenMAPP User Status Update==

===Status Report===
Milestone 2
Read the microarray paper to understand the experiment.
*Read Microarray Paper to understand experiment and find relations between raw data and article.
Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Downloaded sdrf file and opened in excel to determine list that shows correspondence between samples in experiment and raw data file downloaded.
Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Determined 4 replicates based on article and data.
Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Created [[Media: Master Spreadsheet.xls|Master Spreadsheet]] and uploaded it to team wiki.
Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
*Consulted with Dr. Dahlquist on how to process data and recorded steps in [[Dwilliams Project Notebook|Project Notebook]].

===Reflection===
# What were the week’s key accomplishments?
#*The key accomplishments (for my position in the group) were understanding how to run the dChip software and convert and collect the raw data used into a workable format.
# What are next week’s target accomplishments?
#*By next week we would like to perform GenMAPP and MAPPFinder analysis of the data.
# What team strengths were seen this week?
#*Every member on our team accomplishes their role in an efficient and effective manner. If one member needs help with their role, the others are more than willing to help.
# What team weaknesses were seen this week?
#*The Affymetrix data and use of the dChip software were confusing at first, but easily resolved once Dr. Dahlquist was consulted.
-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 21:27, 21 November 2013 (PST)

[[Category:Journal Entry]]
[[Category:Team H(oo)KD]]

Team H(oo)KD Week 13 Status Report

2013-11-22T07:40:18Z

HDelgadi: /* Reflection */ added signature

{{Team H(oo)KD}}

==Coder Status Update==

===Reflection===

==Quality Assurance Status Update==
:The coder, Katrina, and I have completed a full import and export cycle.
===Reflection===
#What were the week’s key accomplishments?
#*Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
#What are next week’s target accomplishments?
#*We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
#What team strengths were seen this week?
#*The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
#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.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 23:40, 21 November 2013 (PST)

==GenMAPP User Status Update==

===Status Report===
Milestone 2
Read the microarray paper to understand the experiment.
*Read Microarray Paper to understand experiment and find relations between raw data and article.
Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Downloaded sdrf file and opened in excel to determine list that shows correspondence between samples in experiment and raw data file downloaded.
Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Determined 4 replicates based on article and data.
Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Created [[Media: Master Spreadsheet.xls|Master Spreadsheet]] and uploaded it to team wiki.
Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
*Consulted with Dr. Dahlquist on how to process data and recorded steps in [[Dwilliams Project Notebook|Project Notebook]].

===Reflection===
# What were the week’s key accomplishments?
#*The key accomplishments (for my position in the group) were understanding how to run the dChip software and convert and collect the raw data used into a workable format.
# What are next week’s target accomplishments?
#*By next week we would like to perform GenMAPP and MAPPFinder analysis of the data.
# What team strengths were seen this week?
#*Every member on our team accomplishes their role in an efficient and effective manner. If one member needs help with their role, the others are more than willing to help.
# What team weaknesses were seen this week?
#*The Affymetrix data and use of the dChip software were confusing at first, but easily resolved once Dr. Dahlquist was consulted.
-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 21:27, 21 November 2013 (PST)

[[Category:Journal Entry]]
[[Category:Team H(oo)KD]]

Team H(oo)KD Week 13 Status Report

2013-11-22T07:39:49Z

HDelgadi: /* Reflection */ adding bullets so numbers are in chronological order

{{Team H(oo)KD}}

==Coder Status Update==

===Reflection===

==Quality Assurance Status Update==
:The coder, Katrina, and I have completed a full import and export cycle.
===Reflection===
#What were the week’s key accomplishments?
#*Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
#What are next week’s target accomplishments?
#*We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
#What team strengths were seen this week?
#*The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
#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==

===Status Report===
Milestone 2
Read the microarray paper to understand the experiment.
*Read Microarray Paper to understand experiment and find relations between raw data and article.
Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Downloaded sdrf file and opened in excel to determine list that shows correspondence between samples in experiment and raw data file downloaded.
Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Determined 4 replicates based on article and data.
Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Created [[Media: Master Spreadsheet.xls|Master Spreadsheet]] and uploaded it to team wiki.
Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
*Consulted with Dr. Dahlquist on how to process data and recorded steps in [[Dwilliams Project Notebook|Project Notebook]].

===Reflection===
# What were the week’s key accomplishments?
#*The key accomplishments (for my position in the group) were understanding how to run the dChip software and convert and collect the raw data used into a workable format.
# What are next week’s target accomplishments?
#*By next week we would like to perform GenMAPP and MAPPFinder analysis of the data.
# What team strengths were seen this week?
#*Every member on our team accomplishes their role in an efficient and effective manner. If one member needs help with their role, the others are more than willing to help.
# What team weaknesses were seen this week?
#*The Affymetrix data and use of the dChip software were confusing at first, but easily resolved once Dr. Dahlquist was consulted.
-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 21:27, 21 November 2013 (PST)

[[Category:Journal Entry]]
[[Category:Team H(oo)KD]]

Team H(oo)KD Week 13 Status Report

2013-11-22T07:39:13Z

HDelgadi: /* Reflection */

{{Team H(oo)KD}}

==Coder Status Update==

===Reflection===

==Quality Assurance Status Update==
:The coder, Katrina, and I have completed a full import and export cycle.
===Reflection===
#What were the week’s key accomplishments?
#*Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
#What are next week’s target accomplishments?
:We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
#What team strengths were seen this week?
:The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
#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==

===Status Report===
Milestone 2
Read the microarray paper to understand the experiment.
*Read Microarray Paper to understand experiment and find relations between raw data and article.
Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Downloaded sdrf file and opened in excel to determine list that shows correspondence between samples in experiment and raw data file downloaded.
Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Determined 4 replicates based on article and data.
Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Created [[Media: Master Spreadsheet.xls|Master Spreadsheet]] and uploaded it to team wiki.
Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
*Consulted with Dr. Dahlquist on how to process data and recorded steps in [[Dwilliams Project Notebook|Project Notebook]].

===Reflection===
# What were the week’s key accomplishments?
#*The key accomplishments (for my position in the group) were understanding how to run the dChip software and convert and collect the raw data used into a workable format.
# What are next week’s target accomplishments?
#*By next week we would like to perform GenMAPP and MAPPFinder analysis of the data.
# What team strengths were seen this week?
#*Every member on our team accomplishes their role in an efficient and effective manner. If one member needs help with their role, the others are more than willing to help.
# What team weaknesses were seen this week?
#*The Affymetrix data and use of the dChip software were confusing at first, but easily resolved once Dr. Dahlquist was consulted.
-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 21:27, 21 November 2013 (PST)

[[Category:Journal Entry]]
[[Category:Team H(oo)KD]]

Team H(oo)KD Week 13 Status Report

2013-11-22T07:38:53Z

HDelgadi: /* Quality Assurance Status Update */ completing the reflection

{{Team H(oo)KD}}

==Coder Status Update==

===Reflection===

==Quality Assurance Status Update==
:The coder, Katrina, and I have completed a full import and export cycle.
===Reflection===
#What were the week’s key accomplishments?
:Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
#What are next week’s target accomplishments?
:We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
#What team strengths were seen this week?
:The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
#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==

===Status Report===
Milestone 2
Read the microarray paper to understand the experiment.
*Read Microarray Paper to understand experiment and find relations between raw data and article.
Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Downloaded sdrf file and opened in excel to determine list that shows correspondence between samples in experiment and raw data file downloaded.
Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Determined 4 replicates based on article and data.
Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Created [[Media: Master Spreadsheet.xls|Master Spreadsheet]] and uploaded it to team wiki.
Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
*Consulted with Dr. Dahlquist on how to process data and recorded steps in [[Dwilliams Project Notebook|Project Notebook]].

===Reflection===
# What were the week’s key accomplishments?
#*The key accomplishments (for my position in the group) were understanding how to run the dChip software and convert and collect the raw data used into a workable format.
# What are next week’s target accomplishments?
#*By next week we would like to perform GenMAPP and MAPPFinder analysis of the data.
# What team strengths were seen this week?
#*Every member on our team accomplishes their role in an efficient and effective manner. If one member needs help with their role, the others are more than willing to help.
# What team weaknesses were seen this week?
#*The Affymetrix data and use of the dChip software were confusing at first, but easily resolved once Dr. Dahlquist was consulted.
-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 21:27, 21 November 2013 (PST)

[[Category:Journal Entry]]
[[Category:Team H(oo)KD]]

Template:HDelgadi

2013-11-22T07:10:29Z

HDelgadi: linking week 13 status report

[[Class Journal Week 1]]

[[Week 1]]

[[Class Journal Week 2]]

[[Week 2]]

[[HDelgadi Week 2]]

[[Class Journal Week 3]]

[[HDelgadi Week 3]]

[[Week 4]]

[[Class Journal Week 4]]

[[HDelgadi Week 4]]

[[Week 5]]

[[HDelgadi Week 5]]

[[Class Journal Week 5]]

* Link: [[http://www.violinet.org/protegen/ Protegen]]

* [[Protegen]]

[[Week 6]]

[[HDelgadi Week 6]]

[[Class Journal Week 6]]

[[Week 7]]

[[HDelgadi Week 7]]

[[Class Journal Week 7]]

[[Week 8]]

[[HDelgadi Week 8]]

[[Class Journal Week 8]]

[[Week 9]]

[[HDelgadi Week 9]]

[[Class Journal Week 9]]

[[Week 10]]

[[HDelgadi Week 10]]

[[Week 11]]

[[Chlamydia trachomatis | Team H(oo)KD]]

[[HDelgadi Week 11]]

*[[Media: Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf]]

[[HDelgadi Project Notebook]]

[[Week 12 Status Report]]

[[Week 13 Status Report]]

[[Category:Journal Entry]]

[[Category:Shared]]

[[Category: Group Projects]]

[[Category: Team H(oo)KD]]

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

HDelgadi Project Notebook

2013-11-22T07:07:02Z

HDelgadi: adding bold lettering

HDelgadi Project Notebook

2013-11-22T07:06:28Z

HDelgadi: additional information about the import and export cycle

Team H(oo)KD Week 13 Status Report

2013-11-22T06:15:17Z

HDelgadi: completing team status report

{{Team H(oo)KD}}

==Coder Status Update==

===Reflection===

==Quality Assurance Status Update==

===Reflection===
:The coder, Katrina, and I have completed a full import and export cycle.

==GenMAPP User Status Update==

===Status Report===
Milestone 2
Read the microarray paper to understand the experiment.
*Read Microarray Paper to understand experiment and find relations between raw data and article.
Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
*Downloaded sdrf file and opened in excel to determine list that shows correspondence between samples in experiment and raw data file downloaded.
Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
*Determined 4 replicates based on article and data.
Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
*Created [[Media: Master Spreadsheet.xls|Master Spreadsheet]] and uploaded it to team wiki.
Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
*Consulted with Dr. Dahlquist on how to process data and recorded steps in [[Dwilliams Project Notebook|Project Notebook]].

===Reflection===
# What were the week’s key accomplishments?
#*The key accomplishments (for my position in the group) were understanding how to run the dChip software and convert and collect the raw data used into a workable format.
# What are next week’s target accomplishments?
#*By next week we would like to perform GenMAPP and MAPPFinder analysis of the data.
# What team strengths were seen this week?
#*Every member on our team accomplishes their role in an efficient and effective manner. If one member needs help with their role, the others are more than willing to help.
# What team weaknesses were seen this week?
#*The Affymetrix data and use of the dChip software were confusing at first, but easily resolved once Dr. Dahlquist was consulted.
-[[User:Dwilliams|Dwilliams]] ([[User talk:Dwilliams|talk]]) 21:27, 21 November 2013 (PST)

[[Category:Journal Entry]]
[[Category:Team H(oo)KD]]

HDelgadi Project Notebook

2013-11-21T18:54:11Z

HDelgadi: added space between the gene database link and the title

HDelgadi Project Notebook

2013-11-21T18:53:12Z

HDelgadi: bold lettering and edited the gene database link pattern

HDelgadi Project Notebook

2013-11-19T18:45:55Z

HDelgadi: Adding Gene Database Link Pattern Information

Template:HDelgadi

2013-11-14T23:07:58Z

HDelgadi: added two more categories- Group Projects and Team H(oo)KD

[[Class Journal Week 1]]

[[Week 1]]

[[Class Journal Week 2]]

[[Week 2]]

[[HDelgadi Week 2]]

[[Class Journal Week 3]]

[[HDelgadi Week 3]]

[[Week 4]]

[[Class Journal Week 4]]

[[HDelgadi Week 4]]

[[Week 5]]

[[HDelgadi Week 5]]

[[Class Journal Week 5]]

* Link: [[http://www.violinet.org/protegen/ Protegen]]

* [[Protegen]]

[[Week 6]]

[[HDelgadi Week 6]]

[[Class Journal Week 6]]

[[Week 7]]

[[HDelgadi Week 7]]

[[Class Journal Week 7]]

[[Week 8]]

[[HDelgadi Week 8]]

[[Class Journal Week 8]]

[[Week 9]]

[[HDelgadi Week 9]]

[[Class Journal Week 9]]

[[Week 10]]

[[HDelgadi Week 10]]

[[Week 11]]

[[Chlamydia trachomatis | Team H(oo)KD]]

[[HDelgadi Week 11]]

*[[Media: Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf]]

[[HDelgadi Project Notebook]]

[[Team Journal Assignment Week 12| Team H(oo)KD Week 12 Status Report]]

[[Category:Journal Entry]]

[[Category:Shared]]

[[Category: Group Projects]]

[[Category: Team H(oo)KD]]

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

Team Journal Assignment Week 12

2013-11-14T23:04:34Z

HDelgadi: QA Status Update of this week accomplishments and further goals

{{Team H(oo)KD}}

==Coder Status Update==

==QA Status Update==
*Obtaining the files GOA file, UniProt XML file, and the GO OBO-XML file were essential to obtain this week. With these files we will begin the importing and exporting of the files Friday November 15th, so we may continue with the exporting of files into the GenMAPP Gene Database next week.

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:46, 14 November 2013 (PST)

==GenMAPP User Status Update==

[[Category:Journal Entry]]

Team Journal Assignment Week 12

2013-11-14T22:51:21Z

HDelgadi: added category journal entry

{{Team H(oo)KD}}

==Coder Status Update==

==QA Status Update==
[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:46, 14 November 2013 (PST)

==GenMAPP User Status Update==

[[Category:Journal Entry]]

HDelgadi Project Notebook

2013-11-14T20:38:15Z

HDelgadi: finishing answers for questions three and four

HDelgadi Project Notebook

2013-11-14T20:16:51Z

HDelgadi: answered first reflection question

HDelgadi Project Notebook

2013-11-14T20:01:40Z

HDelgadi: updating answers

HDelgadi Project Notebook

2013-11-14T18:50:10Z

HDelgadi: adding reflection

Template:HDelgadi

2013-11-14T18:47:16Z

HDelgadi: linking team journal

[[Class Journal Week 1]]

[[Week 1]]

[[Class Journal Week 2]]

[[Week 2]]

[[HDelgadi Week 2]]

[[Class Journal Week 3]]

[[HDelgadi Week 3]]

[[Week 4]]

[[Class Journal Week 4]]

[[HDelgadi Week 4]]

[[Week 5]]

[[HDelgadi Week 5]]

[[Class Journal Week 5]]

* Link: [[http://www.violinet.org/protegen/ Protegen]]

* [[Protegen]]

[[Week 6]]

[[HDelgadi Week 6]]

[[Class Journal Week 6]]

[[Week 7]]

[[HDelgadi Week 7]]

[[Class Journal Week 7]]

[[Week 8]]

[[HDelgadi Week 8]]

[[Class Journal Week 8]]

[[Week 9]]

[[HDelgadi Week 9]]

[[Class Journal Week 9]]

[[Week 10]]

[[HDelgadi Week 10]]

[[Week 11]]

[[Chlamydia trachomatis | Team H(oo)KD]]

[[HDelgadi Week 11]]

*[[Media: Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf]]

[[HDelgadi Project Notebook]]

[[Team Journal Assignment Week 12| Team H(oo)KD Week 12 Status Report]]

[[Category:Journal Entry]]

[[Category:Shared]]

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

Team Journal Assignment Week 12

2013-11-14T18:46:18Z

HDelgadi: added signature

[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:46, 14 November 2013 (PST)

Template:Team H(oo)KD

2013-11-14T18:44:43Z

HDelgadi: erased week 12

<div style="background: #000000; padding: 10px; font-weight:bold; font-size:200%;color:white"><center>Team H(oo)KD</center></div>

<div style="background: #F5F5F5; padding: 10px">
{| style = "width:100%; font-size:120%"
| '''[[Project Manager|<span style="color:black;">'''Project Manager'''</span>]]/[[Coder|<span style="color:black;">'''Coder'''</span>]]: [[User:Ksherbina|Katrina Sherbina]]'''
| '''[[Quality Assurance|<span style="color:black;">'''Quality Assurance'''</span>]]: [[User:HDelgadi|Hilda Delgadillo]]'''
| '''[[GenMAPP User|<span style="color:black;">'''GenMAPP User'''</span>]]: [[User:Dwilliams|Dillon Williams]]'''
|}

<div style="border-width: 2px; border-bottom-width:2px; border-bottom-color:#FFE135; border-bottom-style: solid; width: 100%"></div>

{| style = "width:60%; font-size:%100"
| '''Project Guidelines:'''
| '''[[Gene Database Project]]'''
| '''[[Gene Database Project Report Guidelines|Report Guidelines]]'''
|-
| '''Team Journal Assignments'''
| '''[[Team Journal Assignment Week 12| Team H(oo)KD Week 12 Status Report]]'''
|-
| '''Individual Status Reports:'''
| '''[[HDelgadi Project Notebook]]
|-
| '''Useful Links:'''
| '''[[Main Page|Class Page]]'''
| '''[[Chlamydia trachomatis|Final Project Page]]'''
|}

</div>

H(oo)KD Week 12 Status Report

2013-11-14T18:29:35Z

HDelgadi: adding signature and linking team page

[[Chlamydia trachomatis| Team H(oo)KD]]
[[User:HDelgadi|HDelgadi]] ([[User talk:HDelgadi|talk]]) 10:29, 14 November 2013 (PST)

Template:Team H(oo)KD

2013-11-14T18:29:03Z

HDelgadi: adding week 12 status report

<div style="background: #000000; padding: 10px; font-weight:bold; font-size:200%;color:white"><center>Team H(oo)KD</center></div>

<div style="background: #F5F5F5; padding: 10px">
{| style = "width:100%; font-size:120%"
| '''[[Project Manager|<span style="color:black;">'''Project Manager'''</span>]]/[[Coder|<span style="color:black;">'''Coder'''</span>]]: [[User:Ksherbina|Katrina Sherbina]]'''
| '''[[Quality Assurance|<span style="color:black;">'''Quality Assurance'''</span>]]: [[User:HDelgadi|Hilda Delgadillo]]'''
| '''[[GenMAPP User|<span style="color:black;">'''GenMAPP User'''</span>]]: [[User:Dwilliams|Dillon Williams]]'''
|}

<div style="border-width: 2px; border-bottom-width:2px; border-bottom-color:#FFE135; border-bottom-style: solid; width: 100%"></div>

{| style = "width:60%; font-size:%100"
| '''Project Guidelines:'''
| '''[[Gene Database Project]]'''
| '''[[Gene Database Project Report Guidelines|Report Guidelines]]'''
|-
| '''Status Reports:'''
| '''[[Team H(oo)KD Week 12 Status Report|Week 12]]'''
| '''[[H(oo)KD Week 12 Status Report]]'''
| '''[[HDelgadi Project Notebook]]
|-
| '''Useful Links:'''
| '''[[Main Page|Class Page]]'''
| '''[[Chlamydia trachomatis|Final Project Page]]'''
|}

</div>

HDelgadi Project Notebook

2013-11-14T18:25:07Z

HDelgadi: adding template

Template:HDelgadi

2013-11-14T18:23:36Z

HDelgadi:

[[Class Journal Week 1]]

[[Week 1]]

[[Class Journal Week 2]]

[[Week 2]]

[[HDelgadi Week 2]]

[[Class Journal Week 3]]

[[HDelgadi Week 3]]

[[Week 4]]

[[Class Journal Week 4]]

[[HDelgadi Week 4]]

[[Week 5]]

[[HDelgadi Week 5]]

[[Class Journal Week 5]]

* Link: [[http://www.violinet.org/protegen/ Protegen]]

* [[Protegen]]

[[Week 6]]

[[HDelgadi Week 6]]

[[Class Journal Week 6]]

[[Week 7]]

[[HDelgadi Week 7]]

[[Class Journal Week 7]]

[[Week 8]]

[[HDelgadi Week 8]]

[[Class Journal Week 8]]

[[Week 9]]

[[HDelgadi Week 9]]

[[Class Journal Week 9]]

[[Week 10]]

[[HDelgadi Week 10]]

[[Week 11]]

[[Chlamydia trachomatis | Team H(oo)KD]]

[[HDelgadi Week 11]]

*[[Media: Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf]]

[[HDelgadi Project Notebook]]

[[H(oo)KD Week 12 Status Report]]

[[Category:Journal Entry]]

[[Category:Shared]]

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

Template:HDelgadi

2013-11-14T18:23:06Z

HDelgadi: linking week 12 status report

[[Class Journal Week 1]]

[[Week 1]]

[[Class Journal Week 2]]

[[Week 2]]

[[HDelgadi Week 2]]

[[Class Journal Week 3]]

[[HDelgadi Week 3]]

[[Week 4]]

[[Class Journal Week 4]]

[[HDelgadi Week 4]]

[[Week 5]]

[[HDelgadi Week 5]]

[[Class Journal Week 5]]

* Link: [[http://www.violinet.org/protegen/ Protegen]]

* [[Protegen]]

[[Week 6]]

[[HDelgadi Week 6]]

[[Class Journal Week 6]]

[[Week 7]]

[[HDelgadi Week 7]]

[[Class Journal Week 7]]

[[Week 8]]

[[HDelgadi Week 8]]

[[Class Journal Week 8]]

[[Week 9]]

[[HDelgadi Week 9]]

[[Class Journal Week 9]]

[[Week 10]]

[[HDelgadi Week 10]]

[[Week 11]]

[[Chlamydia trachomatis | Team H(oo)KD]]

[[HDelgadi Week 11]]

*[[Media: Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf]]

[[HDelgadi Project Notebook]]

[[Team H(oo)KD Week 12 Status Report]]

[[Category:Journal Entry]]

[[Category:Shared]]

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

Template:HDelgadi

2013-11-14T18:22:35Z

HDelgadi: linking week 12 status report

[[Class Journal Week 1]]

[[Week 1]]

[[Class Journal Week 2]]

[[Week 2]]

[[HDelgadi Week 2]]

[[Class Journal Week 3]]

[[HDelgadi Week 3]]

[[Week 4]]

[[Class Journal Week 4]]

[[HDelgadi Week 4]]

[[Week 5]]

[[HDelgadi Week 5]]

[[Class Journal Week 5]]

* Link: [[http://www.violinet.org/protegen/ Protegen]]

* [[Protegen]]

[[Week 6]]

[[HDelgadi Week 6]]

[[Class Journal Week 6]]

[[Week 7]]

[[HDelgadi Week 7]]

[[Class Journal Week 7]]

[[Week 8]]

[[HDelgadi Week 8]]

[[Class Journal Week 8]]

[[Week 9]]

[[HDelgadi Week 9]]

[[Class Journal Week 9]]

[[Week 10]]

[[HDelgadi Week 10]]

[[Week 11]]

[[Chlamydia trachomatis | Team H(oo)KD]]

[[HDelgadi Week 11]]

*[[Media: Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf]]

[[HDelgadi Project Notebook]]

[[Chlamydia trachomatis| Team H(oo)KD Week 12 Status Report]]

[[Category:Journal Entry]]

[[Category:Shared]]

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

Template:HDelgadi

2013-11-14T18:21:36Z

HDelgadi: linking week 12 status report

[[Class Journal Week 1]]

[[Week 1]]

[[Class Journal Week 2]]

[[Week 2]]

[[HDelgadi Week 2]]

[[Class Journal Week 3]]

[[HDelgadi Week 3]]

[[Week 4]]

[[Class Journal Week 4]]

[[HDelgadi Week 4]]

[[Week 5]]

[[HDelgadi Week 5]]

[[Class Journal Week 5]]

* Link: [[http://www.violinet.org/protegen/ Protegen]]

* [[Protegen]]

[[Week 6]]

[[HDelgadi Week 6]]

[[Class Journal Week 6]]

[[Week 7]]

[[HDelgadi Week 7]]

[[Class Journal Week 7]]

[[Week 8]]

[[HDelgadi Week 8]]

[[Class Journal Week 8]]

[[Week 9]]

[[HDelgadi Week 9]]

[[Class Journal Week 9]]

[[Week 10]]

[[HDelgadi Week 10]]

[[Week 11]]

[[Chlamydia trachomatis | Team H(oo)KD]]

[[HDelgadi Week 11]]

*[[Media: Presentation on C.trachomatis Genome Paper KS HD DW 20131112.pdf]]

[[HDelgadi Project Notebook]]

[[Teamname Week 12 Status Report]]

[[Category:Journal Entry]]

[[Category:Shared]]

=='''[[User:HDelgadi|Hilda Delgadillo]]'''==

HDelgadi Project Notebook

2013-11-14T18:20:29Z

HDelgadi: added team H(oo)KD team page

HDelgadi Project Notebook

2013-11-14T18:18:30Z

HDelgadi: adding signature

Template:Team H(oo)KD

2013-11-14T18:15:23Z

HDelgadi: adding Hilda's project Notebook

<div style="background: #000000; padding: 10px; font-weight:bold; font-size:200%;color:white"><center>Team H(oo)KD</center></div>

<div style="background: #F5F5F5; padding: 10px">
{| style = "width:100%; font-size:120%"
| '''[[Project Manager|<span style="color:black;">'''Project Manager'''</span>]]/[[Coder|<span style="color:black;">'''Coder'''</span>]]: [[User:Ksherbina|Katrina Sherbina]]'''
| '''[[Quality Assurance|<span style="color:black;">'''Quality Assurance'''</span>]]: [[User:HDelgadi|Hilda Delgadillo]]'''
| '''[[GenMAPP User|<span style="color:black;">'''GenMAPP User'''</span>]]: [[User:Dwilliams|Dillon Williams]]'''
|}

<div style="border-width: 2px; border-bottom-width:2px; border-bottom-color:#FFE135; border-bottom-style: solid; width: 100%"></div>

{| style = "width:60%; font-size:%100"
| '''Project Guidelines:'''
| '''[[Gene Database Project]]'''
| '''[[Gene Database Project Report Guidelines|Report Guidelines]]'''
|-
| '''Status Reports:'''
| '''[[Team H(oo)KD Week 12 Status Report|Week 12]]'''
| '''[[HDelgadi Project Notebook]]
|-
| '''Useful Links:'''
| '''[[Main Page|Class Page]]'''
| '''[[Chlamydia trachomatis|Final Project Page]]'''
|}

</div>

HDelgadi Project Notebook

2013-11-14T18:10:07Z

HDelgadi: Adding italics and bold

HDelgadi Project Notebook

2013-11-14T18:07:36Z

HDelgadi: adding commas to sentences

===HDelgadi Week 12,13,14===
#Week 12
*GO OBO-XML file for C. trachomatis serovar A.
:I clicked on [[Week 9]] and secondly clicked on the link [[Running_GenMAPP_Builder | Perform an export of the ''Vibrio cholerae'' GenMAPP Gene Database following the instructions on this page.]] which is below the subheading '''Exporting a Vibrio cholerae Gene Database'''. I then clicked on 'obo-xml.gz' and the downloading box popped up, so I clicked on Save File and OK. I then opened the file, dragged it to the Desktop, and used the 7-Zip File Manager to unzip the file. I was able to extract the file 'go_daily-termdb_v1_HD_20131107.obo-xml', but I was only able to post the zipped file,[[Media: Go daily-termdb.obo-xml v1 HD 20131107.gz]], on the [[Chlamydia trachomatis | Team H(oo)KD]] page.

HDelgadi Project Notebook

2013-11-14T18:06:46Z

HDelgadi: adding bold lettering

===HDelgadi Week 12,13,14===
#Week 12
*GO OBO-XML file for C. trachomatis serovar A.
:I clicked on [[Week 9]] and secondly clicked on the link [[Running_GenMAPP_Builder | Perform an export of the ''Vibrio cholerae'' GenMAPP Gene Database following the instructions on this page.]] which is below the subheading '''Exporting a Vibrio cholerae Gene Database'''. I then clicked on 'obo-xml.gz' and the downloading box popped up, so I clicked on Save File and OK. I then opened the file dragged it to the Desktop and used the 7-Zip File Manager to unzip the file. I was able to extract the file 'go_daily-termdb_v1_HD_20131107.obo-xml', but I was only able to post the zipped file,[[Media: Go daily-termdb.obo-xml v1 HD 20131107.gz]], on the [[Chlamydia trachomatis | Team H(oo)KD]] page.

HDelgadi Project Notebook

2013-11-14T18:06:15Z

HDelgadi: adding proper link

===HDelgadi Week 12,13,14===
#Week 12
*GO OBO-XML file for C. trachomatis serovar A.
:I clicked on [[Week 9]] and secondly clicked on the link [[Running_GenMAPP_Builder | Perform an export of the ''Vibrio cholerae'' GenMAPP Gene Database following the instructions on this page.]] which is below the subheading 'Exporting a Vibrio cholerae Gene Database'. I then clicked on 'obo-xml.gz' and the downloading box popped up, so I clicked on Save File and OK. I then opened the file dragged it to the Desktop and used the 7-Zip File Manager to unzip the file. I was able to extract the file 'go_daily-termdb_v1_HD_20131107.obo-xml', but I was only able to post the zipped file,[[Media: Go daily-termdb.obo-xml v1 HD 20131107.gz]], on the [[Chlamydia trachomatis | Team H(oo)KD]] page.