File:ReadMe Leishmania 20131212.pdf

2013-12-12T18:15:49Z

Gleis:

Template:Leishmania Major File Updates

2013-12-12T06:32:57Z

Gleis:

#11/5/2013
#*[[Media:A-GEOD-6855.adf_A.txt]] Array Design File
#*[[Media:E-GEOD-10407.idf_A.txt]] Investigation Description File
#*[[Media:E-GEOD-10407.processed.1_A.zip]] Processed Data
#*[[Media:E-GEOD-10407.raw.1_A.zip]] Raw Data
#*[[Media:E-GEOD-10407.sdrf_A.txt]] Sample and Data Relationship File
#11/7/2013
#*[[Media:E-GEOD-10407.sdrf_B.txt]] Leishmania major Chips
#*Completed Import/Export Cycle, conducted a Tally Count, opened .gdb file in Microsoft Access and compared original row counts.
#*Access was missing 2 genes for GeneID and RefSeq, and we had no GO terms in the Tally or in Access.
#11/11/2013
#*[[Media:Leishmania_major_BD.pdf|Leishmania major Genome Reference Article Presentation]]
#11/14/13
#*[[Media:E-GEOD-10407.sdrf_C.txt]] Edited Sample and Data (Ordered based on species and relevant data)
#*[[Media:L.majorCompiledRawData.txt]] L. major raw compiled data
#*[[Media:L.infantumCompliedRawData(A).txt]] L. infantum raw compiled data
#11/19/2013:
#*[[Media:L.majorCompiledRawData_B.txt]] L. major raw compiled data with adjusted dye swap values
#*[[Media:L.infantumCompliedRawData(B).txt]] L. infantum raw compiled data with adjusted dye swap values and sample names
#*[[Media:L.majorCompiledRawData_C.txt]] L. major raw compiled data with adjusted dye swap values and sample names
#11/21/2013
#*[[Media:L.infantumStats.txt]]
#*[[Media:L.infantumStats.xls]]
#*[[File:L.majorStats.xls]]
#*[[File:L.majorStats.txt]]
#*[[File:L.majorStats(A).txt]]
#*[[File:L.infantumStats(A).txt]]
#*[[File:LeishmaniaCompiledStatAnalysis.txt]]
#12/3/2013
#*[[File:LeishmaniaCompiledStatAnalysis(A).txt]]
#*[[File:LeishmaniaCompiledStatAnalysis(A).EX.txt]]
#*[[Media:L.infantumStats_B.xls]] Fixed infantum p-value parenthesis
#*[[Media:LeishmaniaCompiledStatAnalysis(B).txt]]
#*[[Media:LeishmaniaCompiledStatAnalysisLMJFiltered.txt]] Original File That should work in GenMAPP once coding is fixed
#*[[Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).txt]] Quick fix file with underscores to work in GenMAPP until coding is fixed
#*[[Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).EX.txt]]
#*[[Media:LeishmaniaCompiledStatAnalysisLMJFiltered(B).gex]]
#*[[Media:ExceptionFileErrorID.txt]]
#*[[Leishmania Major Group Project Report]]
#*[[Media:Dist Leishmania Lena Gabe 05112013.zip]]
#12/5/2013
#*[[Media:LeishmaniaGDB Lena Gabe 20131205.zip]]
#12/7/2013
#*[[File:LMajorGOMapp-Criterion1-GO.txt ]]
#*[[File:LMajorGOMapp-Criterion0-GO.txt]]
#12/11/2013
#*[[Media:Leishmania schema 20101022.pdf]]
#*[[Media:ReadMe Leishmania 20131211.pdf]]

File:ReadMe Leishmania 20131211.pdf

2013-12-12T06:32:15Z

Gleis:

Template:Leishmania Major File Updates

2013-12-12T06:26:11Z

Gleis:

2013-12-12T01:09:47Z

Gleis:

==Lab Journal==
*Code needed ID changes in Eclipse
*Replaced first period with an "_" and removed second "_"
*Replaced to look like "LMJF_##_####"
*First export failed due to minor error in Eclipse code
*Initiated Gene Database Testing Report
*Began new export with edited code for database
*Need to review errors in GenMAPP
*New export somewhat successful
*Database not catching errors of the form LmjF##.#####
*IDs not present in XML follow the form LmjF01.[0160-1983]
:*Except IDs ending in zero are found in XML for example IDs Lmjf01.0160 and LmjF01.1970 are found but IDs LmjF01.016[1-9] and LmjF01.197[1-9]would not be found

[[Leishmania major]]

[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 22:24, 6 December 2013 (PST)

[[Category:Journal Entry]] [[Category:Leishmania major]]

Template:Leishmania Major File Updates

2013-12-08T01:06:52Z

Gleis:

2013-12-07T06:19:19Z

Gleis: /* Status report as to progress on each milestone that that you have set for the week: */

== Team Journal Assignment Week 15 ==
===Status report as to progress on each milestone that that you have set for the week:===
#GenMAPP users:
#*Did sanity check for the p-values of both L. major and L. infantum
#*Created GenMAPP criteria and colorsets
#*Ran MAPPFiner and are waiting for results
#*:For more details on these steps refer to [[Vkuehn Week 15]] and [[Kevinmcgee Week 15]]
#QA:
#Coder: Initiated Gene Database Testing Report, Edited code for species customization

=== Reflection ===
Each team member should reflect on the team's progress:

[[User:Vkuehn|Viktoria Kuehn]]
# What worked: We successfully looked at the results of our P-values and created the GenMAPP criteria and colorsets.
# What didn't work: We are waiting for MAPPFinder to give us results.
# What will I do next to fix what didn't work: If it does not work within 2 hours we will have to try it again and make sure no errors were made.
[[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 11:03, 5 December 2013 (PST)

'''[[User:Kevinmcgee|Kevin McGee]]'''
#We were able to troubleshoot any problems with uploading our data into GenMAPP by going through everything step by step
#We were held up at times by errors that involved us to wait long amounts of time. For instance, we need to export a new gene database, however we could not because postgress was already being used on the computer we were using. therefore, we had to wait hours for that to finish so we could export our database. We should plan ahead better so we don't have to wait like that.
#I don't know what we could do to fix that other than stay on our computers we had been working on the whole time
[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 11:08, 5 December 2013 (PST)

'''[[User:Gleis|Gabriel Leis]]'''
#Code for species customization was edited twice to ensure ease of use of microarray data in GenMapp. Gene Database Testing report was initiated and nearly completed.
#Errors in the code as well as errors in the formatting of the microarray data held up the group project.
#Test new species customization code, finish gene database testing report
[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 22:16, 6 December 2013 (PST)

{{Template:Leishmania Major Navigation}}
[[Category:Assignment]]
[[Category: Group Projects]]
[[Category: Journal Entry]]

Leishmania major Week 15 Status Report

2013-12-07T06:17:08Z

Gleis: /* Reflection */

== Team Journal Assignment Week 15 ==
===Status report as to progress on each milestone that that you have set for the week:===
#GenMAPP users:
#*Did sanity check for the p-values of both L. major and L. infantum
#*Created GenMAPP criteria and colorsets
#*Ran MAPPFiner and are waiting for results
#*:For more details on these steps refer to [[Vkuehn Week 15]] and [[Kevinmcgee Week 15]]
#QA:
#Coder:

=== Reflection ===
Each team member should reflect on the team's progress:

[[User:Vkuehn|Viktoria Kuehn]]
# What worked: We successfully looked at the results of our P-values and created the GenMAPP criteria and colorsets.
# What didn't work: We are waiting for MAPPFinder to give us results.
# What will I do next to fix what didn't work: If it does not work within 2 hours we will have to try it again and make sure no errors were made.
[[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 11:03, 5 December 2013 (PST)

'''[[User:Kevinmcgee|Kevin McGee]]'''
#We were able to troubleshoot any problems with uploading our data into GenMAPP by going through everything step by step
#We were held up at times by errors that involved us to wait long amounts of time. For instance, we need to export a new gene database, however we could not because postgress was already being used on the computer we were using. therefore, we had to wait hours for that to finish so we could export our database. We should plan ahead better so we don't have to wait like that.
#I don't know what we could do to fix that other than stay on our computers we had been working on the whole time
[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 11:08, 5 December 2013 (PST)

'''[[User:Gleis|Gabriel Leis]]'''
#Code for species customization was edited twice to ensure ease of use of microarray data in GenMapp. Gene Database Testing report was initiated and nearly completed.
#Errors in the code as well as errors in the formatting of the microarray data held up the group project.
#Test new species customization code, finish gene database testing report
[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 22:16, 6 December 2013 (PST)

{{Template:Leishmania Major Navigation}}
[[Category:Assignment]]
[[Category: Group Projects]]
[[Category: Journal Entry]]

Leishmania major Week 15 Status Report

2013-12-07T06:16:51Z

Gleis: /* Reflection */

== Team Journal Assignment Week 15 ==
===Status report as to progress on each milestone that that you have set for the week:===
#GenMAPP users:
#*Did sanity check for the p-values of both L. major and L. infantum
#*Created GenMAPP criteria and colorsets
#*Ran MAPPFiner and are waiting for results
#*:For more details on these steps refer to [[Vkuehn Week 15]] and [[Kevinmcgee Week 15]]
#QA:
#Coder:

=== Reflection ===
Each team member should reflect on the team's progress:

[[User:Vkuehn|Viktoria Kuehn]]
# What worked: We successfully looked at the results of our P-values and created the GenMAPP criteria and colorsets.
# What didn't work: We are waiting for MAPPFinder to give us results.
# What will I do next to fix what didn't work: If it does not work within 2 hours we will have to try it again and make sure no errors were made.
[[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 11:03, 5 December 2013 (PST)

'''[[User:Kevinmcgee|Kevin McGee]]'''
#We were able to troubleshoot any problems with uploading our data into GenMAPP by going through everything step by step
#We were held up at times by errors that involved us to wait long amounts of time. For instance, we need to export a new gene database, however we could not because postgress was already being used on the computer we were using. therefore, we had to wait hours for that to finish so we could export our database. We should plan ahead better so we don't have to wait like that.
#I don't know what we could do to fix that other than stay on our computers we had been working on the whole time
[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 11:08, 5 December 2013 (PST)

[[User:Gleis|Gabriel Leis]]
#Code for species customization was edited twice to ensure ease of use of microarray data in GenMapp. Gene Database Testing report was initiated and nearly completed.
#Errors in the code as well as errors in the formatting of the microarray data held up the group project.
#Test new species customization code, finish gene database testing report
[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 22:16, 6 December 2013 (PST)

{{Template:Leishmania Major Navigation}}
[[Category:Assignment]]
[[Category: Group Projects]]
[[Category: Journal Entry]]

Leishmania major Week 15 Status Report

2013-12-07T03:25:00Z

Gleis: /* Reflection */

== Team Journal Assignment Week 15 ==
===Status report as to progress on each milestone that that you have set for the week:===
#GenMAPP users:
#*Did sanity check for the p-values of both L. major and L. infantum
#*Created GenMAPP criteria and colorsets
#*Ran MAPPFiner and are waiting for results
#*:For more details on these steps refer to [[Vkuehn Week 15]] and [[Kevinmcgee Week 15]]
#QA:
#Coder:

=== Reflection ===
Each team member should reflect on the team's progress:

[[User:Vkuehn|Viktoria Kuehn]]
# What worked: We successfully looked at the results of our P-values and created the GenMAPP criteria and colorsets.
# What didn't work: We are waiting for MAPPFinder to give us results.
# What will I do next to fix what didn't work: If it does not work within 2 hours we will have to try it again and make sure no errors were made.
[[User:Vkuehn|Vkuehn]] ([[User talk:Vkuehn|talk]]) 11:03, 5 December 2013 (PST)

'''[[User:Kevinmcgee|Kevin McGee]]'''
#We were able to troubleshoot any problems with uploading our data into GenMAPP by going through everything step by step
#We were held up at times by errors that involved us to wait long amounts of time. For instance, we need to export a new gene database, however we could not because postgress was already being used on the computer we were using. therefore, we had to wait hours for that to finish so we could export our database. We should plan ahead better so we don't have to wait like that.
#I don't know what we could do to fix that other than stay on our computers we had been working on the whole time
[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 11:08, 5 December 2013 (PST)

[[User:Gleis|Gabriel Leis]]
#Code for species customization was edited twice to ensure ease of use of microarray data in GenMapp. Gene Database Testing report was initiated and nearly completed.
#Errors in the code as well as errors in the formatting of the microarray data held up the group project.
#Test new species customization code, finish gene database testing report
{{Template:Leishmania Major Navigation}}
[[Category:Assignment]]
[[Category: Group Projects]]
[[Category: Journal Entry]]

Leishmania major

2013-12-04T05:28:18Z

Gleis: /* Data Files */

File:Dist Leishmania Lena Gabe 03122013.zip

2013-12-04T05:27:34Z

Gleis:

Gleis Week 15

2013-12-03T18:50:37Z

Gleis: Created page with "==Lab Journal== *Code needed ID changes in Eclipse *Replaced first period with an "_" and removed second "_" *Replaced to look like "LMJF_##_####""

==Lab Journal==
*Code needed ID changes in Eclipse
*Replaced first period with an "_" and removed second "_"
*Replaced to look like "LMJF_##_####"

Template:Workstuff

2013-12-03T18:48:47Z

Gleis:

Important Links

[[User:Gleis|Gabriel Leis]]

[[Leishmania major|Off The Leish]]

[[Week 1]]

[[Week 2]]

[[Week 3]]

[[Week 4]]

[[Week 5]]

[[Week 6]]

[[Week 7]]

[[Week 8]]

[[Week 9]]

[[Week 10]]

[[Week 11]]

[[Week 12]]

[[Week 13]]

[[Class Journal Week 1]]

[[Class Journal Week 2]]

[[Class Journal Week 3]]

[[Class Journal Week 4]]

[[Class Journal Week 5]]

[[Class Journal Week 6]]

[[Class Journal Week 7]]

[[Class Journal Week 8]]

[[Class Journal Week 9]]

[[Gleis Week 2]]

[[Gleis Week 3]]

[[Gleis Week 4]]

[[Gleis Week 5]]

[[Gleis Week 6]]

[[Gleis Week 7]]

[[Gleis Week 8]]

[[Gleis Week 9]]

[[Gleis Week 10]]

[[Gleis Week 11]]

[[Gleis Week 12]]

[[Gleis Week 13]]

[[Gleis Week 14]]

[[Gleis Week 15]]

[[Category:Journal Entry]]