LMU BioDB 2013 - User contributions [en]

Vkuehn Individual Assessment and Reflection

2013-12-16T05:34:57Z

Vkuehn: /* Final Week */ Finished summarizing last minute changes after the presentation

== Statement of Work ==

* Describe exactly what you did on the project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
** Other files or documents
** Code or scripts

=== [[Vkuehn Week 12]]===
* Compiled all of the raw data so that it would be ready to be analysed statistically and normalized
** Chip raw data files compared to SDRF and organized
** Named each chip in a way that gave more information to the project (Chip number from sdrf and species)
** Created the compiled raw data for L. major
*Updated the team page and made wiki improvements
* As the team leader created [[The Plan]] to keep our progress organized and documented
** Created an outline of the project goals and interim deadlines
**Wrote the updates that had to do with GenMAPP users for the team page
===[[Vkuehn Week 13]]===
*Reread the paper and took notes on the specific meaning behind the microarray data and took notes on relevant information
*Scaled and centered microarray data
*Performed statistical analysis
* Edited the wiki and made formatting improvements on the templates so that the page would be easier to update for everyone
***Wrote the updates that had to do with GenMAPP users for the week
===[[Vkuehn Week 15]]===
*Did sanity check on the statistical results from L. major
*imported the mircoarray data to GenMAPP
*Assigned colors to the criteria for GenMAPP
*Ran GenMAPP and GO terms were found
** Found the ones with links to families and looked up the GO terms so that the mapp could be created
* Created the L. major week 15 Status Report Page
**Wrote the updates that had to do with GenMAPP users
===Final Week===
*Wrote my part of paper that corresponds to the journal club for the article and the microarray data compilation and statistical analysis, and made the power point outlining the project and having everyone input their parts [[Media:Leishmania PowerPoint 12122013.pdf]]
*Found and analyzed the results from our GenMAPP and the results in the experiment and compared them
*Looked up the GO terms and the genes that were found to have changed significantly using MAPPFinder and UniProt to organize the genes.
*:Figured out a way to categorize them for the MAPP [[File:Arromatic Compound Catabolic Process Comparative Pathway Map.mapp]]
**Highlighted similarities
* Created a presentation on Google Drive for the group to input the project to presentation
* Reviewed all of the pages and noted all of the requirements that need to be submitted for the project so nothing slips through, and communicated with the group on last minute deadlines
* Redid the statistical analysis of the L. major p-values and fold changes by filtering the excel file down to the relevant information after the presentation [[File:LeishmaniaCompiledStatAnalysis(C).txt ]]
* Wrote the conclusion comparing our results to the results of the article and made general conclusive remarks on the group write up, and made final touches throughout the paper. [[File:LeishmaniaFinalPaper.pdf]]

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
*: I think our team worked very well together. We were always good about communicating where the different members stood and if there were problems everyone worked together to make sure that they would get resolved so that the team could move to the next step. We were very good about planning all of the goals for the weeks and would stay after to make sure everyone was updated for the goals for the next meeting.
* What worked and what didn't work?
*: We all did a good job dividing the workload and the completion of all of the requirements in a timely manner worked well. The set up pf the team page for the initial journal club presentation was hectic and disorganized, but we were still getting familiar with the project.
* What would you do differently if you could do it all over again?
*: Made sure to complete even the last step before finals week because this step did not have a lot of instruction and took a lot of time to understand.
* Evaluate the Gene Database Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#: I am personally very impressed with the quality of our work. With such a large project undestanding all of the details of each step can seem overwhelming, but with the way each team member took a part we were each able to understand all of the details and see the big picture.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#: The organization of the group's wiki could have been improved in my opinion. I think we were in a rush to set it all up in the beginning, so the layout and organization of the information lacked structure. I think that the project was organized though, this just did not translate very well on the wiki page because of the ineffective formatting at the beginning.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*# Yes, our team achieved all of the project objectives. We worked to fix as many of the errors as we could up to the last minute. There are some genes that still did not make it into the database, but the coders worked hard and successfully reduced this number a lot. Other than that, everything was completed.

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
**: I learned the expanse of biological databases and why they are integral to biology today. I also learned the possibilities that these databases provide.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
**: I learned how to manage a long term project so that it does not become unmanageable at the end.
** With your hands (technical skills)?
**: I became more familiar with using computers and learned how to use different ways of manipulating data in different programs.
* What lesson will you take away from this project that you will still use a year from now?
*: The knowledge of how to use databases and how to navigate them to find information.

{{Template: Vkuehn}}

Vkuehn Individual Assessment and Reflection

2013-12-13T20:16:11Z

Vkuehn:

== Statement of Work ==

* Describe exactly what you did on the project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
** Other files or documents
** Code or scripts

=== [[Vkuehn Week 12]]===
* Compiled all of the raw data so that it would be ready to be analysed statistically and normalized
** Chip raw data files compared to SDRF and organized
** Named each chip in a way that gave more information to the project (Chip number from sdrf and species)
** Created the compiled raw data for L. major
*Updated the team page and made wiki improvements
* As the team leader created [[The Plan]] to keep our progress organized and documented
** Created an outline of the project goals and interim deadlines
**Wrote the updates that had to do with GenMAPP users for the team page
===[[Vkuehn Week 13]]===
*Reread the paper and took notes on the specific meaning behind the microarray data and took notes on relevant information
*Scaled and centered microarray data
*Performed statistical analysis
* Edited the wiki and made formatting improvements on the templates so that the page would be easier to update for everyone
***Wrote the updates that had to do with GenMAPP users for the week
===[[Vkuehn Week 15]]===
*Did sanity check on the statistical results from L. major
*imported the mircoarray data to GenMAPP
*Assigned colors to the criteria for GenMAPP
*Ran GenMAPP and GO terms were found
** Found the ones with links to families and looked up the GO terms so that the mapp could be created
* Created the L. major week 15 Status Report Page
**Wrote the updates that had to do with GenMAPP users
===Final Week===
*Wrote my part of paper that corresponds to the journal club for the article and the microarray data compilation and statistical analysis
*Looked at the results from our GenMAPP and the results in the experiment and compared them
**Highlighted similarities
* Created a presentation on Google Drive for the group to input the project to presentation
* Reviewed all of the pages and noted all of the requirements that need to be submitted for the project so nothing slips through

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
*: I think our team worked very well together. We were always good about communicating where the different members stood and if there were problems everyone worked together to make sure that they would get resolved so that the team could move to the next step. We were very good about planning all of the goals for the weeks and would stay after to make sure everyone was updated for the goals for the next meeting.
* What worked and what didn't work?
*: We all did a good job dividing the workload and the completion of all of the requirements in a timely manner worked well. The set up pf the team page for the initial journal club presentation was hectic and disorganized, but we were still getting familiar with the project.
* What would you do differently if you could do it all over again?
*: Made sure to complete even the last step before finals week because this step did not have a lot of instruction and took a lot of time to understand.
* Evaluate the Gene Database Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#: I am personally very impressed with the quality of our work. With such a large project undestanding all of the details of each step can seem overwhelming, but with the way each team member took a part we were each able to understand all of the details and see the big picture.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#: The organization of the group's wiki could have been improved in my opinion. I think we were in a rush to set it all up in the beginning, so the layout and organization of the information lacked structure. I think that the project was organized though, this just did not translate very well on the wiki page because of the ineffective formatting at the beginning.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*# Yes, our team achieved all of the project objectives. We worked to fix as many of the errors as we could up to the last minute. There are some genes that still did not make it into the database, but the coders worked hard and successfully reduced this number a lot. Other than that, everything was completed.

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
**: I learned the expanse of biological databases and why they are integral to biology today. I also learned the possibilities that these databases provide.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
**: I learned how to manage a long term project so that it does not become unmanageable at the end.
** With your hands (technical skills)?
**: I became more familiar with using computers and learned how to use different ways of manipulating data in different programs.
* What lesson will you take away from this project that you will still use a year from now?
*: The knowledge of how to use databases and how to navigate them to find information.

{{Template: Vkuehn}}

Template:Leishmania Major File Updates

2013-12-13T03:14:45Z

Vkuehn:

#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]]
#12/12/13
#* [[File:LeishmaniaCompiledStatAnalysis(C).txt]] The data from L. major only for analyzing statistics

File:LeishmaniaCompiledStatAnalysis(C).txt

2013-12-13T03:13:24Z

Vkuehn:

Vkuehn Individual Assessment and Reflection

2013-12-11T12:36:13Z

Vkuehn:

== Statement of Work ==

* Describe exactly what you did on the project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
** Other files or documents
** Code or scripts

=== [[Vkuehn Week 12]]===
* Compiled all of the raw data so that it would be ready to be analysed statistically and normalized
** Chip raw data files compared to SDRF and organized
** Named each chip in a way that gave more information to the project (Chip number from sdrf and species)
** Created the compiled raw data for L. major
*Updated the team page and made wiki improvements
* As the team leader created [[The Plan]] to keep our progress organized and documented
** Created an outline of the project goals and interim deadlines
**Wrote the updates that had to do with GenMAPP users for the team page
===[[Vkuehn Week 13]]===
*Reread the paper and took notes on the specific meaning behind the microarray data and took notes on relevant information
*Scaled and centered microarray data
*Performed statistical analysis
* Edited the wiki and made formatting improvements on the templates so that the page would be easier to update for everyone
***Wrote the updates that had to do with GenMAPP users for the week
===[[Vkuehn Week 15]]===
*Did sanity check on the statistical results from L. major
*imported the mircoarray data to GenMAPP
*Assigned colors to the criteria for GenMAPP
*Ran GenMAPP and GO terms were found
** Found the ones with links to families and looked up the GO terms so that the mapp could be created
* Created the L. major week 15 Status Report Page
**Wrote the updates that had to do with GenMAPP users
===Final Week===
*Wrote my part of paper that corresponds to the journal club for the article and the microarray data compilation and statistical analysis
*Looked at the results from our GenMAPP and the results in the experiment and compared them
**Highlighted similarities
* Created a presentation on Google Drive for the group to input the project to presentation
* Reviewed all of the pages and noted all of the requirements that need to be submitted for the project so nothing slips through

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
*: I think our team worked very well together. We were always good about communicating where the different members stood and if there were problems everyone worked together to make sure that they would get resolved so that the team could move to the next step. We were very good about planning all of the goals for the weeks and would stay after to make sure everyone was updated for the goals for the next meeting.
* What worked and what didn't work?
*: We all did a good job dividing the workload and the completion of all of the requirements in a timely manner worked well. The set up pf the team page for the initial journal club presentation was hectic and disorganized, but we were still getting familiar with the project.
* What would you do differently if you could do it all over again?
*: Made sure to complete even the last step before finals week because this step did not have a lot of instruction and took a lot of time to understand.
* Evaluate the Gene Database Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#: I am personally very impressed with the quality of our work. With such a large project undestanding all of the details of each step can seem overwhelming, but with the way each team member took a part we were each able to understand all of the details and see the big picture.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#: The organization of the group's wiki could have been improved in my opinion. I think we were in a rush to set it all up in the beginning, so the layout and organization of the information lacked structure. I think that the project was organized though, this just did not translate very well on the wiki page because of the ineffective formatting at the beginning.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

{{Template: Vkuehn}}

Vkuehn Individual Assessment and Reflection

2013-12-11T12:35:40Z

Vkuehn: /* Assessment of Project */

== Statement of Work ==

* Describe exactly what you did on the project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
** Other files or documents
** Code or scripts

=== [[Vkuehn Week 12]]===
* Compiled all of the raw data so that it would be ready to be analysed statistically and normalized
** Chip raw data files compared to SDRF and organized
** Named each chip in a way that gave more information to the project (Chip number from sdrf and species)
** Created the compiled raw data for L. major
*Updated the team page and made wiki improvements
* As the team leader created [[The Plan]] to keep our progress organized and documented
** Created an outline of the project goals and interim deadlines
**Wrote the updates that had to do with GenMAPP users for the team page
===[[Vkuehn Week 13]]===
*Reread the paper and took notes on the specific meaning behind the microarray data and took notes on relevant information
*Scaled and centered microarray data
*Performed statistical analysis
* Edited the wiki and made formatting improvements on the templates so that the page would be easier to update for everyone
***Wrote the updates that had to do with GenMAPP users for the week
===[[Vkuehn Week 15]]===
*Did sanity check on the statistical results from L. major
*imported the mircoarray data to GenMAPP
*Assigned colors to the criteria for GenMAPP
*Ran GenMAPP and GO terms were found
** Found the ones with links to families and looked up the GO terms so that the mapp could be created
* Created the L. major week 15 Status Report Page
**Wrote the updates that had to do with GenMAPP users
===Final Week===
*Wrote my part of paper that corresponds to the journal club for the article and the microarray data compilation and statistical analysis
*Looked at the results from our GenMAPP and the results in the experiment and compared them
**Highlighted similarities
* Created a presentation on Google Drive for the group to input the project to presentation
* Reviewed all of the pages and noted all of the requirements that need to be submitted for the project so nothing slips through

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
*: I think our team worked very well together. We were always good about communicating where the different members stood and if there were problems everyone worked together to make sure that they would get resolved so that the team could move to the next step. We were very good about planning all of the goals for the weeks and would stay after to make sure everyone was updated for the goals for the next meeting.
* What worked and what didn't work?
*: We all did a good job dividing the workload and the completion of all of the requirements in a timely manner worked well. The set up pf the team page for the initial journal club presentation was hectic and disorganized, but we were still getting familiar with the project.
* What would you do differently if you could do it all over again?
*: Made sure to complete even the last step before finals week because this step did not have a lot of instruction and took a lot of time to understand.
* Evaluate the Gene Database Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#: I am personally very impressed with the quality of our work. With such a large project undestanding all of the details of each step can seem overwhelming, but with the way each team member took a part we were each able to understand all of the details and see the big picture.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#: The organization of the group's wiki could have been improved in my opinion. I think we were in a rush to set it all up in the beginning, so the layout and organization of the information lacked structure. I think that the project was organized though, this just did not translate very well on the wiki page because of the ineffective formatting at the beginning.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

Vkuehn Individual Assessment and Reflection

2013-12-11T12:26:43Z

Vkuehn: /* Final Week */

Vkuehn Individual Assessment and Reflection

2013-12-11T12:25:51Z

Vkuehn: /* Final Week */

Vkuehn Individual Assessment and Reflection

2013-12-11T12:25:30Z

Vkuehn: /* Statement of Work */

Vkuehn Week 15

2013-12-11T11:56:13Z

Vkuehn: /* GenMAPP Expression Dataset Manager */

=='''ELECTRONIC NOTEBOOK'''==
==12/5/13==
===Sanity Check===
*P-value less than 0.05: 5303
*P-value less that 0.01: 2130
*P-value less that 0.001: 317
*P-value less that 0.0001: 0
*Out of the 19201 T tests performed, more than 960 results had a P-value less than 0.05. Since 5303 genes passed this cut off it means that there were some significant changes.
*Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC" column to show all genes with an average log fold change greater than zero. These were the ones that increased relative to control. There were 2970
*Genes with an average log fold change less than zero. These were the ones that decreased relative to control. There were: 2334
*Average log fold change of > 0.25 and p < 0.05: 2861
*Average log fold change of < -0.25 and p < 0.05: 2431
===GenMAPP Expression Dataset Manager===
*For exact procedure reference [[Vkuehn Week 13]] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
* The colors were assigned to the two main criterion
**Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored '''blue'''
**Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored '''purple'''

=='''12/7/13'''==
===GO Terms Analysed using MAPPFinder===
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05
:*Came up with 6 results for increased
:*Two GO terms were within the same family. "integral to membrane" and "intrinsic to membrane"
:*:Integral to membrane:Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. (under cellular compnent)
:*:intrinsic to membrane:Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane. (under cellular component)
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05. Number Changed (in column I) greater than or equal to 4 or 5 AND less than 100
:*Came up with 8 results for decreased
:*Found a lot that have to do with catabolic process.
:*"aromatic compound catabolic process" "cellular nitrogen catabolic process" "nucelobase containing compound catabolic process" "heterocyled catabolic process"
:*:aromatic compound catabolic process:The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
:*:cellular nitrogen catablolic process: The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds

===GenMAPP Finder===
Ran genmapp and waiting for results to be generated

{{Template:Vkuehn}}
[[Category: Journal Entry]]

Vkuehn Individual Assessment and Reflection

2013-12-11T10:51:07Z

Vkuehn: Created page with "=== Statement of Work === * Describe exactly what you did on the project. * Provide references or links to artifacts of your work, such as: ** Wiki pages ** Other files or do..."

=== Statement of Work ===

* Describe exactly what you did on the project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
** Other files or documents
** Code or scripts

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
* What worked and what didn't work?
* What would you do differently if you could do it all over again?
* Evaluate the Gene Database Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

Template:Vkuehn

2013-12-11T10:50:48Z

Vkuehn:

* [[Template:vkuehn]]
* [[User:vkuehn|Viktoria Kuehn]]
* [[Week 1 | Week 1 Assignment]]
* [[Class_Journal_Week_1|Class Journal 1]]
* [[Week 2 | Week 2 Assignment]]
* [[Class_Journal_Week_2|Class Journal 2]]
* [[Vkuehn Week 2]]
* [[Week 3 | Week 3 Assignment]]
* [[Class_Journal_Week_3|Class Journal 3]]
* [[Vkuehn Week 3]]
* [[Week 4 | Week 4 Assignment]]
* [[Class_Journal_Week_4#Viktoria_Kuehn|Class Journal 4]]
* [[Vkuehn Week 4]]
* [[Week 5| Week 5 Assignment]]
* [[Vkuehn Week 5]]
* [[Ensembl Database]]
* [[Week 6 | Week 6 Assignment]]
* [[Class_Journal_Week_6|Class Journal 6]]
* [[Vkuehn Week 6]]
* [[Week 7 | Week 7 Assignment]]
* [[Class_Journal_Week_7|Class Journal 7]]
* [[Vkuehn Week 7]]
* [[Week 8 | Week 8 Assignment]]
* [[Class_Journal_Week_8|Class Journal 8]]
* [[Vkuehn Week 8]]
* [[Leishmania major]]
* [[Week 9 | Week 9 Assignment]]
* [[Class_Journal_Week_9|Class Journal 9]]
* [[Vkuehn Week 9]]
* [[Week 10 | Week 10 Assignment]]
* [[Class_Journal_Week_10|Class Journal 10]]
* [[Vkuehn Week 10]]
* [[Leishmania major]]
* [[Week 11 | Week 11 Assignment]]
* [[Vkuehn Week 11]]
*[[Media:Leishmania_major_BD.pdf|Leishmania major Genome Reference Article Presentation]]
*[[Vkuehn Week 12]]
*[[Week 12| Week 12 Assignment]]
*[[Leishmania major Week 12 Status Report]]
*[[Vkuehn Week 13]]
*[[Week 13| Week 13 Assignment]]
*[[Vkuehn Week 15]]
*[[Week 15| Week 15 Assignment]]
*[[Vkuehn Individual Assessment and Reflection]]

[[Category: Journal Entry]]

Vkuehn Week 13

2013-12-10T22:11:39Z

Vkuehn: /* 11/21/13 */

=='''Week 13 Individual Lab Notebook'''==

From this week on, your Individual Journal Assignment will be to complete your electronic laboratory notebook that records your work on your team's final project.
===11/19/13===
:Understanding the array data:
:*data from several independent L. infantum and L. major DNA microarray experiments were compiled and compared
:*compared each gene according to the normalized log2 ratio of the Alexa 647/Alexa 555 signal intensities (amastigotes/promastigotes) and to the signal mean intensity of each spot
:*Transcriptional analyses of L. infantum promastigote compared to L. infantum intracellular amastigote, and L. major promastigote compared to L. major intracellular amastigote
The full-genome DNA microarray includes one 70mer-oligonucleotide probe for each gene of L. infantum and for each gene of L.major LV39
:*Lmj Sample Info: The replicate numbers and sample IDs correspond to our txt files. (22, 24, 25, 28, 30 were dye swaps)
[[File:LmjSampleInfo.PNG]]
:You need to record a narrative that describes all of the methods that you are using in enough detail so that the instructors or your other team members can follow and reproduce your work.
Include links to artifacts you produce (files, images, testing reports, code, etc.)
===11/21/13===
Scaled and Centered the L. major data and performed statistical analysis
*Working with the data:
*#Create new worksheet and copy over all the data
*#Find STDEV and AVG for each column as new rows on top
*#Create new columns next to the sample columns, label name_SC
*#Scale and center doing (Value-AVG)/STDEV for each sample
*Inserted new worksheet called Statistics
*#Added new column: Avg_Log_FC_all
*#Delete the other columns and keep only the SC columns. Delete 2 empty rows on top
*#Compute average log full change for all of the samples ex:(=AVG(B2:E2))
*#T-test: =AVERAGE(samples)/(STDEV(samples)/(SQRT(# of replicates,4))
*#Create new column titled P-Value and Calculated the P-value (lower than 0.05)using TDIST(ABS(tstat),degrees of freedom,tails)
*Created new worksheet titled GenMAPP
*#copy over the data from Statistics worksheet (using values only)
*#Select Fold Changes column and format cells under number tab to 2 decimal places
*#Make 4 decimal places for Tstat and Pvalue
*#Cut Tstat and Pvalue columns and paste to the right of gene ID column
*#Insert "SystemCode" column next to the ID column and input "N" for all rows
*#Save as tab-delimited text file and excel file
'''Excel File''': [[File:L.majorStats.xls]]
'''Text File''': [[File:L.majorStats.txt]]

Template:Vkuehn

2013-12-10T21:31:08Z

Vkuehn: Added Individual Assessment and Reflection

* [[Template:vkuehn]]
* [[User:vkuehn|Viktoria Kuehn]]
* [[Week 1 | Week 1 Assignment]]
* [[Class_Journal_Week_1|Class Journal 1]]
* [[Week 2 | Week 2 Assignment]]
* [[Class_Journal_Week_2|Class Journal 2]]
* [[Vkuehn Week 2]]
* [[Week 3 | Week 3 Assignment]]
* [[Class_Journal_Week_3|Class Journal 3]]
* [[Vkuehn Week 3]]
* [[Week 4 | Week 4 Assignment]]
* [[Class_Journal_Week_4#Viktoria_Kuehn|Class Journal 4]]
* [[Vkuehn Week 4]]
* [[Week 5| Week 5 Assignment]]
* [[Vkuehn Week 5]]
* [[Ensembl Database]]
* [[Week 6 | Week 6 Assignment]]
* [[Class_Journal_Week_6|Class Journal 6]]
* [[Vkuehn Week 6]]
* [[Week 7 | Week 7 Assignment]]
* [[Class_Journal_Week_7|Class Journal 7]]
* [[Vkuehn Week 7]]
* [[Week 8 | Week 8 Assignment]]
* [[Class_Journal_Week_8|Class Journal 8]]
* [[Vkuehn Week 8]]
* [[Leishmania major]]
* [[Week 9 | Week 9 Assignment]]
* [[Class_Journal_Week_9|Class Journal 9]]
* [[Vkuehn Week 9]]
* [[Week 10 | Week 10 Assignment]]
* [[Class_Journal_Week_10|Class Journal 10]]
* [[Vkuehn Week 10]]
* [[Leishmania major]]
* [[Week 11 | Week 11 Assignment]]
* [[Vkuehn Week 11]]
*[[Media:Leishmania_major_BD.pdf|Leishmania major Genome Reference Article Presentation]]
*[[Vkuehn Week 12]]
*[[Week 12| Week 12 Assignment]]
*[[Leishmania major Week 12 Status Report]]
*[[Vkuehn Week 13]]
*[[Week 13| Week 13 Assignment]]
*[[Vkuehn Week 15]]
*[[Week 15| Week 15 Assignment]]
*[[Individual Assessment and Reflection]]

[[Category: Journal Entry]]

Vkuehn Week 15

2013-12-08T00:47:22Z

Vkuehn: /* GO Terms Analysed using MAPPFinder */

=='''ELECTRONIC NOTEBOOK'''==
==12/5/13==
===Sanity Check===
*P-value less than 0.05: 5303
*P-value less that 0.01: 2130
*P-value less that 0.001: 317
*P-value less that 0.0001: 0
*Out of the 19201 T tests performed, more than 960 results had a P-value less than 0.05. Since 5303 genes passed this cut off it means that there were some significant changes.
*Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC" column to show all genes with an average log fold change greater than zero. These were the ones that increased relative to control. There were 2970
*Genes with an average log fold change less than zero. These were the ones that decreased relative to control. There were: 2334
*Average log fold change of > 0.25 and p < 0.05: 2861
*Average log fold change of < -0.25 and p < 0.05: 2431
===GenMAPP Expression Dataset Manager===
*For exact procedure reference [Vkuehn Week 13] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
* The colors were assigned to the two main criterion
**Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored '''blue'''
**Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored '''purple'''

=='''12/7/13'''==
===GO Terms Analysed using MAPPFinder===
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05
:*Came up with 6 results for increased
:*Two GO terms were within the same family. "integral to membrane" and "intrinsic to membrane"
:*:Integral to membrane:Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. (under cellular compnent)
:*:intrinsic to membrane:Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane. (under cellular component)
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05. Number Changed (in column I) greater than or equal to 4 or 5 AND less than 100
:*Came up with 8 results for decreased
:*Found a lot that have to do with catabolic process.
:*"aromatic compound catabolic process" "cellular nitrogen catabolic process" "nucelobase containing compound catabolic process" "heterocyled catabolic process"
:*:aromatic compound catabolic process:The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
:*:cellular nitrogen catablolic process: The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds

===GenMAPP Finder===
Ran genmapp and waiting for results to be generated

{{Template:Vkuehn}}
[[Category: Journal Entry]]

Vkuehn Week 15

2013-12-08T00:46:49Z

Vkuehn: /* 12/7/13 */

=='''ELECTRONIC NOTEBOOK'''==
==12/5/13==
===Sanity Check===
*P-value less than 0.05: 5303
*P-value less that 0.01: 2130
*P-value less that 0.001: 317
*P-value less that 0.0001: 0
*Out of the 19201 T tests performed, more than 960 results had a P-value less than 0.05. Since 5303 genes passed this cut off it means that there were some significant changes.
*Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC" column to show all genes with an average log fold change greater than zero. These were the ones that increased relative to control. There were 2970
*Genes with an average log fold change less than zero. These were the ones that decreased relative to control. There were: 2334
*Average log fold change of > 0.25 and p < 0.05: 2861
*Average log fold change of < -0.25 and p < 0.05: 2431
===GenMAPP Expression Dataset Manager===
*For exact procedure reference [Vkuehn Week 13] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
* The colors were assigned to the two main criterion
**Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored '''blue'''
**Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored '''purple'''

=='''12/7/13'''==
===GO Terms Analysed using MAPPFinder===
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05
:*Came up with 6 results for increased
:*Two GO terms were within the same family. "integral to membrane" and "intrinsic to membrane"
:*:Integral to membrane:Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. (under cellular compnent)
:*:intrinsic to membrane:Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane. (under cellular component)
:Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05. Number Changed (in column I) greater than or equal to 4 or 5 AND less than 100
:*Came up with 8 results for decreased
:*Found a lot that have to do with catabolic process.
:*"aromatic compound catabolic process" "cellular nitrogen catabolic process" "nucelobase containing compound catabolic process" "heterocyled catabolic process"
:*:aromatic compound catabolic process:The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
:*:cellular nitrogen catablolic process: The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds

===GenMAPP Finder===
Ran genmapp and waiting for results to be generated

{{Template:Vkuehn}}
[[Category: Journal Entry]]

Vkuehn Week 15

2013-12-08T00:45:53Z

Vkuehn: /* GO Terms Analysed using MAPPFinder */

=='''ELECTRONIC NOTEBOOK'''==
==12/5/13==
===Sanity Check===
*P-value less than 0.05: 5303
*P-value less that 0.01: 2130
*P-value less that 0.001: 317
*P-value less that 0.0001: 0
*Out of the 19201 T tests performed, more than 960 results had a P-value less than 0.05. Since 5303 genes passed this cut off it means that there were some significant changes.
*Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC" column to show all genes with an average log fold change greater than zero. These were the ones that increased relative to control. There were 2970
*Genes with an average log fold change less than zero. These were the ones that decreased relative to control. There were: 2334
*Average log fold change of > 0.25 and p < 0.05: 2861
*Average log fold change of < -0.25 and p < 0.05: 2431
===GenMAPP Expression Dataset Manager===
*For exact procedure reference [Vkuehn Week 13] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
* The colors were assigned to the two main criterion
**Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored '''blue'''
**Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored '''purple'''

=='''12/7/13'''==
===GO Terms Analysed using MAPPFinder===
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05
**Came up with 6 results for increased
**Two GO terms were within the same family. "integral to membrane" and "intrinsic to membrane"
**:Integral to membrane:Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. (under cellular compnent)
**:intrinsic to membrane:Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane. (under cellular component)
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05. Number Changed (in column I) greater than or equal to 4 or 5 AND less than 100
**Came up with 8 results for decreased
**Found a lot that have to do with catabolic process.
**"aromatic compound catabolic process" "cellular nitrogen catabolic process" "nucelobase containing compound catabolic process" "heterocyled catabolic process"
**:aromatic compound catabolic process:The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
**:cellular nitrogen catablolic process: The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds

===GenMAPP Finder===
Ran genmapp and waiting for results to be generated

{{Template:Vkuehn}}
[[Category: Journal Entry]]

Vkuehn Week 15

2013-12-08T00:36:28Z

Vkuehn: /* GO Terms Analysed */

=='''ELECTRONIC NOTEBOOK'''==
==12/5/13==
===Sanity Check===
*P-value less than 0.05: 5303
*P-value less that 0.01: 2130
*P-value less that 0.001: 317
*P-value less that 0.0001: 0
*Out of the 19201 T tests performed, more than 960 results had a P-value less than 0.05. Since 5303 genes passed this cut off it means that there were some significant changes.
*Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC" column to show all genes with an average log fold change greater than zero. These were the ones that increased relative to control. There were 2970
*Genes with an average log fold change less than zero. These were the ones that decreased relative to control. There were: 2334
*Average log fold change of > 0.25 and p < 0.05: 2861
*Average log fold change of < -0.25 and p < 0.05: 2431
===GenMAPP Expression Dataset Manager===
*For exact procedure reference [Vkuehn Week 13] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
* The colors were assigned to the two main criterion
**Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored '''blue'''
**Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored '''purple'''

=='''12/7/13'''==
===GO Terms Analysed using MAPPFinder===
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05
**Came up with 6 results for increased
**Two GO terms were within the same family. "integral to membrane" and "intrinsic to membrane"
**:Integral to membrane:Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. (under cellular compnent)
**:intrinsic to membrane:Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane. (under cellular component)
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05. Number Changed (in column I) greater than or equal to 4 or 5 AND less than 100
**Came up with 8 results for decreased
**Found a lot that have to do with catabolic process.
**:"aromatic compound catabolic process" "cellular nitrogen catabolic process" "nucelobase containing compound catabolic process" "heterocyled catabolic process"

===GenMAPP Finder===
Ran genmapp and waiting for results to be generated

{{Template:Vkuehn}}
[[Category: Journal Entry]]

Vkuehn Week 15

2013-12-08T00:35:15Z

Vkuehn: /* GenMAPP Expression Dataset Manager */

=='''ELECTRONIC NOTEBOOK'''==
==12/5/13==
===Sanity Check===
*P-value less than 0.05: 5303
*P-value less that 0.01: 2130
*P-value less that 0.001: 317
*P-value less that 0.0001: 0
*Out of the 19201 T tests performed, more than 960 results had a P-value less than 0.05. Since 5303 genes passed this cut off it means that there were some significant changes.
*Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC" column to show all genes with an average log fold change greater than zero. These were the ones that increased relative to control. There were 2970
*Genes with an average log fold change less than zero. These were the ones that decreased relative to control. There were: 2334
*Average log fold change of > 0.25 and p < 0.05: 2861
*Average log fold change of < -0.25 and p < 0.05: 2431
===GenMAPP Expression Dataset Manager===
*For exact procedure reference [Vkuehn Week 13] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
* The colors were assigned to the two main criterion
**Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored '''blue'''
**Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored '''purple'''

===GO Terms Analysed===
'''12/7/13'''
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05
**Came up with 6 results for increased
**Two GO terms were within the same family. "integral to membrane" and "intrinsic to membrane"
**:Integral to membrane:Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. (under cellular compnent)
**:intrinsic to membrane:Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane. (under cellular component)
*Filtered Z Score (in column N) greater than 2
PermuteP (in column O) less than 0.05. Number Changed (in column I) greater than or equal to 4 or 5 AND less than 100
**Came up with 8 results for decreased
**Found a lot that have to do with catabolic process.
**:"aromatic compound catabolic process" "cellular nitrogen catabolic process" "nucelobase containing compound catabolic process" "heterocyled catabolic process"

===GenMAPP Finder===
Ran genmapp and waiting for results to be generated

{{Template:Vkuehn}}
[[Category: Journal Entry]]

Vkuehn Week 15

2013-12-05T19:08:16Z

Vkuehn: /* GenMAPP Finder */

Leishmania major Week 15 Status Report

2013-12-05T19:07:46Z

Vkuehn: /* 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:

=== 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)

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

Leishmania major Week 15 Status Report

2013-12-05T19:03:16Z

Vkuehn: /* Reflection */

== Team Journal Assignment Week 15 ==
===Status report as to progress on each milestone that that you have set for the week:===
#GenMAPP users:
#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)

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

Leishmania major Week 15 Status Report

2013-12-05T18:58:34Z

Vkuehn: /* 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:
#QA:
#Coder:

=== Reflection ===
Each team member should reflect on the team's progress:
# What worked?
# What didn't work?
# What will I do next to fix what didn't work?\

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

The Plan

2013-12-05T18:57:50Z

Vkuehn: /* Timeline */

=='''Leishmania major'''==
Timeline of due dates, helpful links, important updates, etc.
==='''Timeline'''===
*Preparation for Journal Club Individual Journal-- 11/12
*'''Journal Club Presentation-- 11/12'''
*:15 min ppt presentation on genome reference article
*:Finish individual journal by 11/8
*:Meet for work on ppt 11/8-11/10
*:Practice and final touches on ppt, and upload to wiki 11/11
*:[[Week 11]]

*Electronic Lab Notebook on updates on the final project
*:[[Week 12]] due 11/15
*:Please link the lab notebooks here:
*::[[Gleis Week 12]]
*::[[Lena Project Notebook]]
*::[[Vkuehn Week 12]]
*::[[Leishmania major Week 12 Status Report]]

*[[Week 13]] due 11/22
*:GenMAPP users: Perform Statistical Analysis and get ready for Import in to GenMAPP 11/22
*:QA: Get to know System IDs, Characterize regular expression patterns to detect the IDs 11/22

*Week 14
*:GenMAPP users: Run GenMAPP and generate all of the relevant files begin analysis 11/28
*:QA: customize the tally engine setup, add ordered locus IDs 11/28

*[[Week 15]] due 12/6
*: GenMAPP users: Analyze data 12/6
*:QA: Document the relational database schema for the gene database and create the ReadMe with comparisons to MOD for Leishmania 12/6
*: [[Leishmania major Week 15 Status Report]]

*'''Final Project Presentations''' 8-10 am on 12/12

*'''Project Deliverables due''' at 4:30 on 12/13

==='''Important Updates'''===
[[Template:Leishmania Major File Updates]]

Record names of the files as they are updated and edited with dates.
Upload any other relevant files here, and document major progress.

{{Leishmania Major File Updates}}

{{Template:Leishmania Major Navigation}}

Leishmania major Week 15 Status Report

2013-12-05T18:56:40Z

Vkuehn: week 15 made

== Team Journal Assignment Week 15 ==
===Status report as to progress on each milestone that that you have set for the week:===

=== Reflection ===
Each team member should reflect on the team's progress:
# What worked?
# What didn't work?
# What will I do next to fix what didn't work?\

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

Leishmania major

2013-12-05T18:51:45Z

Vkuehn: /* Group Projects */

=='''Team Members:'''==
#[[User:kevinmcgee | Kevin McGee]] : GenMAPP User
#[[User:Lena | Lena Hunt]] : Quality Assurance [[Lena Project Notebook]]
#[[User:vkuehn|Viktoria Kuehn]] : GenMAPP User
#[[User:Gleis| Gabriel Leis]] : Coder
[[Gene Database Project]]

=='''Reference Genome Article'''==
:[http://www.sciencemag.org/content/309/5733/436.long ''The Genome of the Kinetoplastid Parasite, Leishmania major'' (Reference Genome)]
* This article was found via the PubMed database and the key terms used were "Leishmania Major [MeSH Terms] AND Genome [Title]"
** This search resulted in 30 articles, about 5 seemed relevant but this one was the first which had the entire genome
:Citation for paper:
:Alasdair C. Ivens, Christopher S. Peacock, Elizabeth A. Worthey, Lee Murphy, Gautam Aggarwa, Matthew Berriman, Ellen Sisk, Marie-Adele Rajandream, Ellen Adlem, Rita Aert, Atashi Anupama, Zina Apostolou, Philip Attipoe, Nathalie Bason, Christopher Bauser, Alfred Beck, Stephen M. Beverley, Gabriella Bianchettin, Katja Borzym, Gordana Bothe, Carlo V. Bruschi, Matt Collins, Eithon Cadag, Laura Ciarloni, Christine Clayton, Richard M. R. Coulson, Ann Cronin, Angela K. Cruz, Robert M. Davies, Javier De Gaudenzi, Deborah E. Dobson, Andreas Duesterhoeft, Gholam Fazelina, Nigel Fosker, Alberto Carlos Frasch, Audrey Fraser, Monika Fuchs, Claudia Gabel, Arlette Goble, André Goffeau, David Harris, Christiane Hertz-Fowler, Helmut Hilbert, David Horn, Yiting Huang, Sven Klages, Andrew Knights, Michael Kube, Natasha Larke, Lyudmila Litvin, Angela Lord, Tin Louie, Marco Marra, David Masuy, Keith Matthews, Shulamit Michaeli, Jeremy C. Mottram, Silke Müller-Auer, Heather Munden, Siri Nelson, Halina Norbertczak, Karen Oliver, Susan O'Neil, Martin Pentony, Thomas M. Poh, Claire Price, Bénédicte Purnelle, Michael A. Quail, Ester Rabbinowitsch, Richard Reinhardt, Michael Rieger, Joel Rinta, Johan Robben, Laura Robertson, Jeronimo C. Ruiz, Simon Rutter, David Saunders, Melanie Schäfer, Jacquie Schein, David C. Schwartz, Kathy Seeger, Amber Seyler, Sarah Sharp, Heesun Shin, Dhileep Sivam, Rob Squares, Steve Squares, Valentina Tosato, Christy Vogt, Guido Volckaert, Rolf Wambutt, Tim Warren, Holger Wedler, John Woodward, Shiguo Zhou, Wolfgang Zimmermann, Deborah F. Smith, Jenefer M. Blackwell, Kenneth D. Stuart, Bart Barrel, Peter J. Myler (2005) The Genome of the Kinetoplastid Parasite, Leishmania major. Science;309(5733):436-42.

* Pdf of the reference article: [http://www.sciencemag.org/content/309/5733/436.full.pdf''PDF Reference Article'']
**The genome sequencing article was used to do a prospective search on the Web of Knowledge database.
***There were 696 results found that referenced this article, the most recent one was in October 2013.
***Many of the most recent articles that cited this paper were involved in studying drug resistance of Leishmania major and studied related pathogenic parasites using sequence comparative analysis, for example.
*Link to the results page for our reference genome article
Website: http://apps.webofknowledge.com/CitingArticles.do?product=WOS&SID=4BN9U1ila7MPj92Jjlp&search_mode=CitingArticles&parentProduct=WOS&parentQid=3&parentDoc=1&REFID=518694
:
:Below is a screen shot of the results.
[[File:WebOfKnowledge.png]]

=='''[[Leishmania Major Articles| Leishmania Major Articles]]'''==

===Leishmania Major Data Updates===
To update this list edit the following template page: [[Template:Leishmania Major File Updates]]
{{Leishmania Major File Updates}}

====Data Links====
*[http://www.ebi.ac.uk/arrayexpress/ ''Array Express'']
*[http://www.ncbi.nlm.nih.gov/pubmed?holding=calmulib ''PubMed'']
*[http://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=3EzLbnixsjRACypZYp3&preferencesSaved= ''Web of Knowledge'']

{{Leishmania Major Navigation}}

==Group Projects==

:[[Leishmania major Week 12 Status Report]]
:[[Leishmania major Week 13 Status Report]]
:[[Leishmania major Week 15 Status Report]]

[[Media:Leishmania_major_BD.pdf|Leishmania major Genome Reference Article Presentation]]

==Import/Export==
===Export Information===
:Uniprot: 7.12 minutes
:[[Media:UniprotXML Leishmania 05112013 Gabe Lena.xml]]
:GO OBO: 6.32 minutes
:[[Media:Leishmania 05112013 Gabe Lena.obo-xml.gz]]
:GOA: 4.54 minutes
:[[Media:LeishmaniaGOA 05112013 GabeLena.goa]]

===Tally Engine===
[[Image:Screen_shot_2013-11-07_at_10.49.17_AM.png]]

===Original Row Counts Comparison===
*Uniprot has 8041 which is the same the tallycount.
*There were 0 ordered locus, which is the same as the tallycount.
*There were 8315 hits for RefSeq, which is 2 fewer than was seen in the tallycount.
*There were 8315 hits for GeneID, which is 2 fewer than was seen in the tallycount.

==Gene Database Testing Report==
==Export Information==

Version of GenMAPP Builder: gmbuilder2.0-b72

Computer on which export was run: Front row , second computer from the left

Postgres Database name:Leishmania_major_11262013

UniProt XML filename: UniprotXML Leishmania 05112013 Gabe Lena.xml
* UniProt XML version (The version information can be found at [http://uniprot.org/news the UniProt News Page]): UniProt release 2013_10 - October 16, 2013
* Time taken to import: 7.12 minutes

GO OBO-XML filename: Leishmania 05112013 Gabe Lena.obo-xml.gz
* 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): Monday, ‎November ‎04, ‎2013, ‏‎2:03:38 AM
* Time taken to import:6.32 minutes
* Time taken to process: 0.4 minutes

GOA filename:LeishmaniaGOA 19112013 Lena Gabe.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]): 14 November, 2013
12-Nov-2013 11:47 3.0M
* Time taken to import: 4.54 minutes

Name of .gdb file: [[Media:LeishmaniaGDB Lena Gabe 20131203.gdb]]
* Upload your file and link to it here.

Note:

==TallyEngine==

[[Image:Leishmania TallyResults 05122013.PNG]]

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[Image:Leishmania Match Results 05122013 2.PNG]]

Are your results the same as you got for the TallyEngine? Why or why not?
:*We found 8353, we are missing 2 ORFs, but cannot reach the stragglers via coding.

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]]

8350 that match original pattern, 5 stragglers. There is an inconsistancy in patterns where some have underscores, some have periods, some have spaces. We were unable to capture all IDs at once.

==OriginalRowCounts Comparison==

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Benchmark .gdb file: (for the [[Week 9]] Assignment, use the "Vc-Std_External_20101022.gdb" as your benchmark, downloadable from [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download here].

Copy the OriginalRowCounts table and paste it here:

Note:

==Visual Inspection==

Perform visual inspection of individual tables to see if there are any problems.

* Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
* Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?

Note:

==.gdb Use in GenMAPP==

Note:

===Putting a gene on the MAPP using the GeneFinder window===

* Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.

Note:

===Creating an Expression Dataset in the Expression Dataset Manager===

* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?

Note:

===Coloring a MAPP with expression data===

Note:

===Running MAPPFinder===

Note:

Vkuehn Week 15

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Vkuehn: Created page with "=='''ELECTRONIC NOTEBOOK'''== ==12/5/13== ===Sanity Check=== *P-value less than 0.05: 5303 *P-value less that 0.01: 2130 *P-value less that 0.001: 317 *P-value less that 0.00..."

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File:L.infantumStats B.xls

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Leishmania major Week 13 Status Report

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Vkuehn:

==Import/Export GenMAPP==
Name:Leishmania_major_18112013
===Export Information===
:Uniprot: 7.42 minutes
:[[File:UniprotXML Leishmania 05112013 Gabe Lena.xml]]
:GO OBO: 5.96 minutes
:[[File:Leishmania 05112013 Gabe Lena.obo-xml.gz]]
:GOA: 0.04 minutes
:[[File:LeishmaniaGOA 19112013 Lena Gabe.goa]]

==Files==
:'''Newly Updates Database:'''[[File:Leishmania major 19112013 Dist.zip]]
:'''Name of .gdb File:'''[[Media:LeishmaniaGDB 21112013 Lena Gabe.gdb]]
:'''Fixed Microarray Data:'''[[File:L.majorCompiledRawData C 21112013.txt]]

==Reflections==
===[[User:Lena|Lena Hunt]]===
:1.)We got our database to export into GenMAPP. Originally it was showing a generic database, and it wouldn't recognize the OrderedLocusNames. We fixed it in Eclipse and uploaded it to the homepage. We then successfully got GenMAPP to recognize our database. We also updated our microarray data so that the gene IDs did not have extra numbers (we used the : as a separator.) We then went through and changed all the "Error" messages with a 0 so as not to confuse GenMAPP.
:2.)We managed to work through all the things that didn't work this week. At this time we are waiting for the export to complete to test gene database link and microarray data.
:3.)Currently we do not have any problems we are aware of, but after a entire work session of working through problems today, I think we are prepared to work through problems that may come up in the next work session.

===[[User:Gleis|Gabriel Leis]]===
#What worked?
#:
#What didn't work?
#:
#What will I do next to fix what didn't work?
#:

===[[User:Kevinmcgee|Kevin McGee]]===
#We were able to successfully analyze our GenMAPP data to prepare it for import to GenMAPP
#It was hard to relate some of the commands from VC to our data set because there were some major differences in the data that we had.
#Trying to fully understand all the columns and the cells will help us understand what is different from our data compared to VC and therefore how to handle the data differently

[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 11:08, 21 November 2013 (PST)

===[[User:Vkuehn|Viktoria Kuehn]]===
#What worked?
#:We got all of the data ready for import to GenMAPP
#What didn't work?
#:Some of the data had errors instead of values
#What will I do next to fix what didn't work?
#:We already fixed this by making those blank and not using them in the statistical analysis

==GenMAPP Data==
#Centered and Scaled the Microarray data
#Found the Average Fold Change
#Statistical Analysis: Found P-value and T-test
#Formatted to be compatible with GenMAPP
#Saved for GenMAPP as a txt file
#:For more detailed procedure info see [[Vkuehn Week 13]] for major or, for infantum see [[Kevinmcgee Week 13]]
#:The files can be found under [[Leishmania major]] in the File Updates section

Leishmania major Week 13 Status Report

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Vkuehn: /* GenMAPP Data */

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=='''Week 13 Individual Lab Notebook'''==

From this week on, your Individual Journal Assignment will be to complete your electronic laboratory notebook that records your work on your team's final project.
===11/19/13===
:Understanding the array data:
:*data from several independent L. infantum and L. major DNA microarray experiments were compiled and compared
:*compared each gene according to the normalized log2 ratio of the Alexa 647/Alexa 555 signal intensities (amastigotes/promastigotes) and to the signal mean intensity of each spot
:*Transcriptional analyses of L. infantum promastigote compared to L. infantum intracellular amastigote, and L. major promastigote compared to L. major intracellular amastigote
The full-genome DNA microarray includes one 70mer-oligonucleotide probe for each gene of L. infantum and for each gene of L.major LV39
:*Lmj Sample Info: The replicate numbers and sample IDs correspond to our txt files. (22, 24, 25, 28, 30 were dye swaps)
[[File:LmjSampleInfo.PNG]]
:You need to record a narrative that describes all of the methods that you are using in enough detail so that the instructors or your other team members can follow and reproduce your work.
Include links to artifacts you produce (files, images, testing reports, code, etc.)
===11/21/13===
Scaled and Centered the L. major data and performed statistical analysis
*Working with the data:
*#Create new worksheet and copy over all the data
*#Find STDEV and AVG for each column as new rows on top
*#Create new columns next to the sample columns, label name_SC
*#Scale and center doing (Value-AVG)/STDEV for each sample
*Inserted new worksheet called Statistics
*#Added 3 new columns: Avg_Log_FC_A, Avg_Log_FC_B, Avg_Log_FC_C
*#Delete the other columns and keep only the SC columns. Delete 2 empty rows on top
*#Compute average log full change for all of the samples ex:(=AVG(B2:E2))
*#T-test: =AVERAGE(samples)/(STDEV(samples)/(SQRT(# of replicates,4))
*#Create new column titled P-Value and Calculated the P-value (lower than 0.05)using TDIST(ABS(tstat),degrees of freedom,tails)
*Created new worksheet titled GenMAPP
*#copy over the data from Statistics worksheet (using values only)
*#Select Fold Changes column and format cells under number tab to 2 decimal places
*#Make 4 decimal places for Tstat and Pvalue
*#Cut Tstat and Pvalue columns and paste to the right of gene ID column
*#Insert "SystemCode" column next to the ID column and input "N" for all rows
*#Save as tab-delimited text file and excel file
'''Excel File''': [[File:L.majorStats.xls]]
'''Text File''': [[File:L.majorStats.txt]]

File:L.majorStats.txt

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File:L.majorStats.xls

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Vkuehn: Added Statistics Notes

=='''Week 13 Individual Lab Notebook'''==

From this week on, your Individual Journal Assignment will be to complete your electronic laboratory notebook that records your work on your team's final project.
===11/19/13===
:Understanding the array data:
:*data from several independent L. infantum and L. major DNA microarray experiments were compiled and compared
:*compared each gene according to the normalized log2 ratio of the Alexa 647/Alexa 555 signal intensities (amastigotes/promastigotes) and to the signal mean intensity of each spot
:*Transcriptional analyses of L. infantum promastigote compared to L. infantum intracellular amastigote, and L. major promastigote compared to L. major intracellular amastigote
The full-genome DNA microarray includes one 70mer-oligonucleotide probe for each gene of L. infantum and for each gene of L.major LV39
:*Lmj Sample Info: The replicate numbers and sample IDs correspond to our txt files. (22, 24, 25, 28, 30 were dye swaps)
[[File:LmjSampleInfo.PNG]]
:You need to record a narrative that describes all of the methods that you are using in enough detail so that the instructors or your other team members can follow and reproduce your work.
Include links to artifacts you produce (files, images, testing reports, code, etc.)
===11/21/13===
Scaled and Centered the L. major data and performed statistical analysis
*Working with the data:
*#Create new worksheet and copy over all the data
*#Find STDEV and AVG for each column as new rows on top
*#Create new columns next to the sample columns, label name_SC
*#Scale and center doing (Value-AVG)/STDEV for each sample
*Inserted new worksheet called Statistics
*#Added 3 new columns: Avg_Log_FC_A, Avg_Log_FC_B, Avg_Log_FC_C
*#Delete the other columns and keep only the SC columns. Delete 2 empty rows on top
*#Compute average log full change for all of the samples ex:(=AVG(B2:E2))
*#T-test: =AVERAGE(N2:P2)/(STDEV(N2:P2)/(SQRT(# of replicates))
*#Determine if it is significantly different than zero
*#Create new column titled P-Value and Calculated the P-value lower than 0.05 (Got 948 values that were significant).
*Created new worksheet titled GenMAPP
*#copy over the data from Statistics worksheet (using values only)
*#Select all fold changes and format cells under number tab to 2 decimal places
*#Do the same for columns R and S
*#Delete AVG and STDEV rows
*#Insert "SystemCode" column next to the ID column and input "N" for all rows
*#Save as tab-delimited text file

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Vkuehn: added l major data

#11/5/2013
#*[[File:A-GEOD-6855.adf_A.txt]] Array Design File
#*[[File:E-GEOD-10407.idf_A.txt]] Investigation Description File
#*[[File:E-GEOD-10407.processed.1_A.zip]] Processed Data
#*[[File:E-GEOD-10407.raw.1_A.zip]] Raw Data
#*[[file:E-GEOD-10407.sdrf_A.txt]] Sample and Data Relationship File
#11/7/2013
#*[[File: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
#*[[File:E-GEOD-10407.sdrf_C.txt]] Edited Sample and Data (Ordered based on species and relevant data)
#*[[File:L.majorCompiledRawData.txt]] L. major raw compiled data
#*[[File:L.infantumCompliedRawData(A).txt]] L. infantum raw compiled data
#11/19/2013:
#*[[File:L.majorCompiledRawData_B.txt]] L. major raw compiled data with adjusted dye swap values
#*[[File:L.infantumCompliedRawData(B).txt]] L. infantum raw compiled data with adjusted dye swap values and sample names
#*[[File:L.majorCompiledRawData_C.txt]] L. major raw compiled data with adjusted dye swap values and sample names

File:L.majorCompiledRawData C.txt

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Vkuehn: /* Week 13 Individual Lab Notebook */

File:LmjSampleInfo.PNG

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Vkuehn: added new l. major data file

File:L.majorCompiledRawData B.txt

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Vkuehn:

Vkuehn Week 13

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Vkuehn: created page

=='''Week 13 Individual Lab Notebook'''==

:From this week on, your Individual Journal Assignment will be to complete your electronic laboratory notebook that records your work on your team's final project.
:You need to record a narrative that describes all of the methods that you are using in enough detail so that the instructors or your other team members can follow and reproduce your work.
Include links to artifacts you produce (files, images, testing reports, code, etc.)

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Vkuehn:

The Plan

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Vkuehn: /* Timeline */

=='''Leishmania major'''==
Timeline of due dates, helpful links, important updates, etc.
==='''Timeline'''===
*Preparation for Journal Club Individual Journal-- 11/12
*'''Journal Club Presentation-- 11/12'''
*:15 min ppt presentation on genome reference article
*:Finish individual journal by 11/8
*:Meet for work on ppt 11/8-11/10
*:Practice and final touches on ppt, and upload to wiki 11/11
*:[[Week 11]]

*Electronic Lab Notebook on updates on the final project
*:[[Week 12]] due 11/15
*:Please link the lab notebooks here:
*::[[Gleis Week 12]]
*::[[Lena Project Notebook]]
*::[[Vkuehn Week 12]]
*::[[Leishmania major Week 12 Status Report]]

*[[Week 13]] due 11/22
*:GenMAPP users: Perform Statistical Analysis and get ready for Import in to GenMAPP 11/22
*:QA: Get to know System IDs, Characterize regular expression patterns to detect the IDs 11/22

*Week 14
*:GenMAPP users: Run GenMAPP and generate all of the relevant files begin analysis 11/28
*:QA: customize the tally engine setup, add ordered locus IDs 11/28

*[[Week 15]] due 12/6
*: GenMAPP users: Analyze data 12/6
*:QA: Document the relational database schema for the gene database and create the ReadMe with comparisons to MOD for Leishmania 12/6

*'''Final Project Presentations''' 8-10 am on 12/12

*'''Project Deliverables due''' at 4:30 on 12/13

==='''Important Updates'''===
[[Template:Leishmania Major File Updates]]

Record names of the files as they are updated and edited with dates.
Upload any other relevant files here, and document major progress.

{{Leishmania Major File Updates}}

{{Template:Leishmania Major Navigation}}

Template:Leishmania Major Navigation

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Vkuehn: Formatted Template

====Leishmania Major Helpful Links====

'''[[Leishmania major | Leishmania Major Home Page]]'''
:[[Leishmania Major Articles]]
:[[Template:Leishmania Major Navigation]]
:[[Template:Leishmania Major File Updates]]
:[[The Plan]]

Team Members:
:[[User:Vkuehn | Viktoria]] (GenMAPP User, Project Manager)
:[[User:Gleis|Gabriel]] (Coder)
:[[User:Lena|Lena]] (Quality Assurance)
:[[User:Kevinmcgee| Kevin]] (GenMAPP User)

Status Reports:
:[[Leishmania major Week 12 Status Report]]
:[[Leishmania major Week 13 Status Report]]

Relevant Project Links:
:[[Gene Database Project]]
:[[Gene Database Project Report Guidelines]]
:[[Project Manager]]
:[[Coder]]
:[[Quality Assurance]]
:[[GenMAPP User]]

[[Category: Leishmania Major]]
[[Category:Group Projects]]