LMU BioDB 2019 - User contributions [en]

Skinny Genes Deliverables

2019-12-13T21:40:01Z

Ymesfin: /* Data/Files */ uploaded report

{{Skinny Genes}}

==Data/Files==
# Group Report
#*[[Media: SkinnyGenes_BioDB_Final_Paper.pdf | Final Report]]
# Individual statements of work, assessments, reflections
# Group PowerPoint presentation
#* [[Media: Ymesfin_Barreto_Final_Presentation.pdf | Final Presentation]]
# Sample-data relationship table in Excel
#* [[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample-Data Relationship Table]]
# Excel spreadsheet with ANOVA results/stem formatting
#* [[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Data]]
# PowerPoint of ANOVA table, screenshots of stem results, screenshot of black and white GRNsight input network and colored GRNsight output networks
#* [[Media: Ymesfin_Result.pdf ‎| Stem and GRNsight Network]]
# Gene List and GO List files from each significant profile
#* [[Media: SkinnyGenesGeneGOLists.zip | Profile 39 Gene Table & Lists]]
# YEASTRACT "rank by TF" results
#* [[Media: Ymesfin_profile39gene_list.xlsx | Rank by TF list]]
# GRNmap input workbook
#* [[Media: Ymesfin_Barreto_GRNmap_input.xlsx | GRNmap Input]]
# GRNmap output workbook and output plots zipped together
#* [[Media: Ymesfin_Barreto_GRNmap_Output.zip | GRNmap Output]]
# MS Access database, unified by the three teams with expression tables and metadata table(s) created
#* [[Media:BIOL 478 - BioDB CombinedDatabase.zip|MS Access database]]
# ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
#* [[Media:SkinnyGenesDatabaseREADME.pdf|Database README]]
# Query design for populating a GRNmap input workbook from the database
#* [[Media: Ymesfin_Query_1_Design_Production_Rates.PNG | Query Design 1 - Production Rates]]
#* [[Media: Ymesfin_Query_2_Design_Degradation_Rates.PNG | Query Design 2 - Degradation Rates]]
#* [[Media: Ymesfin_Query_3_Design_Fold_Change.PNG | Query Design 3 - Log Fold Changes]]
# Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

File:SkinnyGenes BioDB Final Paper.pdf

2019-12-13T21:39:35Z

Ymesfin:

Skinny Genes

2019-12-13T01:25:34Z

Ymesfin: /* Milestones */ deleted

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Data (MOST UPDATED)]]

[[Media: Copy_ymesfin_Baretto_yeastract_regulation_matrix.xlsx | Network Data]]

[[Media: Ymesfin_Result.pdf ‎| Stem and GRNsight Network]]

[[Media: Wt_profile39_gene_table.txt | Profile 39 Gene Table]]

[[Media: Wt_profile39_GO_table.txt | Profile 39 GO list]]

[[Media: SkinnyGenesGeneGOLists.zip | Profile 39 Gene Table & Lists (.zip)]]

[[Media: Ymesfin_profile39_gene_list.xlsx | Rank by TF list]]

[[Media: Skinny Genes Database.zip|Zip file containing the Skinny Genes group database]]

[[Media: Ymesfin_Barreto_GRNmap_Output.zip | GRNmap Output]]

[[Media: Ymesfin_Barreto_GRNmap_input.xlsx | GRNmap Input]]

[[Image: Barreto_ymesfin_colored_network.PNG]]

[[Media:Skinny_Genes_fresh_GRNmap_run.zip | fresh GRNmap output from @kdahlquist]]
* I redid the input file by copying and Paste special > Paste values into a new .xlsx file
* I then re-ran GRNmap
* Both the input and output files are visualized correctly in GRNsight. I think some formatting of the original input file that got carried through was messing up GRNsight, either that or the "threshold_b" sheet was out of order.

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Assigment for the Week:
*Project Manager: Create Sample/Data Relationship Table
*Data Analysists: download raw data, run ANOVA
*QAs and Coder: standardize the ID and Standard Names of the genes
| 11/19/19
|-
| Assignment for the Week:
*Data Analysists: Run STEM and prepare GRNsight network
*QAs: Discuss standard column headers for database with other groups
*Coder: Design and Create Database
| 11/24/19
|-
| Assignment for the Week:
*Data Analysists: Create GRNmap Input Worksheet and run GRNmap
*QAs and Coder: Finalize the Database
| 12/03/19
|-
|Assignment for the Week:
*Data Analysists, QAs, Coder: Begin working on Research Paper and Presentation
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 00:51, 26 November 2019 (PST)

====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

Skinny Genes Deliverables

2019-12-07T22:04:56Z

Ymesfin:

Skinny Genes

2019-12-07T21:32:34Z

2019-12-07T19:35:44Z

Ymesfin: /* Files */ added colored network

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Data (MOST UPDATED)]]

[[Media: Copy_ymesfin_Baretto_yeastract_regulation_matrix.xlsx | Network Data]]

[[Media: Ymesfin_Result.pdf ‎| Stem and GRNsight Network]]

[[Media: Ymesfin_profile_39_gene_list.xlsx | Profile 39 gene list]]

[[Media: Skinny Genes Database.zip|Zip file containing the Skinny Genes group database]]

[[Media: Ymesfin_GRNmap_output.zip | GRNmap Output Files]]

[[Image: ymesfin_Barreto_GRNsight_color_network.PNG]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Assigment for the Week:
*Project Manager: Create Sample/Data Relationship Table
*Data Analysists: download raw data, run ANOVA
*QAs and Coder: standardize the ID and Standard Names of the genes
| 11/19/19
|-
| Assignment for the Week:
*Data Analysists: Run STEM and prepare GRNsight network
*QAs: Discuss standard column headers for database with other groups
*Coder: Design and Create Database
| 11/24/19
|-
| Assignment for the Week:
*Data Analysists: Create GRNmap Input Worksheet and run GRNmap
*QAs and Coder: Finalize the Database
| 12/03/19
|-
|Assignment for the Week:
*Data Analysists, QAs, Coder: Begin working on Research Paper and Presentation
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 00:51, 26 November 2019 (PST)

====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

==Milestones==

====Milestones 1====
====Milestones 2====
====Milestones 3====
====Milestones 4====
====Milestones 5====
====Milestones 6====
====Milestones 7====

File:Ymesfin Barreto GRNsight color network.PNG

2019-12-07T19:35:06Z

Ymesfin:

File:Ymesfin Barreto GRNsight colored network.PNG

2019-12-07T19:33:22Z

Ymesfin:

Skinny Genes

2019-12-06T00:17:36Z

Ymesfin: /* Files */ deleted file

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Data (MOST UPDATED)]]

[[Media: Copy_ymesfin_Baretto_yeastract_regulation_matrix.xlsx | Network Data]]

[[Media: Ymesfin_Result.pdf ‎| Stem and GRNsight Network]]

[[Media: Ymesfin_profile_39_gene_list.xlsx | Profile 39 gene list]]

[[Media: Skinny Genes Database.zip|Zip file containing the Skinny Genes group database]]

[[Media: Ymesfin_GRNmap_output.zip | GRNmap Output Files]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Assigment for the Week:
*Project Manager: Create Sample/Data Relationship Table
*Data Analysists: download raw data, run ANOVA
*QAs and Coder: standardize the ID and Standard Names of the genes
| 11/19/19
|-
| Assignment for the Week:
*Data Analysists: Run STEM and prepare GRNsight network
*QAs: Discuss standard column headers for database with other groups
*Coder: Design and Create Database
| 11/24/19
|-
| Assignment for the Week:
*Data Analysists: Create GRNmap Input Worksheet and run GRNmap
*QAs and Coder: Finalize the Database
| 12/03/19
|-
|Assignment for the Week:
*Data Analysists, QAs, Coder: Begin working on Research Paper and Presentation
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 00:51, 26 November 2019 (PST)

====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

==Milestones==

====Milestones 1====
====Milestones 2====
====Milestones 3====
====Milestones 4====
====Milestones 5====
====Milestones 6====
====Milestones 7====

Skinny Genes

2019-12-06T00:05:56Z

Ymesfin: /* Files */ uploaded GRNmap output

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media:Ymesfin Barreto ANOVA no duplicates and revised headers.xlsx | ANOVA Data (no duplicates, new headers)]]

[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Data (MOST UPDATED)]]

[[Media: Copy_ymesfin_Baretto_yeastract_regulation_matrix.xlsx | Network Data]]

[[Media: Ymesfin_Result.pdf ‎| Stem and GRNsight Network]]

[[Media: Ymesfin_profile_39_gene_list.xlsx | Profile 39 gene list]]

[[Media: Skinny Genes Database.zip|Zip file containing the Skinny Genes group database]]

[[Media: Ymesfin_GRNmap_output.zip | GRNmap Output Files]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Assigment for the Week:
*Project Manager: Create Sample/Data Relationship Table
*Data Analysists: download raw data, run ANOVA
*QAs and Coder: standardize the ID and Standard Names of the genes
| 11/19/19
|-
| Assignment for the Week:
*Data Analysists: Run STEM and prepare GRNsight network
*QAs: Discuss standard column headers for database with other groups
*Coder: Design and Create Database
| 11/24/19
|-
| Assignment for the Week:
*Data Analysists: Create GRNmap Input Worksheet and run GRNmap
*QAs and Coder: Finalize the Database
| 12/03/19
|-
|Assignment for the Week:
*Data Analysists, QAs, Coder: Begin working on Research Paper and Presentation
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 00:51, 26 November 2019 (PST)

====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

==Milestones==

====Milestones 1====
====Milestones 2====
====Milestones 3====
====Milestones 4====
====Milestones 5====
====Milestones 6====
====Milestones 7====

2019-12-03T23:47:21Z

Ymesfin: /* Files */ uploaded profile 39 gene list

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Data (no duplicates)]]

[[Media:Ymesfin Barreto ANOVA no duplicates and revised headers.xlsx | ANOVA Data (most updated no duplicates, new headers)]]

[[Media: Copy_ymesfin_Baretto_yeastract_regulation_matrix.xlsx | Network Data]]

[[Media: Ymesfin_Results.pdf ‎| Stem and GRNsight Network]]

[[Media: Ymesfin_profile_39_gene_list.xlsx | Profile 39 gene list]]

[[Media: Skinny Genes Database.zip|Zip file containing the Skinny Genes group database]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Team Journal Assignment: Methods and Results thus far
*Project Manager: Create Sample/Data Relationship Table
*Data Analysis: download raw data, run ANOVA
*QA and Coder: standardize the ID and Standard Names of the genes
| 11/21/19
|-
|
| 11/26/19
|-
|
| 11/28/19
|-
|
| 12/03/19
|-
|
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 00:51, 26 November 2019 (PST)

====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

==Milestones==

====Milestones 1====
====Milestones 2====
====Milestones 3====
====Milestones 4====
====Milestones 5====
====Milestones 6====
====Milestones 7====

2019-12-03T22:58:05Z

Ymesfin: /* Files */ uploaded anova

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Data (no duplicates)]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Team Journal Assignment: Methods and Results thus far
*Project Manager: Create Sample/Data Relationship Table
*Data Analysis: download raw data, run ANOVA
*QA and Coder: standardize the ID and Standard Names of the genes
| 11/21/19
|-
|
| 11/26/19
|-
|
| 11/28/19
|-
|
| 12/03/19
|-
|
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 00:51, 26 November 2019 (PST)

====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

==Milestones==

====Milestones 1====
====Milestones 2====
====Milestones 3====
====Milestones 4====
====Milestones 5====
====Milestones 6====
====Milestones 7====

File:Ymesfin Barreto ANOVA no duplicates - Copy.xlsx

2019-12-03T22:57:11Z

Ymesfin: