Difference between revisions of "Emilysimso Week 15"

From LMU BioDB 2015
Jump to: navigation, search
(Added individual reflection, added links)
Line 29: Line 29:
 
*.txt file for GenMAPP
 
*.txt file for GenMAPP
 
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
 
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
 +
 +
==Individual Reflection==
 +
*Statement of Work
 +
**Describe what you did
 +
**Provide references or links to artifacts of your work (wiki, documents)
 +
*Assessment of Project
 +
**Success of project workflow/teamwork
 +
**What worked and what didn’t?
 +
**What would you do differently?
 +
**Evaluate Gene Database Project and Group Report
 +
**Content: what is the quality?
 +
**Organization
 +
**Completeness: did we reach all objectives
 +
*Reflection on the Process
 +
**What did you learn
 +
***With head (bio or CS principles)
 +
***Heart (qualities, teamwork qualities)
 +
***Hands (technical skills)
 +
**What lesson will you take away
 +
 +
 +
I was a GenMAPP User for the group project, meaning I did the raw data analysis from the microarray experiment and worked with the program to analyze the results. I compiled the data from the repletion stage of the experiment (all of the F time points - found on my [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_12 | Week 12 page]) and then combined this data with Ron to perform the statistical analysis on the data. I also created the file we used for [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:UpdatedCompiledRawData_WithGenMAPP_20151210_ES_HMH.xlsx GenMAPP]. I also worked with Josh to enter the data into GenMAPP and then worked with Ron to figure out the criteria for significance of the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion0-GO_20151212_HMH.xlsx increased] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:MAPPFINDER_20151212-Criterion1-GO_20151212_HMH.xlsx decreased] genes. I also created the MAPPs for the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Fatty_Acid_Degradation_Soneidensis_20151213_HMH.mapp Fatty Acid Degradation] and [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Ribosomal_Soneidensis_20151213_HMH.mapp Ribosome] gene pathways. Finally, I created the [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/File:Experimental_Design_Flow_Chart_20151115_HMH.pptx experimental design flow chart].
 +
I think our group worked fairly well together, but we had some issues with communication. Everyone was responsible and got their work done, but sometimes it was unclear when things would be finished or who needed to do which task. I think we should have met more together outside of class to clear up some of these issues, so I would have definitely done that differently. Specifically, Ron and I should have met more to work on the Excel files, since it was unnecessarily complicated doing it apart from each other. Overall, however, I think our group was able to work together to finish the project.
 +
I learned a lot from this project and I think the class as a whole will stay with me beyond undergrad. This course helped solidify the connection between biology and computer science, which is something I had not previously thought much about. I think I learned more about computer science overall, as I had not been exposed to that field before, in terms of database construction, coding, and how various programs can be put together for a final result. In terms of teamwork, this project reminded me how important it is to use people’s skills and work together to make the best project. This project was very specialized, so building off of individual knowledge definitely helped. I think this will help with future projects, especially as they become more involved and specific. For technical skills, I learned how to do some basic coding, database construction, and analysis of a species’ genome. Learning to interpret genomic data is an important skill to start building, as the field is always growing and becoming increasingly relevant to biology.
 +
The biggest lesson I will take away is
 +
  
  
 
{{Template: Esimso entries etc}}
 
{{Template: Esimso entries etc}}

Revision as of 21:39, 14 December 2015

Procedure

  • Calculated averages from split data for each time point and replicate
    • Total of 5409 genes
  • Calculated biological averages of each time point
  • Calculated AverageLogRatio comparing C5, C20, and C60 to C0 and F5, F20, and F60 to C60
    • Subtracted not divided due to log space
  • Performed TTest on the above relationships to get the Pvalue
  • Performed Bonferroni
  • Performed Benjamini & Hochberg
  • Created new sheet forGenMAPP
    • Did adjustments to prepare file for GenMAPP
    • Saved as .txt and uploaded to wiki

GenMAPP

  • Increase criterea = >0.25 AND B-H <0.05
  • Decrease criterea <-0.25 AND B-H <0.05
  • 1441 errors in the raw data
  • Red is increased, green is decreased
  • Uploaded C5-C0, C20-C0, C60-C0, F5-C60, F20-C60, and F60-C60 into GenMAPP

MAPPFinder

  • Criteria: Zscore >2, Permute P<0.05, Number Changed > or equal to 4 < or equal to 100, Percent Changed > or equal to 50%

Files

Individual Reflection

  • Statement of Work
    • Describe what you did
    • Provide references or links to artifacts of your work (wiki, documents)
  • Assessment of Project
    • Success of project workflow/teamwork
    • What worked and what didn’t?
    • What would you do differently?
    • Evaluate Gene Database Project and Group Report
    • Content: what is the quality?
    • Organization
    • Completeness: did we reach all objectives
  • Reflection on the Process
    • What did you learn
      • With head (bio or CS principles)
      • Heart (qualities, teamwork qualities)
      • Hands (technical skills)
    • What lesson will you take away


I was a GenMAPP User for the group project, meaning I did the raw data analysis from the microarray experiment and worked with the program to analyze the results. I compiled the data from the repletion stage of the experiment (all of the F time points - found on my | Week 12 page) and then combined this data with Ron to perform the statistical analysis on the data. I also created the file we used for GenMAPP. I also worked with Josh to enter the data into GenMAPP and then worked with Ron to figure out the criteria for significance of the increased and decreased genes. I also created the MAPPs for the Fatty Acid Degradation and Ribosome gene pathways. Finally, I created the experimental design flow chart. I think our group worked fairly well together, but we had some issues with communication. Everyone was responsible and got their work done, but sometimes it was unclear when things would be finished or who needed to do which task. I think we should have met more together outside of class to clear up some of these issues, so I would have definitely done that differently. Specifically, Ron and I should have met more to work on the Excel files, since it was unnecessarily complicated doing it apart from each other. Overall, however, I think our group was able to work together to finish the project. I learned a lot from this project and I think the class as a whole will stay with me beyond undergrad. This course helped solidify the connection between biology and computer science, which is something I had not previously thought much about. I think I learned more about computer science overall, as I had not been exposed to that field before, in terms of database construction, coding, and how various programs can be put together for a final result. In terms of teamwork, this project reminded me how important it is to use people’s skills and work together to make the best project. This project was very specialized, so building off of individual knowledge definitely helped. I think this will help with future projects, especially as they become more involved and specific. For technical skills, I learned how to do some basic coding, database construction, and analysis of a species’ genome. Learning to interpret genomic data is an important skill to start building, as the field is always growing and becoming increasingly relevant to biology. The biggest lesson I will take away is


Weekly Assignment Information

User: Emilysimso

Assignments

Individual Journal Entries

Class Journal Entries

Group Project

Heavy Metal HaterZ

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Emilysimso_Week_15&oldid=7832"