Difference between revisions of "Marmas Week 12/13"

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(Data and Files: added metadata sheet again, trouble updating)
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==Data and Files==
 
==Data and Files==
 
[[Media:Metadata_Sheet_(1).xlsx | Metadata Sheet]]
 
[[Media:Metadata_Sheet_(1).xlsx | Metadata Sheet]]
*Note: This data sheet is current as of 9:30pm on Nov 11, 2019. Other groups will add information at another time.
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*Note: This data sheet is current as of 11:00pm on Nov 26, 2019. Other groups will add information at another time.
  
 
==Conclusion==
 
==Conclusion==

Revision as of 23:15, 25 November 2019

Michael Armas' User Page
Weekly Pages Individual Journals Shared Journals
Week 1 Individual Journal Week 1 Class Journal Week 1
Week 2 Individual Journal Week 2 Class Journal Week 2
Week 3 Individual Journal Week 3 Class Journal Week 3
Week 4 Individual Journal Week 4 Class Journal Week 4
Week 5 Individual Journal Week 5 Class Journal Week 5
Week 6 Individual Journal Week 6 Class Journal Week 6
Week 7 Individual Journal Week 7 Class Journal Week 7
Week 8 Individual Journal Week 8 Class Journal Week 8
Week 9 Individual Journal Week 9 Class Journal Week 9
Week 10 Individual Journal Week 10 Class Journal Week 10
Week 11 Individual Journal Week 11 Class Journal Week 11
Week 12/13 Individual Journal Week 12/13 Class Journal Week 12/13
Week 15 Individual Journal Week 15 Class Journal Week 15

Purpose

The purpose of the project is to analyze the mircroarray data of a previously performed experiment titled "Effects of the Pesticide Thiuram:  Genome-wide Screening of Indicator Genes by Yeast DNA Microarray" (Kitagawa et al., 2002). The group will begin data analysis and organization of deliverables. Milestones are established to keep up with the workload due by the end of the semester. Milestones are can be found on the Fungals Team Page. For the week of November 18th, the Coder/Designer guild will establish a meta data sheet and universalize column header nomenclature.

Account of Activity

Week 11

  • A Metadata sheet was made with assistance from Mihir Samdarshi and DeLisa Madere. This sheet is used to show ana analyze the relationship between the samples and the corresponding data. Categories remain universal between all groups.
    • Categories chosen for the metadata sheet were article title, PubMed ID, authors, yeast strain, treatment, concentration value, concentration units, time value, and time units.
    • The Metadata sheet can be found in the Data and Files section of this page.
  • To categorize columns, a nomenclature was chosen amongst the three coders/designers to reflect ample information of each sample. The nomenclature for the samples is yeastStrain_treatmentOrMutation_concentrationWithUnits_LogFC_t+timeWithUnits-replicate.
    • For example, to title the column for the log fold change of first replicate of a sample treated with 75uM Thiuram for 15 minutes would be S288C_thiuram_75uM_LogFC_t15m-1.

Week 12/13

  • Worked with Data Analysts to add in column headers according to the nomenclature decided on last week.
  • Little was done on the actual "coding" side of the data analysis. This is due to the wonderful data analysts Kaitlyn and Emma who were more ahead than expected.
    • Thus, we are waiting for STEM analysis to be performed on 11/26 in the computer lab. All worksheets have been checked and are ready to be analyzed on STEM.
  • Additionally, thanks to Mihir Samdarshi, a private server using Microsoft Azure was set up so that MS Access can be used away from the computer lab.
  • Tomorrow (11/26) a database will be started in class to further progress the project

Data and Files

Metadata Sheet

  • Note: This data sheet is current as of 11:00pm on Nov 26, 2019. Other groups will add information at another time.

Conclusion

Acknowledgments

  • I would like to acknowledge Dr. Dahlquist for her continous help with this project.
  • I would like to acknowledge my group, the FunGals, who are helping with reaching deadlines and understanding the material.
  • I would like to acknowledge Mihir Samdarshi for explaining Metadata to me and how to create one.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Marmas (talk) 21:37, 20 November 2019 (PST)