Msamdars Week 12/13

Electronic Lab Notebook

Purpose

This is the electronic notebook recording information regarding my progress towards the final project. I am a member of the designer/coder guild and will be designing the database. Furthermore, I will be helping my group to add and analyze our data from the Barreto et al. paper "The short‐term response of yeast to potassium starvation" (2012).

Methods

• Decided with the help of the group will be using the Azure platform to host a centralized server on which we can all access the Microsoft Access Database.
• Furthermore, we decided on the format for the metadata sheet and the individual data sheets for each article.
  • Sample To Data Table:
    1. Sample ID (PMID + index)[integer]
    2. Pubmed ID [integer]
    3. Control Yeast Strain [string]
    4. Control [String]
    5. Concentration Value [Integer]
    6. Concentration Unit [String]
    7. Time Value [Integer]
    8. Time Units [String]
    9. Number of Replicates [Integer]
  • Citation Table:
    1. PMID [Integer]
    2. Authors [Array[strings]]
    3. Title [String]
    4. DOI [String]
    5. NCBI GEO ID [Integer]
• Attempted to write program using downloaded gene list from Saccharomyces Gene Database. Wrote program using Pandas and NumPy libraries in a Python Jupyter Notebook. Gave up on realizing it was doomed.
• Used the Synergizer website, which was not helpful at all and was not giving the right ids or names.
• Emailed Dr. Dahlquist for help. Received edited gene list.

Conclusion

This week we designed the main part of the database. Next week, I will work on standardizing the expression sheet tables. Furthermore, I will start to build it out in Microsoft Access.

Data & Files

File:Metadata Sheet.xlsx

Acknowledgments

This week my team members are in Skinny Genes which is composed of Jonar Cowan, Aby Mesfin, David Ramirez, Christina Dominguez, & myself. We worked in and out of class together.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source

Other Links

Links
Mihir Samdarshi User Page
Assignment Pages	Personal Journal Entries	Shared Journal Entries
Week 1	Journal Week 1	Class Journal Week 1
Week 2	Journal Week 2	Class Journal Week 2
Week 3	FAS2/YPL231W Week 3	Class Journal Week 3
Week 4	Journal Week 4	Class Journal Week 4
Week 5	Database - AmtDB	Class Journal Week 5
Week 6	Journal Week 6	Class Journal Week 6
Week 7	Journal Week 7	Class Journal Week 7
Week 8	Journal Week 8	Class Journal Week 8
Week 9	Journal Week 9	Class Journal Week 9
Assignment Pages	Personal Journal Entries
Week 10	Journal Week 10
Week 11	Journal Week 11
Week 12/13	Journal Week 12/13
Team Project Links
Skinny Genes Team Page

References

1. LMU BioDB 2019. (2019). Week 12. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
2. MediaWiki (2019). Category: Help. Retrieved November 25, 2019, from https://www.mediawiki.org/wiki/Category:Help