Difference between revisions of "Msamdars Week 12/13"
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==Electronic Lab Notebook== | ==Electronic Lab Notebook== | ||
===Purpose=== | ===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. | + | 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=== | ===Methods=== | ||
Latest revision as of 23:58, 25 November 2019
Contents
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:
- Sample ID (PMID + index)[integer]
- Pubmed ID [integer]
- Control Yeast Strain [string]
- Control [String]
- Concentration Value [Integer]
- Concentration Unit [String]
- Time Value [Integer]
- Time Units [String]
- Number of Replicates [Integer]
- Citation Table:
- PMID [Integer]
- Authors [Array[strings]]
- Title [String]
- DOI [String]
- NCBI GEO ID [Integer]
- Sample To Data Table:
- 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
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
- LMU BioDB 2019. (2019). Week 12. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
- MediaWiki (2019). Category: Help. Retrieved November 25, 2019, from https://www.mediawiki.org/wiki/Category:Help
