Mia Huddleston Week 14

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Electronic Notebook


The purpose of this lab is to analyze and explore a database of our choosing to look at what it holds and the database works. For the second portion of the lab, with the help of my partners, we created an outline based off of the Hebly et al. paper, found thirty definitions of words that we did not know, and fixed the errors found in a previous presentation.

Methods and Results

  1. What database did you access? (link to the home page of the database)
  2. What is the purpose of the database?
  3. What biological information does it contain?
    • This database includes; compounds, cancer-relevant protein targets, compound-target interactions, cell lines, genes (mutations), mutations, and genes (expression) from cancer genomic experiments.
    • http://data-analysis.charite.de/care/
  4. What species are covered in the database?
  5. What biological questions can it be used to answer?
  6. What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])?
    • This database holds sequences of compounds, cancer-relevant protein targets, compound-target interactions, cell lines, genes (mutations), mutations, and genes (expression), and is in house.
    • http://data-analysis.charite.de/care/
  7. What individual or organization maintains the database?
  8. What is their funding source(s)?
  9. Is there a license agreement or any restrictions on access to the database?
  10. How often is the database updated? When was the last update?
  11. Are there links to other databases?
  12. Can the information be downloaded? And in what file formats?
  13. Evaluate the “user-friendliness” of the database.
  14. Is the Web site well-organized?
  15. Does it have a help section or tutorial?
  16. Run a sample query. Do the results make sense?

Group Assignment

The group assignment is located on Matthew Oki's journal 14 page.


The group project portion was completed with my partners, Matthew Oki, Matthew R Allegretti, and Colin Wikholm, with meetings in class and outside of class on Sunday. I would also like to thank Kam D. Dahlquist, Ph.D. for the instruction in class. Even though I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. Mia Huddleston 15:07, 5 December 2016 (EST)


  • Hebly, M., de Ridder, D., de Hulster, E. A. F., de la Torre Cortes, P., Pronk, J. T., & Daran-Lapujade, P. (2014). Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles. Applied and Environmental Microbiology, 80(14), 4433-4449. doi: 10.1128/AEM.00785-14
  • Week 14 Assignment Page

Useful links

User Page: Mia Huddleston

Bioinfomatics Lab: Fall 2016

Class Page: Bioinfomatics Laboratory, Fall 2016

Weekly Assignments Individual Journal Assignments Shared Journal Assignments