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Further Enrichment 2

Exercise 1: Structural biology

Do you love protein structures? There are many interesting standardized file formats that are used in structural biology. Explore some of these datasets:

  • Go to the Protein Data Base:
  • Search for your favorite protein structure
  • Of the search results that pop up, click on an interesting looking entry
  • When you arrive at a given page for an interesting crystal structure, look for the DOWNLOAD FILES pull down menu. Download a PDB file (compressed or uncompressed).

  • Use more/less to browse through the PDB file. Can you figure out how the information is organized? For more information check the PDB file format Wikipedia page
  • Can you count how many oxygens are in your protein?
  • Can you count the number of LYS (lysines) in your protein?

Exercise 2: Pubmed timeline

When you're starting a collection of bibliographic material, it can sometimes be useful to download bibliographic information in bulk from pubmed. Try the following exercise that will create a timeline of publication dates for a given researcher:

  • Enter the name of one of your favorite scientists.
  • Download the results of the search by selecting the pull down menu SEND TO
  • Select FILE
  • Select MEDLINE

  • Download the dataset and browse it in the terminal.
  • Display all the publication dates this person has published on, sorted by year (I couldn't get month sorting to work).

Exercise 3: More databases

There is a wealth of biological data out there. Find a biological database relevant to your field of study and download some datasets. What are the common file types? Which can be read as text files?

Exercise 4: Make your own oligo inventory

Do you order a lot of oligos? If so, the companies typically e-mail you in standardized formats. Try downloading all the e-mails and pulling out relevant information about each oligo based on their standardized format. You can then save these to an .xls sheet or a database program. Your database might be quite basic after Week2 of the course, but after Week4, it may become more sophisticated. If you are interested in making more apps like this, consider taking the python course.

assignments/enrichment2.txt · Last modified: 2018/08/14 16:17 by erin