1. Experiment
   • If possible, we will do an experiment
   • You need your cellphone’s camera
2. Genomic databases
3. Planets

• I will drop an object in front of the class
• The screen will show a timer
• You must record the experiment with your cellphone
• In your computer, open a new text file and write the experimental data
  • three columns: seconds, position, and replica
  • one row for each time the object crosses a mark
• Send your text file to andres.aravena+cmb@istanbul.edu.tr

• https://youtu.be/4pkAFmGZ6_M
• https://youtu.be/nr64gAbiZQw

YouTube has an option to show the video at 0.25 speed. Try that also

Every time a researcher publishes a paper about DNA sequencing, all the sequences are uploaded to several databases.

One of these databases is https://www.ncbi.nlm.nih.gov/sra/

It contains all DNA reads made with New Generation Sequencers

We want to understand how fast this database is growing

• Download the file sra_bases.txt
• Create a new Rmarkdown document. Delete all unnecessary text
  • do not forget to write your student number
• write the code to read the file into your document
• write the code to produce a plot like the one at https://www.ncbi.nlm.nih.gov/sra/docs/sragrowth/

• The growth of databases is usually modeled as a semi-log linear model.
• Build a semi-log model and find
  • what is the factor of growth per day?
  • What will be the database size two years after the last entry in your table?
• write your code and comments in the same Rmarkdown file

• Download the file planets.txt
• In the same Rmarkdown document as the previous question, create a new section
• write the code to read the file into your document
• Draw three plots
  • One using normal scales
  • One using semi-log scales
  • One using log-log scales

• Based on the 3 plots, decide which is the best approach to use a linear model. Explain why you made that decision.
• Build the model and show the coefficients
• Compare your result with Kepler’s third law

• Looking at the log-log plot, do you think that there is something missing?
• Find the Distance and Period for the “missing planet” between Mars and Jupiter

You should send two files to andres.aravena+cmb@istanbul.edu.tr

• The text file with the first part
• The Rmarkdown file with the second and third part

You can send the files in a single email or in two separated ones

Put your student number in the subject

Enjoy!