BioCoding Course:
Python Tutorial Structure:



Variables and print statements
- Lecture
- Quiz/Game

Lists/strings/for loops
- Lecture
_ Quiz/Game

If statements
- Lecture
- Quiz/Game

Basic math
- Lecture
- Quiz/Game

Start project 1:
- Make some code that takes a string called DNA and calculates the percentage of the nucleotides that either C or G (as opposed to A or T)
	- count them up and divide them by the total at the end
	- print out the answer
- Put input validation so it prints a message for every letter in the DNA string that isn't a nucleotide, then make sure you ignore it in the calculations for GC content
- Make all the DNA upper case so you don't have to check a,c,g, and t too. upper(DNA)

Functions
- Lecture

Finish project 1:
- Make project 1 into a function and call it!
- Make a small change to project 1 so it can also work with RNA (U should now be recognized like A and T) (you don't have to change the variable name DNA)


Dictionaries
- Lecture

Choosing the right data structure
- Game

Reverse complement:
- Talk about how DNA is antiparallel and how the bases match each other
- Learn to reverse complement by hand

Project 2:
- write a function called reverse_complement() that gets a string called DNA
- write a dictionary within this function that decodes each A to T, T to A, G to C, and C to G.
- loop through the DNA and decode it one letter at a time: this is the complement
- then reverse the complement using the cool indexing we learned

Teach them about transcription and translation
- how to find a start codon by hand, mark off every 3 nucleotides on paper, and stop at any of the stop codons
- each codon is a code for one amino acid 



Project 3: # we guide them a lot more in this project as it is pretty difficult. I would like to make it a class discussion, and then break them up for each part to actually code what we decided the pseudocode for as a class. The job of the teacher here is to ask questions and guide the discussion without actually giving the answers away.

- the goal is to write a function that transcribes DNA into RNA and then translates it into protein
- parts of this process have already been written and the pieces are broken up neatly into functions
- the students' job is to fill in the rest of the code that is missing 
# Project 3 is pretty difficult, so I have made a framework for it. That way the students can code the simpler parts.  

 


Project 4: Reading a fasta file. Also a bit difficult, but we just want them exploring the file type and how you can look through the lines in the file.












Extras:
	Numpy
	- lecture written already 
	- problem set not written yet


	Matplotlib.pyplot
	- lecture not written yet
	- problem set not written yet