1. Programming Challenge Problem
Chris Haack
Joe Como

3. Programming Challenge Problem Logistics
You can work in groups of 2-3!
Code and brief write up due Tuesday May 21st at 2:30pm
Must be done in python3!
no extensions are going to be provided
You will then make a presentation on your algorithm and ideas!
We will run an in class competition

4. Language Requirement Your code must be written in Python 3.
Why Python?
We want you to focus on your algorithms and not the language optimizations.
Easy to understand what is going on with your code!

5. Challenge Introduction
Implement a function that retrieves the minimum number of steps it takes to generate a string using only tandem duplications from one of the following starts strings [0, 1, 01, 10, 101, 010] as listed in problem 1a on homework one

6. Refresher Problem 1a

7. Tandem Duplication
A tandem duplication of length k is defined as a duplication of a substring of length k next to it’s original position.
For example with a duplication of length 3 at position 2 would become
**note python is 0 indexed, so something at position 1 in python is at position 2 in a string!

8. Duplication Distance
The duplication distance is defined as the minimum number of steps required to generate a given string from a seed by a tandem duplication process.
can be generated from 01 in two ways
01 -> > > ( 3 steps)
01 -> 001 -> (2 steps)
The duplication distance for is then 2 since this is the minimal number of tandem duplications required to generate from seed 01.

9. Duplication Distance Example
What is the duplication distance of string
101 ->
>
>

10. Duplication Distance Example Part 2
How can we get to with just tandem duplications
101 -> 1011
1011 ->
2 steps

11. Reverse?
> > 101

13. Solution
0101
01!

14. Problems?
Once you have completed this you will realize that for large strings it takes a lot of time for your program to grow as the search space becomes much larger.

16. Last Years Winners!

17. Three Points!!!

18. Transition to simple solution and explain code and files here
Transition to simple solution and explain code and files here! This will be done interactively for students at the lecture!

19. 100100
Bio. Info. Channel

20. 100100
SEED: 10
Bio. Info. Channel

21. 100100 SEED: 10 Generate possible duplications: [110, 100, 1010]
Repeat?
Bio. Info. Channel

22. 100100
Now Start from ending string.
Bio. Info. Channel

23. 100100 Possible deduplications: [10010, 10100, 100]
Repeat until you reach a seed.
What do you have to keep count of?
Bio. Info. Channel

24. 100100 Possible deduplications: [10010, 10100, 100]
Repeat until you reach a seed.
What do you have to keep count of?
Second generation:
[1010,
100, 1010
10]
Bio. Info. Channel

25. Optimization
The challenge is to think of ways to optimize this generation process and argue why your solution is good. Please in your solution describe your algorithm and approach. Discuss pros and cons and what things you like/dislike about your algorithm.

26. Tips! Work With Friends! Start Early!
Ask Your TA’s for help and advice

27. Reminders
Write Code in solver.py and have your main solution be in the solve function! Feel free to use any other helper functions!
There is useful template code in helpers.py and a walk through on an initial algorithm in the intro_solver ipython notebook.
If you have questions please reach out to - Joe
- Sidd