Material
Class Date Topics lecture zzzzzZZzzzzzzzz Code and additional material Last Update and comments
1 March 24 Introduction and motivation

Python basics
Intro.pdf

Python_basics1.pdf
basics.py
ex1.py
log1.txt
Also see HW0 under HW tab
To open a .py file, first save it on your computer. Then use the "Edit with IDLE" option.
2 March 31 More Python basics Python_basics2.pdf dna_translate.py
ProtMolWeight.py
count.py

class_exercise2.pdf
IME1.txt
class_sol2.py

log2.txt

add_history.pdf - Useful instructions for configuring keys for command history
3 April 14 Biological Sequences 1 - hashing hash.pdf common_ss.py
frequent_k-mer.py
genomes.zip

Exercise solution:
longest_common_ss.py

log3.txt
4 April 21 Biological Sequences 2 - Regular Expressions and Deterministic Finite Automata (DFA) RE.pdf RE.py

log4.txt
pdf and py updated after class, please download new version (fix in slide 25: 6 states are needed)
5 April 28 Biological Networks 1 - Graph Theory notions and Dijkstra's Shortest Paths Algorithm Graphs1.pdf dijkstra.py
eccentricity.py (ex. 2)

log5.txt
6 May 5 Biological Networks 2 - Boolean models for regulatory network simulation Boolean.pdf bool.py
7 May 11 Biological Images 1 - Digital images representation, Segmentation Images1-intro.pdf

Images2-segmentation.pdf
images.py
segment.py - inside next lecture's zip file

HT29.tif

log7.txt
8 May 19 Biological Images 2 - Erosion, dilation, labeling, noise reduction Images3.pdf image_process.zip

GUI.py

log8.txt
The GUI.py requires installing PIL and swampy

Project guidlines: project.pdf
9 May 26 Discrete models 2 - Cellular automata and the Game of Life CA.pdf ca.py ca.py requires installing PIL and swampy
10 June 2 Computational Complexity - The big problem of computer science: P vs. NP, and how this is related to DNA assembly and other biological problems Complexity.pdf euler.py
11 June 9 Computational Complexity (cont., using last lecture's slides)

Biological Sequences 3- Tries and Suffix Trees

trie.pdf

trie.py
12 June 16 Guest lecture, Dr. Michael Shmoish: R programming language and clustering

Computational Complexity 2- More on NPC and the Halting Problem

"The Invention of the Genetic Code" through the eyes of Combinatorics
R_clustering.pdf


Complexity_and_halting.pdf


lopresti.pdf (courtesy of Prof. Daniel Lopresti, Lehigh University)




See the paper: "The Invention of the Genetic Code", Brian Hayes, American Scientist, 1998.
13 June 23 Guest lecture 1: Prof. Yael Mandel-Gutfreund, Biology and CS, Technion: A novel computational approach for identifying protein relationships

Guest lecture 2: Prof. Benny Chor, Computer Science, Tel-Aviv University: De Novo Assembly

Famous last words (summary)
Yael.pdf




Slides upon request


Summary.pdf


link to previous semester's material-2015

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