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

Python basics

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



add_history.pdf - Useful instructions for configuring keys for command history
3 April 14 Biological Sequences 1 - hashing hash.pdf

Exercise solution:

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

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 (ex. 2)

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

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


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

The requires installing PIL and swampy

Project guidlines: project.pdf
9 May 26 Discrete models 2 - Cellular automata and the Game of Life CA.pdf 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
11 June 9 Computational Complexity (cont., using last lecture's slides)

Biological Sequences 3- Tries and Suffix Trees

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


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)

Slides upon request


link to previous semester's material-2015

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