Material
Class Date Topics Lecture slides zzzzzzzzzzzzz Code and additional material Last Update and comments
1 March 15 Introduction and motivation

Python basics
Intro.pdf


Python_basics1.pdf
basics.py
ex1.py
log1.txt
exercise.pdf
To open a .py file in Windows, first save it on your computer. Then right click and choose the "Edit with IDLE" option.
2 March 22 More Python basics Python_basics2.pdf dna_translate.py
ProtMolWeight.py
ClassEx_count.py

ClassEX2.pdf
IME1.txt
ClassEX2_sol.py

log2.txt

add_history.pdf - Useful instructions for configuring keys for command history
3 March 29 Biological Sequences(1) - hashing hash_new.pdf (updated) common_ss.py

genomes.zip
hash.pdf updated April 2nd
4 April 5 Hashing (cont., using last week's slides)



Biological Sequences(2) - Regular Expressions and Finite State Machines (FSM)



RE.pdf
frequent_kmer.py
Exercise solution:
longest_common_ss.py


RE.py
log4.txt
5 April 12 Biological Networks - Graph theory notions and Dijkstra's shortest paths algorithm networks.pdf dijkstra.py
CA1.py
CA1.txt

log5.txt
6 April 19 Simulation of Biological Systems - A Boolean model for regulatory network simulation boolean.pdf bool.py
7 May 3 Biological Images(1) - Digital images representation, Segmentation Intro.pdf (updated)

Segmentation.pdf
images.py

segment.py

HT29.JPG

log7.txt
Intro.pdf updated May 4th.

Link to install PIL/PILLOW: https://pypi.python.org/pypi/Pillow/3.2.0 (this link is for PILLOW version 3.2, but you can use any version)
8 May 10 Biological Images(2) - Morphological operators, erosion and dilation

Simulation(2) - The Game of Life and cellular automata

Project kickoff
Images3.pdf (updated)


CA.pdf


project_guidelines.pdf
morph.py, edges.py


ca-gui.py


log8.txt
Images3.pdf updated May 17th.
9 May 17 Useful Python packages (numpy, scipy, pandas, matplotlib), and a practical case study
(by Gur Hevroni)

Cellular automata (wrap up, using last time slides)

Biological Images(3) - Labeling, noise reduction
iPython notbook link








Images4.pdf








noise.py
image_GUI.py
1) We did not have time for the noise reduction topic. You are welcome to read the slides on your own and play with the code.

2) To use the image processing GUI, put all the image processing Python files at the same directory: segment.py, morph.py, edges.py, noise.py and image_GUI.py. You will need to install swampy, PILLOW, numpy and scipy packages.
10 May 31 "The Invention of the Genetic Code" through the eyes of Combinatorics - a guided paper reading combinatorics.pdf

lopresti.pdf (courtesy of Prof. Daniel Lopresti, Lehigh University)
The original (fascinating) paper: "The Invention of the Genetic Code", Brian Hayes, American Scientist, 1998.

And the follow up paper: ""Ode to the Code", Brian Hayes, American Scientist, 2004.
11 June 7 A peek into CS theory - and why biologists should care:
Part I: Complexity
complexity.pdf
12 June 14 (cont.):
Part II: Computability and the Halting problem

Course Wrap-up


Presentations of projects - first part
computability16.pdf


wrap-up.pdf



13 June 21 Presentations of projects - second part


link to previous semester's material

Unless otherwise stated, the content of this page is licensed under Creative Commons Attribution-ShareAlike 3.0 License