Material
Class Date Topics Lecture slides zzzzzzzzzzzzz Code and additional material Last Update and comments
1 March 21 Introduction and motivation

Python basics
Intro.pdf


Python_basics.pdf
GC.py
is_dna.py
dna_translate.py
mol_weight.py
log1.txt
To open a .py file in Windows, first save it on your computer. Then right click and choose the "Edit with IDLE" option.

add_history.pdf - Useful instructions for configuring keys for command history
2 March 28 Python Tutorial Class exercise reverse_comp.py
class2Ex_sol.py
IME1.txt
hw1Q3_sol.py
log2.txt
We answered your questions about the reading assignment, then we solved the class exercise, and then solved Q3 of HW1.
3 April 4 Biological Sequences(1) - hashing hash.pdf common_ss.py
frequent_kmer.py

genomes.zip
log3.txt
4 April 18 Hashing: leftovers from previous lecture + exercise



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



RE.pdf
Exercise solution:
longest_common_ss.py


RE.py
log4.txt
5 April 25 Biological Networks - Graph theory notions and Breadth First Search (BFS) Graphs_bfs.pdf BFS.py
toy_examples.py
CA1.py
CA1_data.txt
Some slides were fixed right after class
6 May 9 Graphs: leftovers from previous lecture + exercise

Biological Images -
Digital images representation


Segmentation; Labeling




Images1-intro.pdf

Images2-segmentation-labeling.pdf
diameter.py


images.py
segment.py
HT29.JPG
count_label_example.bmp
7 May 16 Biological Images (2) - Morphological operators, erosion and dilation

Simulation of Biological Systems - The Game of Life and cellular automata
Images3-morph-erosion-dilation.pdf


CA.pdf
morph.py



ca-gui.py
8 May 23 Cellular automata - leftovers

Simulation of Biological Systems (2) - A discrete state graph model for regulatory network simulation
discrete_regulatory_nets.pdf discrete_regulatory_nets.py

The paper mentioned in the slides: The yeast cell cycle network is robustly designed
Also: project kickoff! (see final projects tab
9 June 6 Reflection on modeling and simulation (using last class's slides 35-end)

Computability, the Halting problem and reductions



computability.pdf



collatz.py
pdf updated 13/6
10 June 13 Additional topics:
A glance at Turing test and AI


Randomness


Euler paths in Graphs

Using last class's slides


randomness.pdf


euler.pdf

rand.py


link to previous semester's material


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