Material 2014

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Class Date Topics Material zzzzzZZzzzzzzzz Class exercises zzzzzZZzzzzzzzz Last Update and comments
1 March 4 Introduction and motivation

Python basics
Intro.pdf

Python_basics1.pdf
countA.py
CG.py
CG with prints.py
basics_more.py
log1.txt
polymer_state.py
recitation1(self).pdf
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2 March 11 More Python basics Python_basics2.pdf
dna_translate.py
ProtMolWeight.py
count.py
log2.txt
recitation2.pdf
IME1.txt
recitation2.py
recitation2log.txt
Lecture pdf updated March 11, dna_translate.py bug fixed March 16.

add_history.pdf - Useful instructions for configuring keys for command history
3 March 18 Graph Theory basics, Euler paths Graphs1.pdf
euler_classify.py
log3.txt
recitation3.pdf
recitation3.py
recitation3log.txt
PPI network examples:
Ime1 S.Cerevisiae
GFP C.elegans
4 March 25 Graph Theory (cont.): Sequencing and assembly

Computational Complexity, P vs. NP and NPC; Graph isomorphism, Hamiltonian paths, Traveling salesperson
Graphs2.pdf
euler_path.py
In the lecture slides
5 April 1 Graph Theory (cont. cont.): Sequencing and assembly with Euler paths

Dijkstra's shortest paths algorithm
Graphs3_new.pdf
find_euler.py
log5.txt
In the lecture slides pdf fixed and updated 7/4
6 April 8 Graph Theory (cont. cont. cont.): Dijkstra's algorithms for shortest paths

Reduction

Strings: Trie and suffix tree
dijkstra.py

reduction_new.pdf

trie.pdf
trie.py
sc_dna_c1.txt
In the lecture slides
7 April 22 Suffix trees
Regular Expression and Deterministic Finite Automata
RE.pdf
re_new.py
In the lecture slides
Solutions: re_sol.py
8 April 29 Hash functions and hash tables hash.pdf See next week's material
9 May 13 Hash functions and hash tables


Digital Images
hash2.pdf
common_substring.py
log9.txt


Images_intro.pdf
images.py
guess.jpg
In the lecture slides

Chromosome 1 of Arabidopsis thaliana, divided into fragments of length 100:
at.zip

Genomes of Tuberculosis and Salmonella:
longest_common_ss.zip
10 May 20 Digital Images: segmentation, edge detection Images1_new.pdf
otsu.py
edge.py
HT29.tif
In the lecture slides pdf updated 22/5, with some execution examples for edge detection, plus the reflection slide.
11 May 27 Digital Images: Noise Reduction


Discrete Models: the Game of Life and Cellular Automata
Images2.pdf
rbc.tif
noise.py
local.py
util.py


CA.pdf
life-swampy.py
glider.bmp
In the lecture slides.
Solutions: noise_exercises.py
Images2.pdf updated 29/5, with some minor changes and error fixed
12 Jun 10 Discrete Models (cont.):

Young's skin patterns model (see code in the previous lecture)

Boolean regulatory networks


Young84.pdf

boolean.pdf
bool.py
yeastCC.pdf
We discussed the final projects:
Projects_guidlines.pdf
13 Jun 17 Guest lecture: Prof. Benny Chor

Extensions for the Boolean model for regulatory networks


discrete_space.py
loop_detection.py
14 Jun 24 Research case study: Discrete models the yeast developmental pathways

Summary
discrete_yeast.pdf

Summary.pdf


link to previous semester's material

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