Material 2014

To open py files, right-click and "save-as" on your computer. Then right click the file and "Edit with IDLE".

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	To open py files, right-click and "save-as" on your computer. Then right click the file and "Edit with IDLE".
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