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 |
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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 |
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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 |
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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 |
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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 |
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13 | Jun 17 | Guest lecture: Prof. Benny Chor Extensions for the Boolean model for regulatory networks |
discrete_space.py loop_detection.py |
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14 | Jun 24 | Research case study: Discrete models the yeast developmental pathways Summary |
discrete_yeast.pdf Summary.pdf |
link to previous semester's material