Material
Class | Date | Topics | Lecture slides zzzzzzzzzzzzz | Code and additional material | Last Update and comments |
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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 |
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5 | April 12 | Biological Networks - Graph theory notions and Dijkstra's shortest paths algorithm | networks.pdf | dijkstra.py CA1.py CA1.txt log5.txt |
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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. |
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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 |
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13 | June 21 | Presentations of projects - second part |
link to previous semester's material