Week | Date | Lecture/Lab Topic | Reading | Notes/Lab/Assignments |
---|---|---|---|---|
1 | 8/22 | No lab | ||
8/23 | Intro to class, syllabus Introduction to Computer Science |
Syllabus Handout |
Lec01Green_Introduction.pdf | |
8/25 | Introduction to Bio Variables (DNA) |
Sect. 0.1-0.5 | Lec02Green.pdf | |
2 | Lab | Setting up Python | Print your name, ID, major, year set vars: # A, C, T, G output: total string length, string duplication |
|
8/30 | Introduction to Bio (contd) strings |
Sect. 0.6-0.8 | Lec03Green.pdf | |
9/1 | Sequences & indices & slicing Genbank |
Lec4Green.pdf | ||
3 | 9/5 | No lab: Labor Day | ||
9/6 | Slicing & lists (Proteins) | Sect. 0.9-0.15 | Lec5Green.pdf HW only; no lab (Labor Day) |
|
9/8 | File I/O, Genbank | Lec6Green.pdf genbank.pdf |
||
4 | Lab | File manipulation | Open, read, write, close Read and write to file. Dealing with sequencial reading |
|
9/13 | Functions | Sect. 1.1-1.5 | Lec7Green.pdf | |
9/15 | (%GC, transcription, strand orientation, ORF ) | Lec8Green.pdf | ||
5 | Lab | Functions, map-reduce | ||
9/20 | REVIEW | Lec9Green-Exam1Review.pdf | ||
9/22 | EXAM I | |||
6 | Lab | 3-5 primer test 3-DNA to protein |
||
9/27 | Control flow & first loop: if, elif, else | Sect. 1.6-1.9 (Sect. 3.5) |
Lec10Green.pdf | |
9/29 | Loops: for Pathogenicity |
Sect. 1.9-1.10 | Lec11Green.pdf | |
7 | Lab | For loops | Reverse complement GC content |
|
10/4 | Genes, GC, pathogenesity islands | Sect. 2.1-2.6 | Lec12Green_biology.pdf | |
10/6 | Loops: (Looping over lists, range, functions call functions) |
Lec13Green.pdf | ||
8 | Lab | More for loops | ||
10/11 | Still for loops | Lec14Green.pdf | ||
10/13 | For inside for inside for.... | Sect 3 | Lec15Green.pdf | |
9 | Lab | |||
10/18 | White House Frontiers slides | Pictures from the conference (With captions) | ||
10/20 | Functions return lists | Lec16Green.pdf | ||
10 | Lab | Random numbers | Python documentation | |
10/25 | While loops | Lec17Green.pdf | ||
10/27 | Genetics and heredity | Lec18Green-bio.pdf | ||
11 | Lab | While loops | |
|
11/1 | While loops and loop practice | Lec19Green.pdf | ||
11/3 | REVIEW | |||
12 | Lab | Unequal probabilities | ||
11/8 | EXAM II | |||
11/10 | Unequal probabilities | Lec20Green.pdf | ||
13 | Lab | Plotting in Python | matplotlib examples | |
11/15 | Dictionaries | Sec 7.3 | Lec21Green.pdf | |
11/17 | Models of evolution | |||
14 | Lab | |||
11/22 | Phylogenetic trees | |||
11/24 | NO CLASS Thanksgiving | |||
15 | Lab | |||
11/29 | Review | |||
12/1 | Review | |||
16 | 12/7 3:30-5:30 |
FINAL EXAM | 120 TH |
I | Attachment | Action![]() |
Size | Date | Who | Comment |
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Lec01Green_Introduction.pdf | manage | 3473.7 K | 2016-08-26 - 16:36 | UnknownUser | |
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Lec02Green.pdf | manage | 3329.4 K | 2016-08-26 - 16:38 | UnknownUser | |
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Lec03Green.pdf | manage | 8949.1 K | 2016-08-31 - 01:26 | UnknownUser | |
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Lec10Green.pdf | manage | 1776.8 K | 2016-09-28 - 06:56 | UnknownUser | |
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Lec11Green.pdf | manage | 4465.6 K | 2016-09-29 - 20:38 | UnknownUser | |
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Lec12Green_biology.pdf | manage | 4898.4 K | 2016-10-06 - 18:18 | UnknownUser | |
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Lec13Green.pdf | manage | 831.4 K | 2016-10-06 - 20:54 | UnknownUser | |
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Lec14Green.pdf | manage | 1113.0 K | 2016-10-11 - 21:24 | UnknownUser | |
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Lec15Green.pdf | manage | 2118.7 K | 2016-10-18 - 18:35 | UnknownUser | |
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Lec16green.pdf | manage | 1148.6 K | 2016-10-22 - 18:06 | UnknownUser | |
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Lec17Green.pdf | manage | 550.1 K | 2016-10-31 - 16:53 | UnknownUser | |
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Lec18Green-bio.pdf | manage | 3042.2 K | 2016-10-31 - 16:36 | UnknownUser | |
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Lec19Green.pdf | manage | 415.1 K | 2016-11-03 - 06:23 | UnknownUser | |
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Lec20Green.pdf | manage | 310.5 K | 2016-11-16 - 00:56 | UnknownUser | |
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Lec21Green.pdf | manage | 243.4 K | 2016-11-16 - 00:56 | UnknownUser | |
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Lec4Green.pdf | manage | 5012.5 K | 2016-09-02 - 06:03 | UnknownUser | |
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Lec5Green.pdf | manage | 479.6 K | 2016-09-06 - 21:21 | UnknownUser | |
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Lec6Green.pdf | manage | 297.3 K | 2016-09-12 - 05:13 | UnknownUser | |
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Lec7Green.pdf | manage | 434.1 K | 2016-09-13 - 22:33 | UnknownUser | |
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Lec8Green.pdf | manage | 3943.0 K | 2016-09-20 - 16:58 | UnknownUser | |
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Lec9Green-Exam1Review.pdf | manage | 675.6 K | 2016-09-20 - 21:33 | UnknownUser | |
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genbank.pdf | manage | 4837.9 K | 2016-09-13 - 17:52 | UnknownUser |
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