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CS111 + Bio Schedule and Lecture Notes

(This is a preliminary schedule, to be changed wihtout notice)

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 Dictionaries + review    
11/8 EXAM II    
11/10      
13 Lab      
11/15      
11/17 Recursion I (cell cycle) Sect. 5.1-5.2  
14 Lab      
11/22 Phylogenetic and other trees Sect. 9.1-9.2  
11/24 NO CLASS Thanksgiving    
15 Lab      
11/29 Recursion II (biological hierarchy, TOL) Sect. 5.4-5.5  
12/1      
16 12/7
3:30-5:30
FINAL EXAM    
-- tanyabw - 2016-08-21
Topic attachments
I Attachment Action Size Date Who Comment
PDFpdf Lec01Green_Introduction.pdf manage 3473.7 K 2016-08-26 - 16:36 UnknownUser  
PDFpdf Lec02Green.pdf manage 3329.4 K 2016-08-26 - 16:38 UnknownUser  
PDFpdf Lec03Green.pdf manage 8949.1 K 2016-08-31 - 01:26 UnknownUser  
PDFpdf Lec10Green.pdf manage 1776.8 K 2016-09-28 - 06:56 UnknownUser  
PDFpdf Lec11Green.pdf manage 4465.6 K 2016-09-29 - 20:38 UnknownUser  
PDFpdf Lec12Green_biology.pdf manage 4898.4 K 2016-10-06 - 18:18 UnknownUser  
PDFpdf Lec13Green.pdf manage 831.4 K 2016-10-06 - 20:54 UnknownUser  
PDFpdf Lec14Green.pdf manage 1113.0 K 2016-10-11 - 21:24 UnknownUser  
PDFpdf Lec15Green.pdf manage 2118.7 K 2016-10-18 - 18:35 UnknownUser  
PDFpdf Lec16green.pdf manage 1148.6 K 2016-10-22 - 18:06 UnknownUser  
PDFpdf Lec17Green.pdf manage 550.1 K 2016-10-31 - 16:53 UnknownUser  
PDFpdf Lec18Green-bio.pdf manage 3042.2 K 2016-10-31 - 16:36 UnknownUser  
PDFpdf Lec19Green.pdf manage 415.1 K 2016-11-03 - 06:23 UnknownUser  
PDFpdf Lec4Green.pdf manage 5012.5 K 2016-09-02 - 06:03 UnknownUser  
PDFpdf Lec5Green.pdf manage 479.6 K 2016-09-06 - 21:21 UnknownUser  
PDFpdf Lec6Green.pdf manage 297.3 K 2016-09-12 - 05:13 UnknownUser  
PDFpdf Lec7Green.pdf manage 434.1 K 2016-09-13 - 22:33 UnknownUser  
PDFpdf Lec8Green.pdf manage 3943.0 K 2016-09-20 - 16:58 UnknownUser  
PDFpdf Lec9Green-Exam1Review.pdf manage 675.6 K 2016-09-20 - 21:33 UnknownUser  
PDFpdf genbank.pdf manage 4837.9 K 2016-09-13 - 17:52 UnknownUser  
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Topic revision: r23 - 2016-11-03 - 06:24:28 - Main.tanyabw
 
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