Biological Computing I (C1) Python Programming

 

Semester: Fall 2009, TIGP-BP
Place
: Institute of Information Science, Academia Sinica, New Building, Rm. 107
Time: Thursday mornings, 
10:00-12:00 AM

This course introduces basic aspects of programming language and its application in biomedical analysis. First, fundamental programming language techniques in Python are introduced. After that, this course focuses on the pratical implementation of programs to analyze various biomedical data. Finally, the use of existing available resources from the Internet is incorporated.

 

Introduction to Python programming language

Data types and operators (1): basic built-in object types

Data types and operators (2): container object types

Data types and operators (3): handling files

Basic statements (1): assignment, print, and if statements

Basic statements (2): loop statements

Functions (1): scope rules

Functions (2): passing arguments

Modules: loading modules

Introduction to Biopython resources

Exercise and project implementations

Project demonstrations


Teaching Assistant(助教): George Jau-Ji Lin (林肇基 ) and Emily Chia-Yu Su (蘇家玉)

Note: Please bring a laptop with you for laboratory exercise

Reference: Mark Lutz & David Ascher, Learning Python, 3rd Edition, O'Reilly, 2008

Week

Date

Topics

Project Demonstrations

Slides

Online

1

2009/09/17

No Class

 

   

2

2009/09/24

No Class

 

 

 

3

2009/10/01

Programming Design 1: installation, command prompt, data types

In-class Exercise

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4

2009/10/08

Programming Design 2: loops, branching, handling files, handling texts

In-class Exercise

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5

2009/10/15

Programming Design 3: modules & functions

 

In-class Exercise 

 

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6

2009/10/22

Programming Design 4: regular expression, error handling, object-oriented programming

In-class Exercise

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7

2009/10/29

Project 1: Brute Force Motif Finding Algorithm

 

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8

  2009/11/05  

Project 1 Implementation

 

   

9

2009/11/12

Midterm Exam – No Class

 

   

10

2009/11/19

Project 2: Branch and Bound Motif Finding Algorithm

 

Project 1

 

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11

2009/11/26

Project 2 Implementation

 

 

 

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12

2009/12/03

Project 3: Longest Common Subsequence

Project 2

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13

2009/12/10

 

Project 3 Implementation

 

 

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14

2009/12/17

Project 4: Global Alignment

 

Project 3 

 

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15

2009/12/24

Project 4 Implementation

 

 

 

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16

2009/12/31 

Project 5: Local Alignment

 

Project 4 

   

17

2009/01/08

Programming Review

In-class Programming Exam

   

18

2009/01/14

Final Exam-No Class