Biological Computing I (C1) Python Programming

 

Semester: Fall 2012, TIGP-BP
Place
: Institute of Information Science, Academia Sinica, Old Building, Rm. 108
Time: Tuesday afternoons,  2
:00-4:00 PM

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): Emily Chia-Yu Su (蘇家玉)

Note: Please bring a laptop with you for laboratory exercise

References:

1. Learning Python, Mark Lutz, 3rd Edition, O'Reilly, 2008

2. Python Pocket Reference, Mark Lutz, 3rd Edition, O'Reilly, 2005

3. Programming Python, Mark Lutz, 3rd Edition, O'Reilly, 2006

4. Python for Bioinformatics, Jason Kinser, 1st Edition, Jones & Bartlett Publishers, 2008

Week

Date

Topics

Project Demonstrations

Slides

Online

1

2012/09/18

No Class

 

   

2

2012/09/25

Programming Design 1: installation, command prompt, data types

In-class Exercise

 

 

3

2012/10/02

No Class

 

 

 

4

2012/10/09

Programming Design 2: basic statements: assignment, if, and loops statements

In-class Exercise

 

 

5

2012/10/16

 

Programming Design 3: handling files, handling texts, exception handling

 

In-class Exercise 

 

 

 

6

2012/10/23

Programming Design 4: functions, modules

In-class Exercise

   

7

2012/10/30

Programming Design 5: biopython, regular expression, object-oriented programming

In-class Exercise

 

 

8

  2012/11/06  

Project 1: Brute Force Motif Finding Algorithm

 

 

 

9

2012/11/13

Midterm Exam – No Class (Project 1 Implementation)

 

   

10

2012/11/20

Project 2: Branch and Bound Motif Finding Algorithm

 

Project 1

 

 

 

11

2012/11/27

Project 2 Implementation

 

 

 

 

 

12

2012/12/04

Project 3: Longest Common Subsequence

Project 2

 

 

13

2012/12/11

 

Project 3 Implementation

 

 

   

14

2012/12/18

Project 4: Global Alignment

 

Project 3 

 

 

 

15

2012/12/25

Project 4 Implementation

 

 

 

   

16

2013/01/02 

Project 5: Local Alignment

 

Project 4

 

 

 

17

2013/01/11

Programming Review

@Media conference room, HSSB

In-class Programming Exam

   

18

2013/01/15

Final Exam-No Class