BNFO 135: Programming in Bioinformatics I,
Spring 2014


Instructor: Zhi Wei, Office: GITC 3801, Ph: 973-642-4497, Email: zhiwei@njit.edu
Office hours: Monday 3:30pm-4:30pm, Tuesdays 2:30pm-4:30pm, and by appointment

Teaching assistant: Wei Wang, Email: ww42@njit.edu

Tutor: 11:00 am - 12:30 pm on Friday by Trevor Summerfield, Lower Level of the CAPE-Kupfrian Hall
or by appointment at 2:00 pm- 3:00 pm on Fri.

--> Recommended Websites:
  1. Python for beginners
  2. Codingbat
Recommended Text:
  1. Think Python, by Allen B. Downey, ISBN 978-1449330729, html, pdf
  2. Dive Into Python 3, by Mark Pilgrim, ISBN 978-1430224150, html, pdf
Grading: 2% moodle and class participation, 5% weekly programming asssignments, 30% quiz, 30% midterm, and 35% final.

Course Overview: We will cover the basics of Python and implement programs for comparing DNA and protein sequences.

Tentative weekly course plan (subject to change):

Topic
Date
Readings/Homework
Background and Intro to Python
01/23/14
Chapter 1.
Exercises 2-4
Variables, expressions and statements 01/27/14
Chapter 2.
HW 1
Quiz 1
01/30/14
   
Class cancelled due to snow 02/03/14
 
Strings, For loops 02/06/14
Chapter 7 Iteration, Chapter 8 Strings
CodingBat: String
GooglePython: String
HW 2 ; Sample solution for replacing w with m.
If boolean logic 02/10/14 CodingBat:If-Boolean-Logic Function & Indention
Exercise: CodingBat Warmup-1 Q1-Q6
Class cancelled due to snow
02/13/14
Quiz 2 02/17/14
Lists
02/20/14
Chapter 10 Lists, Excercise: CodingBat List-1 Q1-Q6
HW 3, Sample Solution for count_evens(nums)
File and Keyboard Input  02/24/14
Chapter 14 Files, dna file1, Keyboard Input Example
Quiz 3 02/27/14
 
Lab (Write a script) 03/03/14
Exercise1, Solution including ex1b.py, HW 4
Lab (for loop)
03/06/14
Exercise: big_diffExercise2, Sample dna file, Solution
Midterm Review 03/10/14
 
Midterm Exam  03/13/14
 
 Spring Break 03/17/14  
 Spring Break 03/20/14  
Midterm Solution 03/24/14  
while loop 03/27/14 HW 5
break/continue in loop 03/31/14 Exercise: Guessing Game, Solution
 
Dictionary / DNA complements 04/03/14 Chapter 11 Dictionaries. HW6, Solution
Transcription and translation 04/07/14
Codon to amino acid map
 Quiz 4 04/10/14
Quiz 4 solution and Transcript and Translate Exercise solution 04/14/14 Transcript and Translate Exercise: Solution
HW7 Solution
Commonly used list/string methods 04/17/14 HW 8 For Input File http://web.njit.edu/~zhiwei/BNFO135/data1/Ng.txt , Sample Output: N=10, N=15
solution
Exercise for HW 8 04/21/14
Quiz 5 + Excercise:  Ex1Ex2  (Sample dna file) 04/24/14  
Review (1) String and Logic 04/28/14  
Review (2) List and Loop 05/01/14
Review (3) Dictionary and Function 05/05/14