BNFO 135: Programming in Bioinformatics I
Fall 2012

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Mon and Wed 2:30-4pm, Thu 2-4pm, and by appointment
Email: usman@cs.njit.edu

Teaching assistant: Ying Chen
Email: yc354@njit.edu

Recommended Text:
  1. Bioinformatics Programming Using Python by Mitchell Model

Grading: 15% weekly programming asssignments, 25% two exams, and 35% final

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

Course plan:

Topic
Date
Remarks
Background and Intro to Python
09/05/12
Basic molecular biology
Intro to Python
Lists, input and output 09/10/12
See previous slides
Lists, input and output 09/12/12
See slides from first lecture
HW 1
For loop 09/17/12
See slides from first lecture
HW 2
More loops
09/19/12
HW 3
More loops
09/24/12
HW 4
More loops
09/26/12
HW 5
DNA complements
10/01/12
HW 6
Transcription and translation
10/03/12
HW 7
Codon to amino acid map
Translation 10/08/12
HW 8
Translation and review 10/10/12
First exam 10/15/12
Sequence alignment
10/17/12
Sequence alignment
HW 9
Exam solution 10/22/12
HW 10
Conserved columns 10/24/12
Hands-on bioinformatics exercise
HW 11
NJIT closed due to hurricane Sandy
10/29/12
NJIT closed due to hurricane Sandy
10/31/12
Conserved columns
11/05/12 HW 11 reassigned
Conserved columns
11/07/12 HW 12
Conserved columns, data formats (FASTA and PHYLIP), and while loops
11/12/12 FASTA and PHYLIP formats
HW 13
Split function, data formats, and dictionaries 11/14/12 HW 14
11/19/12 HW 15
Practice problem
NJIT classes follow Friday schedule 11/21/12
11/26/12 HW 16
11/28/12
Second exam 12/03/12
Second exam solution 12/05/12 HW 17
Extra credit assignment 12/10/12 Extra credit assignment
BLOSUM 62 matrix
alignments2.fasta
Review 12/12/12 Substring alignment problem
Genome assembly problem
Final exam 12/20/12 FMH 310, 8:30 to 11am