Welcome to the home page for Bioinformatics Programming II, course catalog numbers BINF 6112 and ITCS 8112. This class is the second semester of the two semester series Bioinformatics Programming, a core course in the Bioinformatics program at UNC Charlotte. Your instructor is Prof. Ann Loraine. For more information about Dr. Loraine's background and research interests, visit the Loraine Lab Web site.
Wei Song (wsong4uncc.edu) is the Teaching Assistant for the class.
Python links and resources
Java textbook and resources
Class Meeting times Spring 2011: Class meets Wednesday and Friday, 09:30-10:45am, in the Bioinformatics building computer lab.
The class repository is accessible from https://cci-subv.uncc.edu/svn/binf_prog
To check out a copy, do something like:
svn co https://cci-subv.uncc.edu/svn/binf_prog --username=alorainesubstituting your user name.
Week 1 Jan 12 - Jan 14
Class 1: Welcome Back! BINF 6111 review
Class 2: Review
Week 2 Jan 19 - Jan 21
Class 1: Exam
Class 2: Analysis of Algorithms
Week 3 Jan 26 - Jan 28
Class 1: Analysis of Algorithms
Homework: Analysis of algorithms
Extra Credit: More questions about algorithms
Class 2: Analysis of Algorithms
Week 4 Feb 2 - Feb 4
Class 1: Biopython
Assignment: Biopython Intro
Due: Analysis of algorithms
Due (Extra Credit): More questions about algorithms
Class 2: Biopython
Week 5 Feb 9 - 11Class 1: Review (led by Wei)
Week 7 Feb 16 - Feb 18
Class 1: Welcome to Java
Reading Assignment for next class:: Chapters 1, 2, and 3, Eck Textbook
Prepare for next class: Answers to Chapter 1-3 Questions
Assignment: NetBeans and Java
Reference: Searchable Javadocs Source code: TextIO.java
Class 2: Development Tools and Introduction to Java
Reading Assignment for next class Chapters 4 and 5, Eck textbook
In-class Discussion: Eck Chapters 1-3 questions
Prepare for next class: Answers to Chapter 4-5 Questions
Java links, history of C-like languages:
Week 8 Feb 23 - Feb 25
Class 1: Programming in Java
In-class discussion: Eck textbook Chapter 4-5 Questions
Due: NetBeans and Java
Assignment: From Python to Java.
Reference: Searchable Javadocs
Class 2: Programming in Java
Reference: How to write comments for the Javadoc Tool (javadocs)
Reference: Java API
Week 9 Mar 2 - Mar 4
Week 10 March 9 - 11 Spring Break
Week 11 March 16 - 18Class 1: Unit testing in Java
Week 12 March 23 - March 25Class 1: Graphical User Interface (GUI) Programming
Class 2: GUI programming
Assignment: A simple GUI Reading: Chapter 6, Sections 6.4-6.8, Eck textbook
Reading: Writing an event producer
Reading: Using the EventObject class
Week 13 March 30 - April 1
Class 1: GUI programming, cont.
Due: Graphics and drawing in Java
Class 2: NetBeans GUI builder
Reading: Designing a Swing GUI in NetBeans IDE - Tutorial
Reading: Introduction to GUI Building - Tutorial
Week 14 April 6 - April 8
Class 1: Using Java samtools
Assignment: GUI for BAM
Due: A simple GUI
Class 2: Using Java samtools, con't
Week 15 April 13 - April 15Class 1: Java Web Start (Quick Start Guide)
Week 16 April 20 - April 22
Class 1: Exam3
Class 2: No class (holiday)
Week 17 April 27 - April 29
Class 1: Demo your app
Due: Java Web Start deployment of your GUI for BAM
In-class Assignment: Interactive testing.
Grades update: Scoring and grade range.
Class 2: Testing follow-up - demos.
Congratulations - you are now a bioinformatics programmer!