Biocomputing, part of MVE311, 2.5 credits

Course info
The course Introduction to bioinformatics, systems biology and biocomputing (MVE310) consists of two blocks: Introduction to Bioinformatics and Systems Biology (5 credits) and Biocomputing (2.5 credits). This web page is intended for the biocomputing part.

Latest news
100912: Course web site updated and files added.
100825: Course web site updated.

Examiner and lecturer
Responsible teacher for the biocomputing block is Alexandra Jauhiainen.
For files related to the project, see the following site.

Projects
Depending on previous programming experience, different projects are available. A project description for a protein strucutre project supervised by Graham Kemp can be found here (access within Chalmers and GU only). A sequence bioinformatics related project concerning motif searching and visualization can be found here. For students also following the course Programming for Science (DAT161), we recommend a more general project in Java. The aim of the project is to learn about program design. During the labs, help will be provided on the projects, and also on assignments given in DAT161, if needed. Files for the sequence bioinformatics project will be distributed by Alexandra. For a project description and relevant files for the Java project (called Balls in a Box), see the above site.

Course literature
If you program in Java, we recommend Java Concepts 6th Edition (ISBN 978-0-470-56159-1) by Cay Horstmann, which is also used in the JAVA part of the course Programming for science (DAT161).

Preliminary plan for labs
Day
Time
Room
Contents
 100901  09:00-11:45  MVF24  Introduction
 100908  09:00-11:45  MVF24  Project.
 100915  09:00-11:45  MVF24  Continued work on the project.
 100922  09:00-11:45  MVF24  Lab and tutorial. Introduction to the MVC architecture (for students doing the general Java project).
 100929  09:00-11:45  MVF24  Lab

Examination
For those who follow the main track of the course (the Balls in a Box project), the examination of the biocpomuting part will be to

1. Demonstrate a fully functioning balls in a box program.
2. Hand in a lab report including code.

The program should be designed according to MVC with a control class, viewer class, main class and two model classes. You must have modified the program so that the balls cannot leave the box.You have two options concerning the control class:

1. Implement a control class which also visualizes the buttons (i.e. extends JPanel) which corresponds to the design suggested in Assignment 5 in DAT161.
2. Implement a control class and a specific viewer class for the buttons (pure MVC).

The minimum requirement for the functionality of the program is to implment a button that can move either (i) all the balls one step or (ii) a button and JComboBox that makes you choose which ball to move one step. Further functionality (not compulsory) would be to implement a button that moves all the balls 100 steps.

Deadline to be decided.

For other special projects in the course, please contact either Graham Kemp or Alexandra Jauhiainen for details concerning the examination.