Resources: COMPSCI 369 Semester 1, City Campus

Learning ourcomes

Learning outcomes for the course are presented here

Materials for the course

A local java applet illustrating several pairwise sequence alignment algorithms is given here

A number of useful materials including interactive applets can be found in
US National Resource for Computational Science Education (SHODOR),
in particular, in its MASTER (Modelling and Simulation Tools for Education Reform) section.

Supplementary materials for lectures: Examples, questions, answers

• Lecture 2: Taylor series; Newton root finder; Gaussian elimination
• Lectures 3, 4, 5: Eigenvectors, eigenvalues, SVD (singular value decomposition)
  • C-file sources.c with three subroutines:
    • for computing SVD of an m × n matrix; m ≥ n (svd.c) and
    • reading (readFilePGM_PPM) and writing (writeFilePGM_PPM)
      greyscale and colour digital images in PGM and PPM formats, respectively.
      Note: the reading subroutine was modified by Jeremy Meese on 11-03-2012
      to work not only in the Unix/Linux, but also the Windows OS environment.
    • Useful examples on computing eigenvectors: see the web-resource
      S.O.S. MATHematics by M. A. Khamsi.
• Lectures 6, 7: Unconstrained optimisation
  • Useful examples of gradient search: see the corresponding web-page in
    Wikipedia.
• Lecture 8: Constrained optimisation
• Lectures 9, 10: Least squares
• 1 May: Random walk and Poisson process simulators

Materials for Assignment 2

Sample file containing 10000 simulations: simulation2012.csv.

Article: Pritchard et al, 1999, Population Growth of Human Y Chromosomes.

Materials for Assignment 1

C-subroutines for SVD and input/output of grayscale (format PGM) and colour (format PPM)
digital images are also given here.

Java public class PGM_PPM_Handler for input and output of pgm and ppm images
developed in 2011 by Andrew Probert and refined by Gabriel (Jin Koo) Niersbach
is given here (working with arrays in char format).

Java Matrix algebra package developed by the US Nat. Inst. for Standards and Technology (NIST):
see JAMA website. This package implements the same algorithms as MATLAB and LINPACK.
The corresponding jar library is available from the above website and also is placed here.
The online documentation for its usage can be found here.

Test images "Baboon" 120 × 100:

Grayscale pgm file

Colour ppm file