COSC348

COSC348 Labs

Each lab from week 2 produces a deliverable (brief report or program code) that is worth 1% of your final mark. To submit your code or report that you produced in the lab, use the submit348 script on either a mac or a linux OS - that puts files or whole directories of files into the /coursework/348/submit directory. Name your file/directory with your name and lab number.

Lab access

Cosc348 will have labs in Owheo Lab B on Tuesdays 11:00-12:50. The lab can be used at other times too.

MacOSX
This uses the same login and password as the rest of the machines you can use in the department.

Lab schedule

  1. 07 July:   The Macro and the Micro (Videos about human genetic dispersion and DNA.)
  2. 14 July:   Finding Data (Review of sources of online information: ExPASy, GenBank, Ensembl. )
  3. 21 July:   Coding of exact string search
  4. 28 July:   Sequence alignment, finding genes and motifs
  5. 04 Aug:   Hidden Markov Model 1/2 ( Coding of, generating and scoring sequences according to HMM. )
  6. 11 Aug:   Hidden Markov Model 2/2
  7. 18 Aug:   Phylogeny inference 1/3 ( Coding trees.)

    22 Aug -- 30 Aug:     MID-SEMESTER BREAK

  8. 01 Sept:   Phylogeny inference 2/3 ( Adding the Fitch cost.)
  9. 08 Sept:   Phylogeny inference 3/3 (Finishing previous labs and graphical visualisation of trees.)
  10. 15 Sept:   Microarray data analysis 1/2 ( Discuss the scientific paper on microarray data analysis. Then you can start working on data analysis. )
  11. 22 Sept:   Microarray data analysis 2/2 ( Perform microarray data analysis on real medical data using NeuCom, Windows software for data analysis. )
  12. 29 Sep:   Gene regulatory network (GRN) ( Ising-like model of the dynamics of an abstract GRN. )
  13. 06 Oct:   2D visualisation of the DNA/RNA sequences ( Chaos game representation of symbolic sequences or the completion of the previous lab. )