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BIOL 595

Computing in Life Sciences, Spring 2009


Syllabus
This course is based on case studies and projects. We will mainly use R throughout this course. Basic Linux will also be introduced. Other necessary software tools, such as MEGA and BLAST will also be used.

Lectures and labs

  1. Computer basics
  2. An overview of R
  3. Basic programming in R; Keys to exercise
  4. Input, ouput, plots, packages; homework1
  5. Quiz1 (functions, loops, input, output)
  6. Computational thinking and p-value; t-test and p-value
  7. distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;
  8. Libya HIV case;
  9. Microarry, clustering analysis, Prostate cancer case;
  10. Protein structure and protein networks, (Graduating seniors should write a one-page summary on the paper, Kim, et al, 2006, Science. "Relating 3-dimentioal structures to protein networks provides evolutionary insights". Your summary should explain the key findings and methods used, point out a few weakness. )
  11. Modeling of aging and genetic changes;
  12. QUIZ 2;
  13. Regression, Peanut genotypes and phenotypes association;
  14. Probability and likelihood estimation;

Reading materials:

  1. R reference card
  2. An Introduction to R, pdf
  3. Contributed docs on R at CRAN
  4. R, UW
  5. R online tutorial, ISU
  6. R online tutorial, Mercury
  7. Programming in R, UC Riverside

Software tools

  1. R (Windows) installation

Papers

  1. Libya HIV
  2. Kelly 2008 Light drinking in pregnancy, a risk forbehavioural problems and cognitive deficits at 3 years of age?

  3. Siege of Athens
  4. yeast tiling array
  5. yeast LOH and life span
  6. Human metabolic profile variation

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