|
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
- Computer basics
- An overview of R
- Basic programming in R; Keys to exercise
- Input, ouput, plots, packages; homework1
- Quiz1 (functions, loops, input, output)
- Computational thinking and p-value; t-test and p-value
- distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;
- Libya HIV case;
- Microarry, clustering analysis, Prostate cancer case;
- 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. )
- Modeling of aging and genetic changes;
- QUIZ 2;
- Regression, Peanut genotypes and phenotypes association;
- Probability and likelihood estimation;
Reading materials:
- R reference card
- An Introduction to R, pdf
- Contributed docs on R at CRAN
- R, UW
- R online tutorial, ISU
- R online tutorial, Mercury
- Programming in R, UC Riverside
Software tools
- R (Windows) installation
Papers
- Libya HIV
- Kelly 2008 Light drinking in pregnancy, a risk forbehavioural problems and cognitive deficits at 3 years of age?
- Siege of Athens
- yeast tiling array
- yeast LOH and life span
- Human metabolic profile variation
Related sites:
|
|