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BIOL 320

Computing in Genomics and Proteomics

These are course materials based on R. This course was offered in Spring of 2010, 2011, 2012. Later materials are in Spel.eLearn site and http://sunrays.spelman.edu/hqin/

Announcements

• Final take home quiz will be posted on April 28th. Your R codes, discussion of results and conclusions should be emailed to the instructor by May 3rd, 5pm. Discussion of the results and conclusions should be written in WORD document. This is an independent test. No collaboration is allowed. Late submission will not be accepted.

• Final quiz is here. Good luck.

• Final written reports are due on May 4, 5pm. This report should be written in the style of a scientific publication. In addition to your reports, R codes and running results, and necessary supporting materials should all be electronically submitted to the instructor. Please see your syllabus for detailed requirement.

• Oral presentation is on April 27 in class. Rubric will be provided.

Lectures and labs

• An overview of R;

• Basic programming in R;

• Quiz 1

• Input, output, plots, packages;

• Assignment 1, due Tuesday Feb 9, 2010

• KaKs, growth fitness, protein connectivity in yeast PIN
• Assignment 2

• Computational thinking, simulation and p-value
• Permutation to calculate the p-value of Ka difference in interacting protein pairs
• Assignment 2, continued

• Quiz 2. Your answers should be emailed to the instructor by 12:00pm on Feb 23, Tuesday, 2010.
• Keys to #3,#4 in Quiz2

Reading materials:

1. Computer basics
2. Beginner R by Mathews;
3. R for Bioinformatics by Krijnen;
4. Essential Bioinformatics, by J Xiong
5. First course in statistical programming using R, by WJ Braun & DJ Murdoch
6. R reference card,1
7. R reference card,2
8. An Introduction to R, pdf
9. Documents at CRAN

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Software tools

• R for windows
• Notepad++

Reference 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

Papers

1. essential genes and connectivity
2. Gasch expression
3. yeast LOH and life span

Related sites:

• http://ocw.mit.edu/ans7870/6/6.891/f04/labs/lab1.html
• http://ocw.mit.edu/ans7870/6/6.891/f04/labs/laboratory2.htm
• http://www.sys-bio.org/sbwWiki/sysbiolabmembers/498_systems_and_synthetic_biology_spring_2008
• http://www.sys-bio.org/index.htm
• http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-Science/6-895Fall-2005/LectureNotes/index.htm
• Number Count
• Meeting at GaTech, March 26-28, 2010

Old contents

• 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
• Modeling of aging and genetic changes;
• QUIZ 2;
• Regression, Peanut genotypes and phenotypes association;
• Probability and likelihood estimation

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