Computational Thinking in Life Sciences : BIOL 595

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Credits: 3
Location: Milbank 403
Time: Wed,3-6pm pm

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Syllabus

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Syllabus \\

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Special Readings

Special readings

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Please turn in your homework 1 and your solution to quiz1.

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.

Quiz2 on April 8 on distance, distance matrix, and clustering

Survey on April 8

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Regression, Peanut data;

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Regression, Peanut genotypes and phenotypes association;

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QUIZ 2;

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QUIZ 2;

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Regression analysis

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Regression, Peanut data;

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QUIZ 2;

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Modeling of aging and genetic changes;

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Modeling of aging and genetic changes;

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Quiz2 on April 8

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Quiz2 on April 8 on distance, distance matrix, and clustering

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Survey on April 8

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Probability and likelihood estimation; Models on aging;

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Modeling of aging and genetic changes;

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Probability and likelihood estimation;

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Quiz2 on April 8

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%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.

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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.

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%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.

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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 shortcomings )

to:

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. )

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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 shortcomings )

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Libya HIV case;
distance matrix and gene expression analysis; Prostate cancer data

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Microarry, clustering analysis, Prostate cancer case;

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Libya HIV case;

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more on distance matrix and phylogeny Libya HIV case;

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Libya HIV case;

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Special Readings

Special readings

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Probability and likelihood estimation; Models on aging;
Regression analysis

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distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;

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distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;

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t-test and p-value distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;

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distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;

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distance between sequences
distance matrix, clustering, and trees; Libya HIV case; SARS 2003 outbreak

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t-test and p-value distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;
more on distance matrix and phylogeny Libya HIV case;

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Please turn in your homework 1. Arrange for make-up quizs.

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Please turn in your homework 1 and your solution to quiz1.

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Announcment: Quiz on Feb 11 (topics:function,loops,input,output)

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Please turn in your homework 1. Arrange for make-up quizs.

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quiz1 (functions, loops, input, output)

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Quiz1 (functions, loops, input, output)

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quiz1

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quiz1 (functions, loops, input, output)

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quiz1

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distance matrix and trees; Libya HIV case; SARS 2003 outbreak

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distance matrix, clustering, and trees; Libya HIV case; SARS 2003 outbreak

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distance between sequences
distance matrix and trees; Libya HIV case; SARS 2003 outbreak
distance matrix and gene expression analysis; Prostate cancer data

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Computational thinking and p-value; t-test and p-value

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Computational thinking and p-value; t-test and p-value

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Computational thinking and p-value; t-test and p-value

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Input, ouput, plot, packages; homework1

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Input, ouput, plots, packages; homework1

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Announcment: Quiz on Feb 11 (topics:function,loops,input,output)

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Input, ouput, plot, packages

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Input, ouput, plot, packages; homework1

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An overview R

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An overview of R

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Input, ouput, plot, packages

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Basic programming in R Keys to exercise

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Basic programming in R; Keys to exercise

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Basic programming in R

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Basic programming in R Keys to exercise

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Time: Wed,3-5:30pm

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Time: Wed,3-6pm pm

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Introduction to R

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An overview R
Basic programming in R

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

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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) will also be used.

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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.

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Time: Wed, Thu, 3pm-4:30pm (We will discuss the schedule on the first lecture)

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Time: Wed,3-5:30pm

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Introduction to R

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Introduction to R

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Introduction to R

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R reference card

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Siege of Athens

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Number Count

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http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-Science/6-895Fall-2005/LectureNotes/index.htm

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http://www.sys-bio.org/index.htm

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http://www.sys-bio.org/sbwWiki/sysbiolabmembers/498_systems_and_synthetic_biology_spring_2008

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Relative sites:

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Related sites:

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http://ocw.mit.edu/ans7870/6/6.891/f04/labs/laboratory2.htm

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http://ocw.mit.edu/ans7870/6/6.891/f04/labs/lab1.html
http://ocw.mit.edu/ans7870/6/6.891/f04/labs/laboratory2.htm

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Human metabolic profile variation

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Human metabolic profile variation

Relative sites:

http://ocw.mit.edu/ans7870/6/6.891/f04/labs/laboratory2.htm

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computer basics

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Computer basics

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Credit: 3\\

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Credits: 3\\

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Time: Wed, Thu, 3pm-4:30pm (We will discuss the schedule on the first class)

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Time: Wed, Thu, 3pm-4:30pm (We will discuss the schedule on the first lecture)

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This course is based on case studies and projects. We will mainly use R throughout this course. Basic Linux will also be introduced.

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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) will also be used.

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Time: Wed, Thu, 3pm-4:30pm (We discuss the schedule on the first class)

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Time: Wed, Thu, 3pm-4:30pm (We will discuss the schedule on the first class)

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Time: Wed, Thu, 3pm-4:30pm.

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Time: Wed, Thu, 3pm-4:30pm (We discuss the schedule on the first class)

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yeast LOH and life span

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Collection of docs on R

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Contributed docs on R at CRAN

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Collection of docs on R

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Libya HIV
yeast tiling array

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Papers

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Papers

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Software tools

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R (Windows) installation

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Lectures and labs

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Reading materials:

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Reading materials:

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This course is based on case studies and projects. We will mainly use R throughout this course. Basic Linux will also be introduced.

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This course is based on case studies and projects. We will mainly use R throughout this course. Basic Linux will also be introduced.

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computer basics

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Syllabus

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Syllabus

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\\

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Syllabus

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Time: Schedule will be decided by interested students. Tentatively Wed, Thu, 3pm-4:30pm.

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Time: Wed, Thu, 3pm-4:30pm.

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Papers

Human metabolic profile variation

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Reading materials:

An Introduction to R, pdf
R, UW
R online tutorial, ISU
R online tutorial, Mercury
Programming in R, UC Riverside

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Time: Tentatively Wed, Thu, 3pm-4:30pm.

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Time: Schedule will be decided by interested students. Tentatively Wed, Thu, 3pm-4:30pm.

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Location: Milbank 403

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Location: Milbank 403 \\

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Mon, Wed, 3-4:30pm \\

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Time: Tentatively Wed, Thu, 3pm-4:30pm.

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This course is based on case studies and projects. We will mainly use R throughout this course.

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This course is based on case studies and projects. We will mainly use R throughout this course. Basic Linux will also be introduced.

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This project based course will focus on case studies. We will mainly use R throughout this course.

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This course is based on case studies and projects. We will mainly use R throughout this course.

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Location: Milbank 403 \\

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Location: Milbank 403

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This project based course will focus on case studies. We will mainly use R throughout this course.

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This project based course will focus on case studies. We will mainly use R throughout this course.

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Location: Milbank 403 \\

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Location: Milbank 403 \\ \\

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Location: Milbank 403

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Location: Milbank 403 \\

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Credit: 3 Mon, Wed, 3-4:30pm Location: Milbank 403

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Credit: 3
Mon, Wed, 3-4:30pm
Location: Milbank 403

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Computing in Life Sciences, Spring 2009

Credit: 3 Mon, Wed, 3-4:30pm Location: Milbank 403

This project based course will focus on case studies. We will mainly use R throughout this course.

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Main.BIOL595 History

Special Readings

Please turn in your homework 1 and your solution to quiz1.

Quiz2 on April 8 on distance, distance matrix, and clustering

Survey on April 8

Quiz2 on April 8

Quiz2 on April 8 on distance, distance matrix, and clustering

Survey on April 8

Quiz2 on April 8

Special Readings

Please turn in your homework 1. Arrange for make-up quizs.

Please turn in your homework 1 and your solution to quiz1.

Announcment: Quiz on Feb 11 (topics:function,loops,input,output)

Please turn in your homework 1. Arrange for make-up quizs.

Announcment: Quiz on Feb 11 (topics:function,loops,input,output)

Papers

Software tools

Lectures and labs

Reading materials:

Computing in Life Sciences, Spring 2009