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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[[http://www.bioinformatics.org/ctls/download/biol595/syllabus.doc | Syllabus]]

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[[http://www.bioinformatics.org/ctls/download/biol595/syllabus.doc | Syllabus]]
\\

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!!%blue% Special Readings
#[[http://www.bioinformatics.org/ctls/download/biol595/bullock.readings.zip | Special readings]]

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!!%blue% Please turn in your homework 1 and your solution to quiz1.

%blue% 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.

!!%blue% Quiz2 on April 8 on distance, distance matrix, and clustering
!!%blue% Survey on April 8

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# [[http://www.bioinformatics.org/ctls/download/biol595/regression.peanut.data.zip | Regression, Peanut data]];

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# [[http://www.bioinformatics.org/ctls/download/biol595/lec11.regression.peanut.data.zip | Regression, Peanut genotypes and phenotypes association]];

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* [[http://www.bioinformatics.org/ctls/download/biol595/quiz2.zip | QUIZ 2 ]];

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# [[http://www.bioinformatics.org/ctls/download/biol595/quiz2.zip | QUIZ 2 ]];

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# Regression analysis

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# [[http://www.bioinformatics.org/ctls/download/biol595/regression.peanut.data.zip | Regression, Peanut data]];

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* [[http://www.bioinformatics.org/ctls/download/biol595/quiz2.zip | QUIZ 2 ]];

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# Modeling of aging and genetic changes;

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# [[http://www.bioinformatics.org/ctls/download/biol595/aging.mutation.zip | Modeling of aging and genetic changes]];

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!!%blue% Quiz2 on April 8

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!!%blue% Quiz2 on April 8 on distance, distance matrix, and clustering

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!!%blue% 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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!!%blue% 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.

to:

%blue% 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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# [[http://www.bioinformatics.org/ctls/download/biol595/lec8.microarray.Prostate.cancer.zip | Libya HIV case ]];

# distance matrix and gene expression analysis; Prostate cancer data

to:

# [[http://www.bioinformatics.org/ctls/download/biol595/lec8.microarray.Prostate.cancer.zip | Microarry, clustering analysis, Prostate cancer case ]];

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# [[http://www.bioinformatics.org/ctls/download/biol595/lec8.microarray.Prostate.cancer.zip | Libya HIV case ]];

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# more on distance matrix and phylogeny Libya HIV case;

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# [[http://www.bioinformatics.org/ctls/download/biol595/LibyaHIV.zip | Libya HIV case ]];

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!!%blue% Special Readings
#[[http://www.bioinformatics.org/ctls/download/biol595/bullock.readings.zip | Special readings]]

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# Probability and likelihood estimation; Models on aging;
# Regression analysis

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# [[http://www.bioinformatics.org/ctls/download/biol595/permutation.pvalue.020709.R | distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda ]];

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# [[http://www.bioinformatics.org/ctls/download/biol595/dist.mat.and.trees.zip | distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda ]];

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# [[http://www.bioinformatics.org/ctls/download/biol595/permutation.pvalue.020709.R | t-test and p-value]] distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;

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# [[http://www.bioinformatics.org/ctls/download/biol595/permutation.pvalue.020709.R | 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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# [[http://www.bioinformatics.org/ctls/download/biol595/permutation.pvalue.020709.R | 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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!!%blue% Please turn in your homework 1. Arrange for make-up quizs.

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!!%blue% Please turn in your homework 1 and your solution to quiz1.

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

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

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# quiz1 (functions, loops, input, output)

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# [[http://www.bioinformatics.org/ctls/download/biol595/quiz1.R | 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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#[[http://www.bioinformatics.org/ctls/download/biol595/computational.thinking.and.p-value.ppt | Computational thinking and p-value]]; [[t-test and p-value]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/computational.thinking.and.p-value.ppt | Computational thinking and p-value]]; [[http://www.bioinformatics.org/ctls/download/biol595/permutation.pvalue.020709.R | t-test and p-value]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/computational.thinking.and.p-value.ppt | Computational thinking and p-value]]; [[t-test and p-value]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plot, packages]]; [[homework1]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plots, packages]]; [[homework1]]

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

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#[[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plot, packages]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plot, packages]]; [[homework1]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/lec2.R.zip | An overview R]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/lec2.R.zip | An overview of R]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plot, packages]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/basic.programming.in.R.ppt| Basic programming in R]] [[Keys to exercise]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/basic.programming.in.R.ppt| Basic programming in R]]; [[ Keys to exercise]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/basic.programming.in.R.ppt| Basic programming in R]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/basic.programming.in.R.ppt| 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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#[[http://www.bioinformatics.org/ctls/download/biol595/lec2.R.zip | Introduction to R]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/lec2.R.zip | An overview R]]
#[[http://www.bioinformatics.org/ctls/download/biol595/basic.programming.in.R.ppt| 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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#[[http://www.bioinformatics.org/ctls/download/biol595/ | Introduction to R]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/lec2.R.zip | Introduction to R]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/ | Introduction to R]]

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# [[http://http://cran.r-project.org/doc/contrib/Short-refcard.pdf | R reference card]]

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# Siege of Athens

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*[[http://www.bioquest.org/NumbersCount/agnesscott_2009/resources.php | 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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# [[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000282#s5 | Human metabolic profile variation]]

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# [[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000282#s5 | Human metabolic profile variation]]

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

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#[[http://www.bioinformatics.org/ctls/download/biol595/computer.basics.ppt | computer basics]]

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#[[http://www.bioinformatics.org/ctls/download/biol595/computer.basics.ppt | 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 (We discuss the schedule on the first class)

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#

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# yeast LOH and life span

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# [[http://mirrors.ibiblio.org/pub/mirrors/CRAN/ | Collection of docs on R ]]

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# [[http://mirrors.ibiblio.org/pub/mirrors/CRAN/ | Contributed docs on R at CRAN ]]

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# [[http://mirrors.ibiblio.org/pub/mirrors/CRAN/ | Collection of docs on R ]]

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# Libya HIV
# yeast tiling array
#

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Papers

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!!%blue% Papers

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!!%blue% Software tools

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# [[ http://mirrors.ibiblio.org/pub/mirrors/CRAN/ | R (Windows) installation ]]
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!!%blue% Lectures and labs

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Reading materials:

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!!%blue% 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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#[[http://www.bioinformatics.org/ctls/download/biol595/computer.basics.ppt | computer basics]]

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->[[http://www.bioinformatics.org/ctls/download/biol595/syllabus.doc | Syllabus]]

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[[http://www.bioinformatics.org/ctls/download/biol595/syllabus.doc | Syllabus]]

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\\

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->[[http://www.bioinformatics.org/ctls/download/biol595/syllabus.doc | 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
# [[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000282#s5 | Human metabolic profile variation]]

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Reading materials:
# [[http://cran.r-project.org/doc/manuals/R-intro.pdf | An Introduction to R, pdf]]

# [[http://faculty.washington.edu/tlumley/Rcourse/ | R, UW ]]

# [[http://www.math.ilstu.edu/dhkim/Rstuff/Rtutor.html | R online tutorial, ISU]]

# [[http://mercury.bio.uaf.edu/mercury/R/R.html | R online tutorial, Mercury ]]

# [[http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_Programming.html | 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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!! %blue% 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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