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Main.BIOL320 History
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February 01, 2012, at 09:48 AM
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These are course materials based on R. This course was offered in Spring of 2010 and 2011.
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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/
September 18, 2011, at 01:38 PM
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June 03, 2011, at 03:00 PM
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These are course materials based on R. This course was offered in Spring of 2010 and 2011.
June 03, 2011, at 02:59 PM
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%center% %blue% Hong Qin, Spring 2010, Spelman Changed lines 3-5 from:
%center% %blue% 9am-11:30am, Tue & Thur, Sci 246
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* [[http://www.spelman.edu/researchday/index.shtml| Spelman Research Day, April 16, 2010 ]]
April 27, 2010, at 02:56 PM
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* [[http://www.bioinformatics.org/ctls/download/biol320/q3.zip| Final quiz is here]]. Good luck.
April 27, 2010, at 10:01 AM
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* Final written reports are due on May 1, 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.
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* 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.
April 24, 2010, at 08:27 AM
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* Final take home quiz will be posted on April 30th. 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 written reports are due on April 27, 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.
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* 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 written reports are due on May 1, 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.
April 23, 2010, at 03:01 PM
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* Final written reports are due on April 27, 5pm. Late reports will not be accepted. 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.
to:
* Final written reports are due on April 27, 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.
April 10, 2010, at 02:01 PM
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* Final written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication. In addition to your reports, codes, running results, and necessary supporting materials should all be electronically submitted to the instructor. Please see your syllabus for detailed requirement.
to:
* Final written reports are due on April 27, 5pm. Late reports will not be accepted. 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.
April 10, 2010, at 01:28 AM
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* Final written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication.
* Oral presentation is on April 27 in class.
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* Final written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication. In addition to your reports, codes, 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.
April 10, 2010, at 01:24 AM
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* Final take home quiz will be posted on April 30th. 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.
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* Final take home quiz will be posted on April 30th. 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.
April 10, 2010, at 01:24 AM
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Final take home quiz will be posted on April 30th. 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 written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication.
Oral presentation is on April 27 in class.
to:
* Final take home quiz will be posted on April 30th. 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 written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication.
* Oral presentation is on April 27 in class.
April 10, 2010, at 01:23 AM
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Final take home quiz will be posted on April 30th. 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 written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication.
Oral presentation is on April 27 in class.
April 06, 2010, at 07:20 PM
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Old contents
* [[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plots, packages]]; [[homework1]]
* [[http://www.bioinformatics.org/ctls/download/biol595/quiz1.R | Quiz1 ]] (functions, loops, input, output)
* [[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]]
* [[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 ]];
* [[http://www.bioinformatics.org/ctls/download/biol595/LibyaHIV.zip | Libya HIV case ]];
* [[http://www.bioinformatics.org/ctls/download/biol595/lec8.microarray.Prostate.cancer.zip | Microarry, clustering analysis, Prostate cancer case ]];
* Protein structure and protein networks
* [[http://www.bioinformatics.org/ctls/download/biol595/aging.mutation.zip | Modeling of aging and genetic changes]];
* [[http://www.bioinformatics.org/ctls/download/biol595/quiz2.zip | QUIZ 2 ]];
* [[http://www.bioinformatics.org/ctls/download/biol595/lec11.regression.peanut.data.zip | Regression, Peanut genotypes and phenotypes association]];
* Probability and likelihood estimation;
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Old contents
* [[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plots, packages]]; [[homework1]]
* [[http://www.bioinformatics.org/ctls/download/biol595/quiz1.R | Quiz1 ]] (functions, loops, input, output)
* [[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]]
* [[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 ]];
* [[http://www.bioinformatics.org/ctls/download/biol595/LibyaHIV.zip | Libya HIV case ]];
* [[http://www.bioinformatics.org/ctls/download/biol595/lec8.microarray.Prostate.cancer.zip | Microarry, clustering analysis, Prostate cancer case ]];
* Protein structure and protein networks
* [[http://www.bioinformatics.org/ctls/download/biol595/aging.mutation.zip | Modeling of aging and genetic changes]];
* [[http://www.bioinformatics.org/ctls/download/biol595/quiz2.zip | QUIZ 2 ]];
* [[http://www.bioinformatics.org/ctls/download/biol595/lec11.regression.peanut.data.zip | Regression, Peanut genotypes and phenotypes association]];
* Probability and likelihood estimation
April 06, 2010, at 07:12 PM
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* [[http://www.bioinformatics.org/ctls/download/biol320/q2key.zip| Keys to #3,#4 in Quiz2]]
March 18, 2010, at 06:07 PM
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!! Abstract submission for Research Day is due on March 15, Monday.
March 07, 2010, at 09:33 PM
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Abstract submission for Research Day is due on March 15, Monday.
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!! Abstract submission for Research Day is due on March 15, Monday.
March 07, 2010, at 09:33 PM
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All groups should email their draft research abstract to the instructor by the end of March 5
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Abstract submission for Research Day is due on March 15, Monday.
March 02, 2010, at 09:26 AM
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All groups should email their draft research abstract to the instructor by the end of March 5
February 19, 2010, at 04:57 PM
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* [[Quiz 2]] on Feb 23, Tuesday
*[[http://www.bioinformatics.org/ctls/download/biol320/quiz2.zip| Quiz 2]] on Feb 23, Tuesday.
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*[[http://www.bioinformatics.org/ctls/download/biol320/quiz2.zip| Quiz 2]]. Your answers should be emailed to the instructor by 12:00pm on Feb 23, Tuesday, 2010.
February 19, 2010, at 04:55 PM
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*[[http://www.bioinformatics.org/ctls/download/biol320/quiz2.zip| Quiz 2]] on Feb 23, Tuesday.
February 18, 2010, at 08:45 AM
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* [[Quiz 2]] on Feb 23, Tuesday
February 11, 2010, at 09:18 AM
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* [[ http://bioinformatics.org/ctls/download/biol320/5.zip | Computational thinking, permutation and p-value]] to:
* [[ http://bioinformatics.org/ctls/download/biol320/5.zip | Computational thinking, simulation and p-value]] February 08, 2010, at 09:17 PM
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* [[Assignment 1]], due Tuesday Feb 9, 2010
February 08, 2010, at 09:17 PM
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# [[ Assignment 2, continued]]
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* [[ Assignment 2, continued]]
February 08, 2010, at 09:15 PM
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* [[ http://bioinformatics.org/ctls/download/data/PIN.KaKs.zip | KaKs, growth fitness, protein connectivity in yeast PIN]] [[Assignment 2]]
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* [[ http://bioinformatics.org/ctls/download/data/PIN.KaKs.zip | KaKs, growth fitness, protein connectivity in yeast PIN]]
*[[Assignment 2]]
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* [[ http://bioinformatics.org/ctls/download/biol320/permutation.R | Permutation to calculate the p-value of Ka difference in interacting protein pairs]]
[[ Assignment 2, continued]]
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* [[ http://bioinformatics.org/ctls/download/biol320/permutation.r | Permutation to calculate the p-value of Ka difference in interacting protein pairs]]
# [[ Assignment 2, continued]]
February 08, 2010, at 09:15 PM
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* [[ http://bioinformatics.org/ctls/download/biol320/5.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
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* [[ http://bioinformatics.org/ctls/download/biol320/5.zip | Computational thinking, permutation and p-value]]
* [[ http://bioinformatics.org/ctls/download/biol320/permutation.R | Permutation to calculate the p-value of Ka difference in interacting protein pairs]]
[[ Assignment 2, continued]]
February 08, 2010, at 09:11 PM
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* [[ http://bioinformatics.org/ctls/biol320/5.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
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* [[ http://bioinformatics.org/ctls/download/biol320/5.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
February 08, 2010, at 09:11 PM
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* [[ http://bioinformatics.org/ctls/biol320/5.comp.thinking.permutation.pvalue.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
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* [[ http://bioinformatics.org/ctls/biol320/5.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
February 08, 2010, at 09:09 PM
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* [[ http://bioinformatics.org/ctls/biol320/5.computationl.thinking,permutation.pvalue.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
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* [[ http://bioinformatics.org/ctls/biol320/5.comp.thinking.permutation.pvalue.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
February 08, 2010, at 09:08 PM
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* [[ http://bioinformatics.org/ctls/biol320/5.computationl.thinking.permutation.pvalue.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
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* [[ http://bioinformatics.org/ctls/biol320/5.computationl.thinking,permutation.pvalue.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
February 08, 2010, at 09:07 PM
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* [[ http://bioinformatics.org/ctls/biol320/5.computationl.thinking.permutation.pvalue.zip | Computational thinking, permutation and p-value]] [[Assignment 2, continued]]
February 06, 2010, at 12:14 PM
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%center% %blue% Hong Qin
%center% %blue% Spring 2010, Spelman to:
%center% %blue% Hong Qin, Spring 2010, Spelman February 06, 2010, at 12:13 PM
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* [[ http://bioinformatics.org/ctls/download/data/PIN.KaKs.zip | KaKs, growth fitness analysis, protein connectivity in yeast PIN]] [[Assignment 2]]
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* [[ http://bioinformatics.org/ctls/download/data/PIN.KaKs.zip | KaKs, growth fitness, protein connectivity in yeast PIN]] [[Assignment 2]]
February 04, 2010, at 11:01 AM
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* [[ http://bioinformatics.org/ctls/download/data/PIN.KaKs.zip | KaKs, growth fitness analysis, protein connectivity in yeast PIN]]
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* [[ http://bioinformatics.org/ctls/download/data/PIN.KaKs.zip | KaKs, growth fitness analysis, protein connectivity in yeast PIN]] [[Assignment 2]]
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* [[ http://bioinformatics.org/ctls/download/data/PIN.KaKs.zip | KaKs, growth fitness analysis, protein connectivity in yeast PIN]]
February 02, 2010, at 09:45 AM
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-> [[http://www.bioinformatics.org/ctls/download/biol320/input.output.plot.R | script for salary example]];
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-> [[http://www.bioinformatics.org/ctls/download/biol320/input.output.plot.R | input.output.plot.R]];
February 02, 2010, at 09:45 AM
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-> [[http://www.bioinformatics.org/ctls/download/biol320/input.output.plot.R | script for salary example]];
February 01, 2010, at 02:20 PM
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!!%blue% Lectures and labs
* [[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]];
-> [[http://www.bioinformatics.org/ctls/download/biol320/salary.R | script for salary example]];
->Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
*[[http://www.bioinformatics.org/ctls/download/biol320/lec2.R.programming.zip| Basic programming in R]];
* [[Quiz 1]]
*[[http://www.bioinformatics.org/ctls/download/biol320/lec3,input.output.plot.zip| Input, output, plots, packages]];
* [[Assignment 1]]
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----
!!%blue% Lectures and labs
* [[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]];
-> [[http://www.bioinformatics.org/ctls/download/biol320/salary.R | script for salary example]];
->Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
*[[http://www.bioinformatics.org/ctls/download/biol320/lec2.R.programming.zip| Basic programming in R]];
* [[Quiz 1]]
*[[http://www.bioinformatics.org/ctls/download/biol320/lec3,input.output.plot.zip| Input, output, plots, packages]];
* [[Assignment 1]]
to:
February 01, 2010, at 02:19 PM
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* [[http://www.seec.biology.gatech.edu/ | Meeting at GaTech, March 26-28, 2010]] Added lines 78-79:
* [[http://www.seec.biology.gatech.edu/ | Meeting at GaTech, March 26-28, 2010]]
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*[[http://www.bioinformatics.org/ctls/download/biol320/lec3.input.output.plot.zip| Input, output, plots, packages]]; to:
*[[http://www.bioinformatics.org/ctls/download/biol320/lec3,input.output.plot.zip| Input, output, plots, packages]]; February 01, 2010, at 11:12 AM
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*[[http://www.bioinformatics.org/ctls/download/biol320/lec3.input.output.plot.zip| Input, output, plots, packages]];
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January 21, 2010, at 10:40 AM
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[[http://www.bioinformatics.org/ctls/download/biol320/salary.R | script for salary example]]; to:
-> [[http://www.bioinformatics.org/ctls/download/biol320/salary.R | script for salary example]]; January 21, 2010, at 10:40 AM
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[[http://www.bioinformatics.org/ctls/download/biol320/salary.R | script for salary example]]; January 21, 2010, at 09:03 AM
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* Spelman Research Day, April 16, 2010
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* [[http://www.spelman.edu/researchday/index.shtml| Spelman Research Day, April 16, 2010 ]]
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!!%blue% Announcements
* [[http://www.seec.biology.gatech.edu/ | Meeting at GaTech, March 26-28, 2010]]
* Spelman Research Day, April 16, 2010
---- January 21, 2010, at 08:55 AM
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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/biol320/lec2.R.programming.zip| Basic programming in R]];
January 20, 2010, at 10:03 PM
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!!%blue% Please install the following software on your computers
* [[http://notepad-plus.sourceforge.net/uk/site.htm | Notepad++]]
* [[ http://mira.sunsite.utk.edu/CRAN/ | R for windows]]
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!!%blue% Software tools
* [[ http://mira.sunsite.utk.edu/CRAN/ | R for windows]]
* [[http://notepad-plus.sourceforge.net/uk/site.htm | Notepad++]]
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# [[http://http://cran.r-project.org/doc/contrib/refcard.pdf | R reference card,1]]
# [[http://http://cran.r-project.org/doc/contrib/Short-refcard.pdf | R reference card,2]] to:
# [[http://cran.r-project.org/doc/contrib/refcard.pdf | R reference card,1]]
# [[http://cran.r-project.org/doc/contrib/Short-refcard.pdf | R reference card,2]] January 20, 2010, at 07:06 PM
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# [[http://http://cran.r-project.org/doc/contrib/Short-refcard.pdf | R reference card]] to:
# [[http://http://cran.r-project.org/doc/contrib/refcard.pdf | R reference card,1]]
# [[http://http://cran.r-project.org/doc/contrib/Short-refcard.pdf | R reference card,2]] January 18, 2010, at 10:17 AM
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# [[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]]; Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
#[[http://www.bioinformatics.org/ctls/download/biol595/basic.programming.in.R.ppt| Basic programming in R]];
#[[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plots, packages]]; [[homework1]]
# [[http://www.bioinformatics.org/ctls/download/biol595/quiz1.R | Quiz1 ]] (functions, loops, input, output)
#[[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]]
# [[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 ]];
# [[http://www.bioinformatics.org/ctls/download/biol595/LibyaHIV.zip | Libya HIV case ]];
# [[http://www.bioinformatics.org/ctls/download/biol595/lec8.microarray.Prostate.cancer.zip | Microarry, clustering analysis, Prostate cancer case ]];
# Protein structure and protein networks
# [[http://www.bioinformatics.org/ctls/download/biol595/aging.mutation.zip | Modeling of aging and genetic changes]];
# [[http://www.bioinformatics.org/ctls/download/biol595/quiz2.zip | QUIZ 2 ]];
# [[http://www.bioinformatics.org/ctls/download/biol595/lec11.regression.peanut.data.zip | Regression, Peanut genotypes and phenotypes association]];
# Probability and likelihood estimation;
to:
* [[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]];
->Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
*[[http://www.bioinformatics.org/ctls/download/biol595/basic.programming.in.R.ppt| Basic programming in R]];
* [[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plots, packages]]; [[homework1]]
* [[http://www.bioinformatics.org/ctls/download/biol595/quiz1.R | Quiz1 ]] (functions, loops, input, output)
* [[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]]
* [[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 ]];
* [[http://www.bioinformatics.org/ctls/download/biol595/LibyaHIV.zip | Libya HIV case ]];
* [[http://www.bioinformatics.org/ctls/download/biol595/lec8.microarray.Prostate.cancer.zip | Microarry, clustering analysis, Prostate cancer case ]];
* Protein structure and protein networks
* [[http://www.bioinformatics.org/ctls/download/biol595/aging.mutation.zip | Modeling of aging and genetic changes]];
* [[http://www.bioinformatics.org/ctls/download/biol595/quiz2.zip | QUIZ 2 ]];
* [[http://www.bioinformatics.org/ctls/download/biol595/lec11.regression.peanut.data.zip | Regression, Peanut genotypes and phenotypes association]];
* Probability and likelihood estimation;
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#[[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]]
->Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
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# [[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]]; Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
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->Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
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#[[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]]\\ Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
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#[[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]]
\\
Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
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#[[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]] Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
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#[[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]]\\ Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
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#[[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]]
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#[[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]] Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.
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# 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 to:
# essential genes and connectivity
# Gasch expression Changed lines 57-58 from:
# [[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000282#s5 | Human metabolic profile variation]]
to:
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#[[http://www.bioinformatics.org/ctls/download/biol595/lec2.R.zip | An overview of R]] to:
#[[http://www.bioinformatics.org/ctls/download/biol320/lec1.R.an.overview.zip | An overview of R]] January 17, 2010, at 08:30 PM
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# [[ http://cran.r-project.org/other-docs.html | Documents at CRAN ]]
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#[[http://www.bioinformatics.org/ctls/download/biol595/computer.basics.ppt|Computer basics]] Deleted line 23:
#[[http://www.bioinformatics.org/ctls/download/biol595/computer.basics.ppt|Computer basics]] January 14, 2010, at 09:13 PM
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#[[http://www.bioinformatics.org/ctls/download/R-materials/Marthews-BeginnersRcourse.zip | Begginer R by Mathews]]; to:
#[[http://www.bioinformatics.org/ctls/download/R-materials/Marthews-BeginnersRcourse.zip | Beginner R by Mathews]]; January 14, 2010, at 09:10 PM
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%center% %blue% 9am-11:30am, Tue & Thur, Sci 246 January 14, 2010, at 04:47 PM
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!! %blue% Computing in Genomics and Proteomics, Spring 2010, Spelman to:
!!%center% %blue% Computing in Genomics and Proteomics
%center% %blue% Spring 2010, Spelman January 14, 2010, at 04:45 PM
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!! %blue% Computing in Genomics and Proteomics, Spring 2010 to:
!! %blue% Computing in Genomics and Proteomics, Spring 2010, Spelman January 14, 2010, at 04:19 PM
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# [[http://mirrors.ibiblio.org/pub/mirrors/CRAN/ | Contributed docs on R at CRAN ]] January 14, 2010, at 04:19 PM
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# [[http://http://cran.r-project.org/doc/contrib/Short-refcard.pdf | R reference card]]
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# [[http://http://cran.r-project.org/doc/contrib/Short-refcard.pdf | R reference card]]
# [[http://cran.r-project.org/doc/manuals/R-intro.pdf | An Introduction to R, pdf]]
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# Essential Bioinformatics
# First course in statistical programming using R
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# [[ http://www.amazon.com/Essential-Bioinformatics-Jin-Xiong/dp/0521600820 | Essential Bioinformatics, by J Xiong]]
# [[http://www.amazon.com/First-Course-Statistical-Programming/dp/0521694248/ref=tmm_pap_title_0 | First course in statistical programming using R, by WJ Braun & DJ Murdoch]]
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#[[http://www.bioinformatics.org/ctls/download/R-materials/Marthews-BeginnersRcourse.zip | Begginer R by Mathews]];
#[[http://www.bioinformatics.org/ctls/download/R-materials/Krijnen-IntroBioInfStatistics.pdf | R for Bioinformatics by Krijnen ]]; Changed lines 15-17 from:
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# Essential Bioinformatics
# First course in statistical programming using R
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!!%blue% Reading materials:
# [[http://http://cran.r-project.org/doc/contrib/Short-refcard.pdf | R reference card]]
# [[http://cran.r-project.org/doc/manuals/R-intro.pdf | An Introduction to R, pdf]]
# [[http://mirrors.ibiblio.org/pub/mirrors/CRAN/ | Contributed docs on R at CRAN ]]
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!!%blue% Reference materials: Added line 42:
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!!%blue% Software tools
# [[ http://mirrors.ibiblio.org/pub/mirrors/CRAN/ | R (Windows) installation ]]
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Please install the following software on your computers
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!!%blue% Please install the following software on your computers January 14, 2010, at 09:40 AM
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Please install the following software on your computers
* [[http://notepad-plus.sourceforge.net/uk/site.htm | Notepad++]]
* [[ http://mira.sunsite.utk.edu/CRAN/ | R for windows]]
---- January 13, 2010, at 12:37 PM
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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 weakness. ) to:
# Protein structure and protein networks January 13, 2010, at 12:37 PM
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#[[http://www.bioinformatics.org/ctls/download/biol595/computer.basics.ppt | Computer
basics]] to:
#[[http://www.bioinformatics.org/ctls/download/biol595/computer.basics.ppt|Computer basics]] January 13, 2010, at 12:36 PM
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!! %blue% Computing in Genomics and Proteomics, Spring 2010
\\
----
!!%blue% Lectures and labs
#[[http://www.bioinformatics.org/ctls/download/biol595/computer.basics.ppt | Computer
basics]]
#[[http://www.bioinformatics.org/ctls/download/biol595/lec2.R.zip | An overview of R]]
#[[http://www.bioinformatics.org/ctls/download/biol595/basic.programming.in.R.ppt| Basic programming in R]];
#[[http://www.bioinformatics.org/ctls/download/biol595/lec4.zip | Input, ouput, plots, packages]]; [[homework1]]
# [[http://www.bioinformatics.org/ctls/download/biol595/quiz1.R | Quiz1 ]] (functions, loops, input, output)
#[[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]]
# [[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 ]];
# [[http://www.bioinformatics.org/ctls/download/biol595/LibyaHIV.zip | Libya HIV case ]];
# [[http://www.bioinformatics.org/ctls/download/biol595/lec8.microarray.Prostate.cancer.zip | 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. )
# [[http://www.bioinformatics.org/ctls/download/biol595/aging.mutation.zip | Modeling of aging and genetic changes]];
# [[http://www.bioinformatics.org/ctls/download/biol595/quiz2.zip | QUIZ 2 ]];
# [[http://www.bioinformatics.org/ctls/download/biol595/lec11.regression.peanut.data.zip | Regression, Peanut genotypes and phenotypes association]];
# Probability and likelihood estimation;
----
!!%blue% Reading materials:
# [[http://http://cran.r-project.org/doc/contrib/Short-refcard.pdf | R reference card]]
# [[http://cran.r-project.org/doc/manuals/R-intro.pdf | An Introduction to R, pdf]]
# [[http://mirrors.ibiblio.org/pub/mirrors/CRAN/ | Contributed docs on R at CRAN ]]
# [[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]]
----
!!%blue% Software tools
# [[ http://mirrors.ibiblio.org/pub/mirrors/CRAN/ | R (Windows) installation ]]
----
!!%blue% 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
# [[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000282#s5 | Human metabolic profile variation]]
----
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
*[[http://www.bioquest.org/NumbersCount/agnesscott_2009/resources.php | Number Count]]
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