CS299: Class schedule, Fall 2011
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Slot numberDateTopicReading assignment (due date!)Homework assignment (due date!)Additional reading (more information on the topic)
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1Tues 8/30Course overview
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2Thur 9/1The Central Dogma of Molecular BiologyHunter Chapter 1 and http://bit.ly/l0sELCLPTHW exercises 0-2
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3Tues 9/6From DNA to Protein: DNA to mRNALPTHW exercises 3-14; fill in office hours poll (address under announcements on the web site)http://genomebiology.com/2010/11/5/206
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4Thurs 9/8Python programming and the LPTHW exercises so farSee additional reading - not due today, but this is highly recommended study materialLPTHW exercises 15-22http://www.ncbi.nlm.nih.gov/books/NBK21050/ http://www.ncbi.nlm.nih.gov/books/NBK26887/
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5Tues 9/13From DNA to Protein: mRNA to Protein Redo LPTHW exercises that you had trouble with (Bio students), and focus on exercise 22. Review the additional reading for Thursday 9/8 in detail (CS students). This is NOT a night off of homework - you're going to be quizzed on this material next week!http://www.ncbi.nlm.nih.gov/books/NBK26829/
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6Thurs 9/15EvolutionHunter Chapter 2LPTHW exercises 24-31 NOTE: we're skipping 23 for now
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7Tues 9/20Evolution and introduction to sequence searching and alignmentLPTHW exercises 32-35, modified exercise 36; EMAIL ME YOUR PROGRAMMING NOTEBOOKS BEFORE CLASS!http://evolution-textbook.org/content/free/contents/ch27.html
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8Thurs 9/22Evolution and introduction to sequence searching and alignment; brief introduction to PyCogentHunter Chapter 3, 5.1Exercise 36 continued, LPTHW exercises 37- and start 38 - for exercise 38, use code from PyCogent or QIIME
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9Tues 9/27Amino acid substitution matrices, sequence alignment, phylogeny reconstruction"BLASTing through the kingdoms of life" (GRADED - turn in on paper in class)
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10Thurs 9/29Amino acid substitution matrices, sequence alignment, phylogeny reconstructionHunter Chapter 5Exercise 38 continued, Exercises 39-40
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11Tues 10/4Amino acid substitution matrices, sequence alignment, phylogeny reconstruction; brief intro to software testingwork through lecture 9 notes in the same way you work through LPTHY exercises (you can copy/paste the BLOSUM50 matrix)
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12Thurs 10/6Class Cancelled Modified LPTHW exercises 41-44 (start)
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13Tues 10/11python modules: matplotlib, pycogentHunter Chapter 4; http://genomebiology.com/2007/8/8/R171Modified LPTHW exercises 41-44
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14Thurs 10/13Midterm Exam reviewStudy! Review the Hunter text, LPTHW, and the lecture slides!Modified LPTHW exercises 41-44
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15Tues 10/18Midterm Exam reviewStudy! Review the Hunter text, LPTHW, and the lecture slides!Modified LPTHW exercises 41-44 due! Email these to me BEFORE CLASS! Review recent LPTHW exercises; note in your programming notebook which exercises you're working though again
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16Thurs 10/20Midterm Exam (in class)Study! Review the Hunter text, LPTHW, and the lecture slides!
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17Tues 10/25The Structure of Python ProgramsEmail me programming notebooks before class!
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18Thurs 10/27Working on the Amazon Cloudhttp://qiime.org/svn_documentation/tutorials/working_with_aws.html http://dl.dropbox.com/u/2868868/Science-2011-Fox-406-7.pdfBring laptops today if possible
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19Tues 11/1Evaluating bioinformatics software; application presentation (Dr. Caporaso)http://dl.dropbox.com/u/2868868/cs299_slides_XCFGcsdFGGad/QIIME_NM_2010.pdf http://dl.dropbox.com/u/2868868/cs299_slides_XCFGcsdFGGad/QIIME_NM_2010_supp.pdfResubmission of Programming Assignment 1 Submission of Extra Credit Assignment 1 Submission of Midterm Exam corrections (py files by email; exam on paper)
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20Thurs 11/3Amplicon sequencing and microbial ecology
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21Tues 11/8Microbial Ecology (continued) and OTU pickingEdgar 2010 (emailed to class mailing list)
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22Thurs 11/10Metagenomics; application presentation (student group)http://bioinformatics.oxfordjournals.org/content/27/8/1159.long
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23Tues 11/15Sequence coevolution and method comparisons in bioinformatics; application presentation (student group)http://dl.dropbox.com/u/2868868/cs299_slides_XCFGcsdFGGad/Genome%20Res.-2009-Parks-1896-904.pdfProgramming assignment 2 due!
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24Thurs 11/17Sequence coevolution algorithms; application presentation (student group)http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044276/pdf/1471-2105-12-S1-S21.pdfBring laptops today if possible
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25Tues 11/22Class Cancelled
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Thurs 11/24No class: Thanksgiving Break
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26Tues 11/29Genome assembly; application presentation (student group)http://www.mcponline.org/content/5/8/1520.full.pdf+html
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27Thurs 12/1Genome assembly (continued); application presenation (student group)http://genomebiology.com/2010/11/8/R86
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28Tues 12/6Genome assembly (continued); Final Exam review
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29Thurs 12/8Final Exam reviewProgramming assignment 3 due!
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Thurs 12/15Final Exam: 12:30-2:30pm
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