Bio/CS 299: Introduction to Bioinformatics (NAU, Spring 2013)
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Lecture numberDateTopicLecture slidesLecture notebooksHomework assignment (due date!) See http://bit.ly/bio299-hwReading assignments -- this column and ALL to the right!! (due date!)ReadingReading
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11/14/2013Introductionhttps://speakerdeck.com/gregcaporaso/bio-299-lecture-1-nau-fall-2013
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21/16/2013TA Lecture: In class exercise/homework 1
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1/21/2013No Class: Martin Luther King Jr Day
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31/23/2013Biology review: biological informationhttps://speakerdeck.com/gregcaporaso/bio-299-lecture-3-nau-fall-2013#Homework 1 due!http://www.ncbi.nlm.nih.gov/books/NBK21050/http://www.ncbi.nlm.nih.gov/books/NBK26887/http://www.ncbi.nlm.nih.gov/books/NBK26829/
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41/28/2013IPython Notebook; Introduction to sequence evolution; Prep for sequence searching and alignmenthttps://speakerdeck.com/gregcaporaso/bio-299-lecture-4-nau-fall-2013#http://nbviewer.ipython.org/4657175/Lecture4.ipynbhttp://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2012123a.html
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51/30/2013Sequence evolution; IPython Notebook exercise; parallel/cloud computing; how does this relate to sequence searching?https://speakerdeck.com/gregcaporaso/bio-299-lecture-5-nau-fall-2013#http://www.ncbi.nlm.nih.gov/books/NBK1734/
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62/4/2013Guest lecture: Nancy JohnsonHomework 2 due!https://dl.dropbox.com/u/2868868/bio299_spring2013/JohnsonPNAS_2010.pdf
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72/6/2013Guest lecture: Brad Butterfieldhttps://dl.dropbox.com/u/2868868/bio299_spring2013/plant_trait_ontology.pdf
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82/11/2013Sequence searching and alignmenthttps://speakerdeck.com/gregcaporaso/bio-299-lecture-8-10-nau-fall-2013#http://nbviewer.ipython.org/4657175/Lecture8.ipynbGuest lecture reports duehttp://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0020206
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92/13/2013Sequence searching and alignmenthttps://speakerdeck.com/gregcaporaso/bio-299-lecture-8-10-nau-fall-2013#
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102/18/2013Sequence searching and alignmenthttps://speakerdeck.com/gregcaporaso/bio-299-lecture-8-10-nau-fall-2013#http://nbviewer.ipython.org/4657175/Lecture10.ipynb
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112/20/2013Snow day...
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122/25/2013Evaluating bioinformatics software; application presentation by Dr. Caporasohttps://speakerdeck.com/gregcaporaso/bio-299-lecture-11-nau-fall-2013http://nbviewer.ipython.org/4657175/Lecture11-caporaso-application-presentation-demo.ipynbhttps://dl.dropbox.com/u/2868868/reprints/QIIME_NM_2010.pdfhttps://dl.dropbox.com/u/2868868/reprints/QIIME_NM_2010_supp.pdf
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132/27/2013Python programming topicshttp://nbviewer.ipython.org/4657175/Lecture13.ipynb
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143/4/2013Midterm reviewHomework 3 due!
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153/6/2013Mideterm exam
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163/11/2013Group application presentations: Groups 1 and 2http://bioinformatics.oxfordjournals.org/content/early/2010/08/12/bioinformatics.btq461.full.pdf+htmlhttp://bioinformatics.oxfordjournals.org/content/suppl/2010/08/11/btq461.DC1/supp_mat_rev2.pdfhttp://dl.dropbox.com/u/2868868/cs299_slides_XCFGcsdFGGad/Genome%20Res.-2009-Parks-1896-904.pdf
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173/13/2013Group application presentations: Groups 3 and 4http://genomebiology.com/2010/11/8/R86http://www.mcponline.org/content/5/8/1520.full.pdf+html
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3/18/2013No class: Spring Break
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3/20/2013No class: Spring Break
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183/25/2013Phylogeny reconstructionhttps://speakerdeck.com/gregcaporaso/bio-299-lecture-18-nau-fall-2013http://evolution-textbook.org/content/free/contents/ch27.html
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193/27/2013Phylogeny reconstructionhttps://speakerdeck.com/gregcaporaso/bio-299-lecture-18-nau-fall-2013Homework 4 due!
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204/1/2013Topic 1: Amplicon sequencing and microbial ecologyhttps://speakerdeck.com/gregcaporaso/bio-299-lecture-20-22-nau-fall-2013https://dl.dropbox.com/u/2868868/reprints/QIIME_NM_2010.pdfhttps://dl.dropbox.com/u/2868868/reprints/QIIME_NM_2010_supp.pdf
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214/3/2013Topic 1: Amplicon sequencing and microbial ecologyhttps://speakerdeck.com/gregcaporaso/bio-299-lecture-20-22-nau-fall-2013https://dl.dropbox.com/u/2868868/reprints/Science-2013-Smith-548-54.pdf
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224/8/2013Topic 1: Amplicon sequencing and microbial ecologyhttps://speakerdeck.com/gregcaporaso/bio-299-lecture-20-22-nau-fall-2013
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234/10/2013Topic 2: Human Genomics (lecture by Mr. Chase); NO OFFICE HOURS TODAYhttps://speakerdeck.com/johnchase/lecture-23-mol-gen
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244/15/2013Topic 2: Human Genomics (lecture by Mr. Chase)https://speakerdeck.com/johnchase/pop-genHomework 5 due
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254/17/2013Topic 2: Human Genomics (lecture by Mr. Chase)https://speakerdeck.com/johnchase/25-pop-gen
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264/22/2013Ordination https://speakerdeck.com/gregcaporaso/bio-299-lecture-20-22-nau-fall-2013Homework 6 due
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274/24/2013Ordination wrap-up; Bioinformatics record keepinghttps://speakerdeck.com/gregcaporaso/bio-299-lecture-27-28-nau-fall-2013
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284/29/2013Software testinghttps://speakerdeck.com/gregcaporaso/bio-299-lecture-27-28-nau-fall-2013http://arxiv.org/pdf/1210.0530v3.pdf
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295/1/2013Experimental design in Bioinformatics https://speakerdeck.com/gregcaporaso/bio-299-lecture-29-nau-fall-2013Homework 7 due; browse the link under reading assignments for today - you don't need to read the full article in detail. http://www.theskepticsguide.org/resources/logicalfallacies.aspx
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5/7/2013No final exam: Final project due at 5pm!
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