Bio599: Computational Biology course schedule (Fall 2012)
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Slot numberDateTopicLecture notesHomework assignment (due date!) See http://bit.ly/bio599-hwReading assignments -- this column and ALL to the right!! (due date!)ReadingReading
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18/28/2012Course overview and introductions from students: Describe your research project. Why are you interested in this course?https://speakerdeck.com/gregcaporaso/bio-599-lecture-1-nau-fall-2012
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28/30/2012Working with genomes: pulling data to your computer and getting started with text manipulationhttps://speakerdeck.com/gregcaporaso/bio-599-lecture-2-nau-fall-2012Text editorPCFB 1, (and Appendix 1 for those not working on Mac), start on PCFB 2https://dl.dropbox.com/u/2868868/PCFB_Appendix1a.pdfhttps://dl.dropbox.com/u/2868868/PCFB_Appendix1b.pdf
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39/4/2012Regular expressionshttps://speakerdeck.com/gregcaporaso/bio-599-lecture-3-nau-fall-2012GC contentPCFB 2
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49/6/2012Regular expressionshttps://speakerdeck.com/gregcaporaso/bio-599-lecture-4-nau-fall-2012PCFB 3, Appendix 2
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59/11/2012Regular expressionshttps://speakerdeck.com/gregcaporaso/bio-599-lecture-5-nau-fall-2012Catch up on reading! PCFB 1-3
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69/13/2012Parallel computing, cloud computing and working on Amazon Web Serviceshttps://speakerdeck.com/gregcaporaso/bio-599-lecture-6-nau-fall-2012Appendix 3http://dl.dropbox.com/u/2868868/Science-2011-Fox-406-7.pdf
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79/18/2012Connecting to Amazon Web Services instanceshttps://speakerdeck.com/gregcaporaso/bio-599-lecture-7-nau-fall-2012Regular ExpressionsPCFB 4https://dl.dropbox.com/u/2868868/Angluoli2011.pdf
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89/20/2012Working with the shell on Amazon Web Serviceshttps://speakerdeck.com/gregcaporaso/bio-599-lecture-8-nau-fall-2012
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99/25/2012More working with the shell and Quiz 1https://speakerdeck.com/gregcaporaso/bio-599-lecture-9-nau-fall-2012QUIZ!PCFB 5
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109/27/2012Shell scripting: turning a text file into softwarehttps://speakerdeck.com/gregcaporaso/bio-599-lecture-10-nau-fall-2012PCFB 6
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1110/2/2012Shell scripting: turning a text file into softwarehttps://speakerdeck.com/gregcaporaso/bio-599-lecture-11-nau-fall-2012Catch up on reading! Review Appendix 3
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1210/4/2012Guest Lecture: Jason Sahl "Lessons learned from a food-borne outbreak of E. coli in Germany, 2011"https://dl.dropbox.com/u/2868868/cs399_public/Rasko2011.pdfWork through PCFB Chapter 6 examples! These are extremely valuable and will help with the Shell Script assignment.
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1310/9/2012QIIME data analysis and microbiomicshttps://speakerdeck.com/gregcaporaso/bio-599-lecture-13-and-14-nau-fall-2012Shell scripthttp://dl.dropbox.com/u/2868868/cs399_public/QIIME_NM_2010.pdfhttp://dl.dropbox.com/u/2868868/cs399_public/QIIME_NM_2010_supp.pdf
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1410/11/2012QIIME and microbiomics (continued)https://speakerdeck.com/gregcaporaso/bio-599-lecture-13-and-14-nau-fall-2012http://www.pnas.org/content/107/14/6477.longhttp://www.ibm.com/developerworks/aix/library/au-gnu_screen/
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1510/16/2012Class cancelledhttp://www.nature.com/ismej/journal/v6/n8/full/ismej20128a.htmlSkim PCFB 16
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1610/18/2012Guest Lecture: Andy KrohnPCFB 20
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1710/23/2012Questions on PCFB 16 and 20; QIIME and microbiomics (continued)https://speakerdeck.com/gregcaporaso/bio-599-lecture-17-nau-fall-2012
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1810/25/2012Ordinationhttps://speakerdeck.com/gregcaporaso/bio-599-lecture-18-nau-fall-2012QIIME analysishttp://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html
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1910/30/2012Python programming and the IPython Notebookhttps://speakerdeck.com/gregcaporaso/bio-599-lecture-19-nau-fall-2012QUIZ!PCFB 7http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2012123a.html
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2011/1/2012Writing a first programhttps://speakerdeck.com/gregcaporaso/bio-599-lecture-20-nau-fall-2012PCFB 8
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2111/6/2012Guest Lecture: Stephen Beckstrom-Sternberg "SNP analysis and in-silico genotyper (ISG)"https://dl.dropbox.com/u/2868868/bio599/readings/SolSNP.r1.pdf
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2211/8/2012Python programming: conditional statements and loopshttp://nbviewer.ipython.org/3994000/Lecture22.ipynbProgramming assignment 1PCFB 9
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2311/13/2012Python programming: lists, list indexing, nested for loopshttp://nbviewer.ipython.org/3994000/Lecture23.ipynb
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2411/15/2012Python programming: nested for loops, functions, reviewing Programming Assignment 2http://nbviewer.ipython.org/3994000/Lecture24.ipynbProgramming assignment 2PCFB 10
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2511/20/2012Python programming: File I/O, command line interfaces, review functionshttp://nbviewer.ipython.org/3994000/Lecture25.ipynbQUIZ!: Hint, review the page listed under the Reading Assignment for today http://learnpythonthehardway.org/book/ex28.html
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11/22/2012Thanksgiving holidaySee some notes on the argv function in the reading assignment column for today:http://learnpythonthehardway.org/book/ex13.htmlLooking for some interesting reading over the long weekend? See this book chapter - I promise it will help you with your thesis:https://dl.dropbox.com/u/2868868/bio599/readings/Tufte_VDoQI_CH1.pdf
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2611/27/2012Questions on Programming Assignment 3; Bioinformatics provenance tracking: record keeping and reproducibilityhttps://speakerdeck.com/gregcaporaso/bio-599-lecture-26-nau-fall-2012Create an account at https://github.com/; review the lectures in the first reading assignment and skim the document in the second reading assignment http://software-carpentry.org/4_0/vc/https://docs.google.com/document/d/1fUpTyCgpYZDK-He62WPWq4P4aXP2GZxmI9tPgzPxnYU/edit#heading=h.xqljmciqzk81PCFB 11
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2711/29/2012Python programming: moduleshttp://nbviewer.ipython.org/3994000/Lecture27.ipynbPCFB 12
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2812/4/2012Python programming: PyCogent, The Python Comparative Genomics Toolkithttp://nbviewer.ipython.org/3994000/Lecture28.ipynbProgramming assignment 3http://genomebiology.com/2007/8/8/R171
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2912/6/2012Python programming: Introduction to software testinghttps://speakerdeck.com/gregcaporaso/bio-599-lecture-29-nau-fall-2012QUIZ!
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Final project12/13/2012DUE at 9:30am (i.e., end of final exam time)NO EXAM! Final project due!
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