Bio/CS 399: Projects in Bioinformatics course schedule
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Slot numberDateTopicHomework assignment (due date!)NotesReading assignments -- this column and ALL to the right!! (due date!)
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1Tues 1/17Course overview; introduction to microbial ecology; introduction of student microbiome research project
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2Thurs 1/19Cloud computing: Working on AWSFill in office hours poll; email me to join the class mailing list. This is a graded assignment, and is due Thusday 1/19 before class!Bring laptops if possiblehttp://qiime.org/tutorials/working_with_aws.htmlhttp://qiime.org/tutorials/unix_commands.htmlhttps://docs.google.com/document/d/1Orjuc5ESU3ojsTT2hsbrPklPRdEfAf2W9irLTlKnDs0/edit
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3Tues 1/24Cloud computing: Working on AWSBring laptops if possiblehttp://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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4Thurs 1/26QIIME data analysisBring laptops if possible
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5Tues 1/31QIIME data analysis (continued)Bring laptops if possiblehttp://www.pnas.org/content/107/14/6477.longhttp://www.qiime.org/svn_documentation/documentation/biom_format.html
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6Thurs 2/2Project discussion and assignmentsQIIME tutorial on Fierer et al data on AWS (see assignments page)http://qiime.org/svn_documentation/documentation/biom_format.htmlhttp://www.json.org
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7Tues 2/7Bioinformatics record keeping
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8Thurs 2/9Testing software: PyUnithttp://dl.dropbox.com/u/2868868/cs399_public/Rother2011.pdfhttp://www.python.org/doc//current/library/unittest.html
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9Tues 2/14Testing software: PyUnit (Lecture/hands-on)Group assignment 1: QIIME data analysis and reportBring laptops if possible
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10Thurs 2/16Python generators
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11Tues 2/21Bioinformatics experimental designhttp://docs.python.org/reference/expressions.html#yieldexprhttp://docs.python.org/library/itertools.html
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12Thurs 2/23Catch-up day/midterm reviewPyUnit homework due; course mid-way evaluations due!
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13Tues 2/28Midterm reviewRead group assignment 1 for all three groups (in AWS bucket)
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14Thurs 3/1Midterm Exam
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15Tues 3/6Guest Lecture: Jason Sahl: "Changing the paradigm of Escherichia coli pathotypes: lessons learned from the 2011 German outbreak"http://dl.dropbox.com/u/2868868/cs399_public/Rasko2011.pdfhttp://dl.dropbox.com/u/2868868/cs399_public/Rasko2008.pdf
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16Thurs 3/8No classGroup assignment 2: Experimental outline report; Schedule group meeting with Dr. Caporaso
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Tues 3/13Spring Break
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Thurs 3/15
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17Tues 3/20UniFrac and Distance matricesReport on Sahl guest lecture due!
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18Thurs 3/22Group presentationsEmail presentation slides
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19Tues 3/27Clustering and ordination techniqueshttp://www.southampton.ac.uk/~re1u06/teaching/upgma/http://ordination.okstate.edu/PCA.htm
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20Thurs 3/29Presenting Bioinformatics ResultsRedo of UniFrac Exam question for extra credit duehttp://dl.dropbox.com/u/2868868/qiime-r2868/tutorials/open_reference_illumina_processing.html
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21Tues 4/3No classhttp://dl.dropbox.com/u/2868868/cs399_public/Ramette2007.pdf
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22Thurs 4/5Monte Carlo simulations in bioinformaticshttp://udel.edu/~mcdonald/statttest.html
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23Tues 4/10Monte Carlo simulations in bioinformatics
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24Thurs 4/12Monte Carlo simulations in bioinformatics
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25Tues 4/17Wrap up Monte Carlo; Developing, documenting and testing command line interfaceshttp://docs.python.org/library/optparse.html?highlight=optparse#optparse
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26Thurs 4/19UPGMA and jackknifingGroup assignment 3: Progress updates due
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27Tues 4/24StarClusterhttp://web.mit.edu/star/cluster/docs/latest/overview.htmlhttp://web.mit.edu/star/cluster/about.htmlhttp://web.mit.edu/star/cluster/docs/latest/quickstart.html
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28Thurs 4/26Group presentationsE-mail presentation slides
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29Tues 5/1Catch-up day/final reviewFinal papers due; email presentation slides
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30Thurs 5/4Final review
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Thurs 5/10Final Exam 7:30am
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