| Meets: | Lectures 8:30-9:50 am, Mon Wed, Biology Learning Center, Koffler 209 | |
| Discussion Section (Optional) 9 - 9:50 am, Fri, BioSciences West 321 | ||
| Instructors: | Dr. Mike Barker; BioSciences West 321E; 520-621-2213; msbarker@email.arizona.edu | |
| Tao Shi; BioSciences West 321D; scotty323@email.arizona.edu | ||
| Office Hours: | 4:00-5:00 PM, Tuesday, BioSciences West 321D (Shi) | |
| 11:00-12:00 PM, Thursday, BioSciences West 321E (Barker) | ||
| Group Paper Instructions! | ||
| Advice from Bill Birky on Writing Papers & Giving Talks! | ||
| Full Syllabus | ||
| Perl Cheat Sheet | ||
| Unix/Linux CL Reference | ||
| vi Cheat Sheet |
| Date | Topic | Lecturer | Readings/HomeWork | Slides | ||||||||||
| 1/11 | Introduction to the Course & The Unix Command Line | Barker | None | Introduction | ||||||||||
| 1/18 | Working on the Unix Command Line | Barker | None | Unix Introduction | ||||||||||
| 1/23 | Introduction to Perl | Barker | seqsHW01.txt, HW01.pdf, Learning Perl Chapters 1 & 5 | Perl Introduction | ||||||||||
| 1/25 | Basics of Perl Scripting | Barker | est_cluster.txt, HW02.pdf, Learning Perl Chapters 2 & 3 | Scalars & Arrays | ||||||||||
| 1/30 | Perl Scripting Continued | Barker | HW03.pdf, Ceratopteris1.fasta, Ceratopteris2.fasta, Learning Perl Chapters 6, 7, 8, 9, and 10 | More Perl | ||||||||||
| 2/1 | Wrapping up Perl Intro | Barker | Blast Search Introduction PDF or Link Example Solutions to Previous HW: Mike_HW03.zip | |||||||||||
| 2/6 | Introduction to Biological Databases, Search Algorithms, and Clustering Sequences | Barker | HW04.pdf | Genomic Databases & BLAST Intro | ||||||||||
| 2/8 | Advanced BLAST Searching | Barker | HW05.pdf, Readings: Genome Sequence Assembly Primer and Assembly of Large Genomes using Second-Generation Sequencing | Advanced BLAST Searching | ||||||||||
| 2/13 | Shotgun Sequencing | Barker | Shotgun Sequencing | |||||||||||
| 2/15 | Assembling Genomic Data | Barker | Genome Assembly | |||||||||||
| 2/20 | Data Assembly Cont. | Barker | HW06.pdf Example BLAST Parsing Scripts blast_parsers.zip | Data Assembly Cont | ||||||||||
| 2/22 | Circumscribing Gene Families | Barker | HW07.pdf Step by Step Guide to Building a Phylogeny Harrison & Langdale 2006 | Gene Families | ||||||||||
| 2/27 | Exam Review | |||||||||||||
| 2/29 | Multiple Sequence Alignment and Distance Trees | Barker | MSA & Distance Trees | |||||||||||
| 3/5 | Midterm 1 | |||||||||||||
| 3/7 | Comparative Genomics and Synteny Evolution | Lyons | Comparitive Genomics from Genes to Genomes Schnable & Lyons 2011 | |||||||||||
| 3/19 | Tree Thinking | Barker | HW08.pdf, plant_rbcl.fasta | Tree Thinking | ||||||||||
| 3/21 | MP and ML | Barker | HW09.pdf | MP & ML | ||||||||||
| 3/26 | SATe & Orthology | Barker | HW10.pdf | SATe & *logs | ||||||||||
| 3/28 | Gene Ontology and Annotation | Barker | GO & Functional Annotation | |||||||||||
| 4/4 | Neutral Theory and Genetic Variation | Barker | HW11.pdf | NT & Genomic Tests of Selection | ||||||||||
| 4/9 | PAML LRT | Shi & Barker | ||||||||||||
| 4/11 | Analyses of Variation in Gene Expression | Barker | Gene Expression | |||||||||||
| 4/16 | Exam Review | |||||||||||||
| 4/18 | Midterm 2 | |||||||||||||
| 4/23 | Biogeographic Data and Niche Modeling | |||||||||||||
| 4/25 | Group Presentations | |||||||||||||
| 4/30 | Group Presentations | |||||||||||||
| 5/2 | Group Presentations |
