Weekly Calendar
Fall 2008
| Class Meetings | Major Topic | Class notes | Assignments |
|---|---|---|---|
| Wed: 9/3 | Background & Basics | Class 1: Introduction to Bioinformatics Biology as an information science Language of Bio and CS | |
| Mon: 9/8 | Class 2 (Prof Smith attending CPA2008): Guest Speaker: Greg Priest-Dorman Security, Access and Usage of bioinf cluster Lab: Accessing the bioinf Cluster Navigating with Linux commands Project 0 | ||
| Wed: 9/10 | Class 3 (Prof Smith attending CPA2008): Genomes and Central Dogma | UB: Chapters 1 - 3 | |
| Mon: 9/15 | Class 4: Dealing with large scale data cs353-pedna-ch1.ppt cs353-pedna-ch3.ppt Lab: Computational string analysis | PEDNA: 1, 3 Project 1: Assigned (Playing with Strings) |
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| Wed: 9/17 | Class 5: Guest speakers: Mickey Thaler and Felix Steiny AiptasiaWiki | Assigned reading: Cyberinfrastructure Review | |
| Mon: 9/22 | Class 6: Proj1 Discussion Translation and Blast Lab: The BLAST algorithm Proj1 completion | UBChapter 4 Project 1 Due |
|
| Wed: 9/24 | Class 7: Regular Expressions cs353-pedna-ch4.ppt | Literature Assignment | |
| Mon: 9/29 | Class 8: Paper presentations Lab: More regex | Presentations due Project 2: Assigned (Playing with Regular Expressions) |
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| Wed: 10/1 | Class 9: Implementing an algorithm if-else statements cs353-pedna-ch6.ppt | PEDNA Chapter 6 | |
| Mon: 10/6 | Class 10: Dr. Garrett: Introduction to phosphatidylated proteins Discussion of bioinformatic appproach Lab: if elsif and while loops | ||
| Wed: 10/8 | Class 11: Intro to Subroutines Garrett Project Gabriel Finite State Machine | PEDNA Capter 7 | |
| Mon: 10/13 | Class 12: Sequence Alignment Sequence Alignment | UB: Chapters 4, 5, 7 | |
| Wed: 10/15 | Class 13 | |
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| Mon: 10/20 | Fall Break | ||
| Wed: 10/22 | Fall Break | ||
| Mon: 10/27 | Class 14: Jodi not home from CA yet! Submit your Proj. 3 code Prepare 5-min pres. for Prof. Garrett A Random Lecture (in Jodi’s absense): cs353-pedna-ch13.ppt | UB: Ch. 6, Sec. 6.2 | |
| Wed: 10/29 | Class 15: Presentations for Prof. Garrett (first half hour) | Proj4: Due Monday 11/3: local_vs_global_alignments.doc | |
| Mon: 11/3 | Class 16: More about alignments Sequence Logo Headcount for CSHL | ||
| Wed: 11/5 | Class 17: Hidden Markov Models | ||
| Mon: 11/10 | Class 18: Project 5: Assigned (Modeling Molecular Evolution) | ||
| Wed: 11/12 | Class 19 | Final Project Assignment Due in stages |
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| Mon: 11/17 | Class 20 Final Project Teams Sam and Phil: Identification of non-coding RNAs in Drosophila Carrie and Dan: Topic to be refined Jenny: Evolution simulator Gabe: Topic to be refined Amory: Hydrophobicity prediction tool | ||
| Wed: 11/19 | Class 21 | ||
| Fri: 11/21 | CSHL Field Trip Itinerary and Directions! http://www.cshl.edu/public/SCIENCE/lucito.html Robert Lucito: Cancer Genome http://www.cshl.edu/public/SCIENCE/ware.html Dooreen Ware: microRNA Evolution | ||
| Mon: 11/24 | Class 22: CSHL Discussion Proj 5 Alg Design Final Projects | ||
| Wed: 11/26 | Class 23: No class! | ||
| Thur: 11/27 | Thanksgiving | ||
| Mon: 12/1 | Class 24: Final Project Milestone: Draft of Introduction and Materials and Methods sections Lab: mutation_stats.pl Alignment File | ||
| Wed: 12/3 | Class 25 | ||
| Fri: 12/5 | Draft of Results and Discussion sections | ||
| Mon: 12/8 | Class 26 Independent research presentations and pizza!!! | ||
| Mon: 12/15 | Final Paper due |
