Weekly Calendar
Spring 2012
| Class Meetings | Class notes | Assignments (Reading, Labs, Projects) |
|---|---|---|
| Fundamentals of Bioinformatics: Genomics and Algorithms | ||
| Thu: 1/19 | Class 1: Eric Lander Interview Introduction to Bioinformatics Biology as an information science Language of Bio and CS BLASTing TED Talk Paul Rothemund Time permitting | |
| Tue: 1/24 | Class 2: Guest Speaker: Ben Stoutenburgh Security, Access and Usage of jr Lab: Accessing the jr Cluster Field Trip: to CIS to meet jr! | Navigating with Linux commands Project 0 Watson and Crick Structure of DNA UB: Chapters 1–3 ubchapter1.pdf |
| Thu: 1/26 | Class 3: Genomic Biology Dealing with large scale data: cs353-pedna-ch1.ppt cs353-pedna-ch3.ppt | Reading: EB: Ch. 1 PEDNA: 1, 3 pedna-ch1.pdf pedna-ch3.pdf Project 1: Assigned (Playing with Strings) Mystery Sequence (in fasta format) Blast Assignment: due Tuesday |
| Tue: 1/31 | Class 4: * More about blast * Questions about the Blast assignment * PEDNA: Chapter 3 sample code | (Playing with Strings) Literature Assignment: Due Thur Feb 9 |
| Thu: 2/2 | Class 5: * Finish PEDNA Ch. 3 * Codewalks! | Literature Search Assignment |
| Tue: 2/7 | Class 6: * Literature Search Assignment: upload papers and start ppts * Regular Expressions (PEDNA Ch 4) * cs353-pedna-ch4.ppt | |
| Thu: 2/9 | Class 7: * Presentations * PEDNA: Substitutions with regex * Command line BLAST | Literature assignment: due Project 2: assigned (Playing with Strings with regex) |
| Tue: 2/14 | Class 8: * Happy Valentine’s Day! * More regex matching * More perl: if and while * cs353-pedna-ch6.ppt * Scoring Alignments: Blast and Clustal * Command line BLAST | |
| Thu: 2/16 | Class 9: * Running Blast from the Command Line * Scoring Alignments: Blast and Clustal Clustalw (time permitting) | Reading: UB: Ch. 4-6 (Sequence Alignments) Optional: BLAST (Altschul et al, 1990) Gapped Blast (Altschul et al., 1997) Review BLOSUM Matrix (Eddy 2004) Proj2 Due |
| Tue: 2/21 | Class 10: * CSHL Field Trip Discussion Introduction to miRNAs and SNPs * Project 2 code walks * PEDNA Ch. 8 (File I/O) * Finite State Machine Parsing (time permitting) | Reading: PEDNA Ch. 7 (Subroutines) PEDNA: Ch. 8 (Accessing Files of Sequences) |
| Thu: 2/23 | Class 11: Field Trip to Cold Spring Harbor Lab Leave campus at 11:30am | CSHL Itinerary Hammell, 2009. Predicting microRNAs. Schatz, 2010. Cloud Computing for DNA Schatz, 2009. Mining SNPs. Dr. Michael Schatz Website Dr. Molly Hammell (Shared Bioinformatic Resources) |
| Tue: 2/28 | Class 12: * Course feedback * Jodi’s Blast results file! * PEDNA Ch. 8 (File I/O) * Finite State Machine Parsing | Reading: PEDNA Ch. 7 (Subroutines) PEDNA: Ch. 8 (Accessing Files of Sequences) Assignment: Project 3: Prediction of 5’ UTRs in Aiptasia * Due: after spring break |
| Thu: 3/1 | Class 13: * Symbiosis/Cnidarian Biology Lab * Meet in Olmsted room 314 * Marc away:SIGCSE 2012 | Read the following papers Weis: Coral Symbiosis Bioprospecting in Corals using Deep Sequencing |
| Tue: 3/6 | Spring Vacation | |
| Thu: 3/8 | Spring Vacation | |
| Tue: 3/13 | Spring Vacation | |
| Thu: 3/15 | Spring Vacation | |
| First Collaboration: BiTT Project | ||
| Tue: 3/20 | Class 14: Guest Researchers Dr. Jenni Kennell and Laure-Alix Clerbaux Identification of miRNA targets in Drosophila | Gerin, et al. Mir33 Expression |
| Thu: 3/22 | Class 15: * Project 3 Lab * BiTT Project Lab | |
| Tue: 3/27 | Class 16: * Questions for Dr. Jenni Kennell and Laure-Alix Clerbaux * BiTT Project Lab | |
| Thu: 3/29 | Class 17: * Discussion re. Class 16 * Randomness * Work on BiTT Projects in Groups | PEDNA: 13 (Random) cs353-pedna-ch13.ppt |
| Tue: 4/3 | Class 18: * Collaboration survey (anonymous) * Start thinking about final projects and possible partners * Subroutines * Arrays * BiTT Project | PEDNA Ch. 7 PEDNA Ch. 9 |
| Thu: 4/5 | Class 19: * Final project discussion * Work on BiTT Project | Searching for symbiont genes in a host transcriptome Finding transcription factor binding sites |
| Final Research Project | ||
| Tue: 4/10 | Class 20: Presentations “Predicting targets of mir33 in Drosophila” | |
| Thu: 4/12 | Class 21: Individual group meetings to discuss project ideas | |
| Tue: 4/17 | Class 22: Lightening talks Blog Feedback Schedule Poster Session Group work on Final Projects | |
| Thu: 4/19 | Class 23: Progress updates Arrays and Hashes | Submit draft of poster with the Poster Title and the Introduction section |
| Tue: 4/24 | Class 24: Progress updates | Submit draft of poster with the Methods section |
| Thu: 4/26 | Class 25: Progress updates | Submit draft of poster with the Results section |
| Tue: 5/1 | Class 26: * Grant Proposal Guidelines * Bioinformatics: a Retrospective * CEQs * Prep for Poster Session | Submit Final Poster ready for printing Grant proposal assignment instructions |
| Study Week May 2–8 | Poster Session and Pizza: Thur. May 3, 3-5:30pm | |
| Final Exam Period May 9–15 | Grant Proposal Due May 9 5pm | |
