==Introduction to Computers and Biology==
- Introduction, overview (8/30/2012)
Go over syllabus, quick Intro to Bioinformatics
- Intro to molecular biology (9/4/2012)
Rehash syllabus, attendance policy, glue server instructions (need to know for homework #1)
Log in to grace, go over homework and project submission
Discuss basic mol bio concepts: genetic code, DNA, etc- Homework:
- Required reading
- Supplemental material
==Bionformatics programming and DBs==
- Programming for Bioinformatics and DBs (9/6/2012)
- Clarifications
- Piazza class site
- Denisovan genome comments
- Anyone read the article?
- Here is an image of the bone that was sequenced
- Questions on HW1?
- rehash
- Due before start of class next Tuesday
- Please direct HW related email to mgholami at cs
- Slides
- Project Specification (Overall and Part 1)
- Required readings for next lecture
- Supplemental material
- In the news -- Sept. 5th 2012
- Now in the queue:
- Homework #1: Due start of next class
- Project part 1: Due in two weeks
==Dynamic Programming & Sequence Alignment==
- Part I: String comparison/Global Sequence Alignment (9/11/2012)
- Milad's office hours:
- Now TUESDAYS and Wednesdays, 9-11am
- Glue server:
- Most able to submit, see Piazza thread for details on resolving PATH issues with submit script
- Lecture:
- Homework:
- Homework #1 due!
- Homework #2 handed out (Due 11:00am 10/02/2012)
- Part II: Local Sequence Alignment (9/13/2012)
- In the news
- Local alignment
- Required readings
- Lecture #5
- Now in the queue:
- Project part 1: Due 9/20/2012
- Homework #2: Due 9/25/2012
- DNA sequencing & assembly, Lander-Waterman statistics (9/18/2012)
- Guest lecture: Dr. Sergey Koren
- Lecture #6
- In the news:
- Required readings
- Now in the queue:
- Project part 1: Due 9/21/2012
- Homework #2: Due 9/27/2012
- Review of global alignment, project help, etc (9/20/2012)
- Local alignment and affine gap penalties (9/25/2012)
- Lecture #8
- Brief Midterm Review (3 weeks from today!)
- Go over what likely will be on it
- In the news:
- Required readings
- Project part 2:
- Now in the queue:
- Homework #2: Due 9/27/2012
- Project part 2: Due 10/9/2012
- Affine gap penalties (9/27/2012)
- Lecture #9
- Required reading
==MSA and Data Structures for string queries==
- MSA (10/02/2012)
- Review Project part 1 results
- Collect Homework #2
- Lecture #10
- Homework
- Now in the queue:
- Project part 2: Due 10/09/2012
- Midterm: Due 10/16/2012
- Required reading for 10/04
- MSA recap, suffix trees (10/04/2012)
- Housekeeping
- Project part 1 results
- Grades now posted on grades.cs.umd.edu
- Project part 2 questions and clarifications
- Midterm questions
- In class assignment
- Graded as complete/incomplete, contact me if you missed class
- Lecture #11
- Required reading for 10/09/2012:
- Suffix trees and generalized suffix trees(10/09/2012)
- In the news
- Housekeeping
- BioPerl, BioJava now available
- BioPython, BioRuby should be available this week
- Project part 2 due today by 11:59pm
- HW2 returned
- A few missing
- Return by next Tuesday start of class for opportunity to improve grade (with no penalty)
- All regrade requests must be received via email by 10/11
- QZ2 returned on 10/11
- Collect from those that missed class
- Guest lecture on Thursday
- Midterm moved to 1 week from Thursday (10/18)
- Lecture #12
- Project help last 15 minutes of class
- Free to go if already submitted
- Required reading for 10/11/2012:
- Project part 3 posted:
- Efficient large-scale alignment (whole genome alignment w/ MUMmer) (10/11/2012)
- Wrap-up and midterm prep (10/16/2012)
- Hand back Quiz 2 and go over answers
- Homework 2
- Review previous lectures and potential midterm questions
- Practice questions
- Midterm (10/18/2012)
- Midterm review (10/23/2012)
- Go over midterm grades and answers to questions
- Lecture on Substitution/scoring matrices
- Affine gaps, suffix arrays(10/25/2012)
- In the news
- Lecture slides
- Useful for project part 3
- Code review
- Project part 3 spec
- Required reading for next lecture:
- NO CLASS UMD CLOSED DUE TO HURRICANE SANDY (10/30/2012)
- Suffix arrays and BWT(11/1/2012)
- In the news
- Code review presentations
- HW #3 posted, DUE 11/20
- Lecture 15: Suffix arrays and BWT
- Required reading for next lecture
- Project part 3 sequences to be posted today
- BWT, DS wrap up, HMMs (11/6/2012)
- In the news
- Review project part 3 test sequences and discuss deadline extension
- Lecture 16: Review of BWT and BWT algorithms, HMMs
- Required reading for next lecture (same as last time)
- HMMs and repeats (11/08/2012)
- Announcements
- Project part 3 now DUE 11/13 at 11:59pm
- HW3 now DUE 11/20
- Lecture 17: Repeats and HMMs
- Required reading for next lecture
- Lecture 18 HMMs(11/13/2012)
- Quiz 3 handed back, grades
- Final project handed out (part 4) DUE 12/11 @ 11:59pm
- Project part 3 due today @ 11:59pm!
- Lecture 18: Viterbi decoding
- HMMs, viterbi decoding gene finding (11/15/2012)
- Final project, HMMs review (11/20/2012)
- In the news
- Project part 3 comments
- Milad is having trouble compiling/running some of your programs. You can resubmit your README with more detailed instructions on how to run your program for the test dataset.
- I'll let you know at start of class
- Viterbi algorithm review
- Lecture slides, might go over solutions to HW3, etc
- Final project review/useful links/etc
- More on local alignment heuristics
- What's left?
- Sequence Clustering
- Phylogenetics
- Required reading
==Thanksgiving break, no class (11/22/2012)==
- Intro to Clustering/TBD (11/27/2012)
- Final project questions/update
- Test sequences and output now available on grace
- K-mer size? Initiate SW on any two reads with a shared k-mer of length 11 or 13
- Program will be evaluated on final output (contig file), so make sure you know how to use AMOS
- Grades
- In class assignment #3
- Homework #3
- Project part 3
- Intro to Clustering
- In class assignment
- Bioscience Research Day
- Poster session in Stamp Student Union @ 11:30am
- Required reading
- Genome Assembly, AMOS, k-means Clustering (11/29/2012))
- Announcements
- Final project discussion
- Genome Assembly,AMOS refresher
- k-means Clustering
- Note: only 2 more lectures
- Project (part 3, final) and Motifs (12/4/2012)
- Final project discussion
- Lecture:
- Project part 3 discussion with Milad
- Motif finding/Gibbs and bonus (12/6/2012)
- FINAL lecture
- lecture material:
- Final review day (12/11/2012)
- Final project DUE at 11:59pm
- Material:
- Material from Midterm plus:
- Local alignment with affine gaps
- Suffix trees
- Suffix arrays
- BWTs
- HMMs
- Clustering
- Phylogenetics
- Motif finding
- Final Exam (12/13/2012)
- 8-10am, CSI 1121 (12/13/2012)