Announcements
- 01.22.2010: Welcome to CS 795 Biological Sequence Analysis class. The schedule and syllabus is up.
- 01.26.2010: Assignment 1 is up.
- 01.30.2010: Excellent Learning Resource on Genetics Basics from the University of Utah: Link Here.
- 02.06.2010: Readings and Slides have been updated. Plan for next class is to finish gap modeling & multiple sequence alignment. See you all on Monday
- 02.07.2010: George Mason will be closed on Monday 02.08 . As such office hours and classes are canceled. We will have extra office hours on Tuesday 02.09.2010 from 4:00-5:00 pm.
- 02.08.2010: There is a chance of another storm on Tue 02.09.2010. Please keep an eye on the Alerts page maintained by GMU .
- 02.08.2010: Since Mason is closed on Tue 02.09.2010; I am scheduling special office hours on Thursday 02.11.2010 - 4:30-5:30 pm
- 02.11.2010: Finally we are open this Friday. Two important announcements. Firstly, the assignment due date will be Thursday 02.18.2010 (before 11:59 pm EST). Secondly, I will have special office hours on Friday 02.12.2010 between 3:30-4:30 pm in Engineering Building 4423.
- 02.15.2010: DNA technologies: promises and computational challenges on Friday 02.19.2010 1-2 pm in Engineering Building 3507 by Dr. Mihai Pop from University of Maryland. I would encourage everyone to attend. Click here for more information
- 02.16.2010: Please email your assignments to rangwala at cs [.] gmu [.] edu and put in the subject line CS_795_A1. Also for the LSA there is some issue as to what the row-order first cell means, hence I will accept any lsa solution but the score needs to be unique.
- 02.18.2010: Slides and Readings updated. There will be no office hours on 02.22.2010.
- 02.21.2010: Please could you vote on make-up class options . I had like to have a make-up class for the snow day before spring break for maintaining the structure and balance for the class. The last week of this class is unsuitable for this purpose. Thanks for your help.
- 02.23.2010: Assignment 2 is up. Due date: 03.15.2010 before class begins. The assignment asks you to develop a progressive UPGMA algorithm for multiple sequence alignments. You can chose to do the Markovian model development as part of your class project.
- 03.01.2010: Optional Assignment 3 is up. You can do this one instead of a class project or your mid-term as well. If you do it instead of the mid-term then it will be 20% of your grade (Due Date: 04.10.2010). If you do it in lieu of your project it will be 30% (Due Date: 05.05.2010). Confusing but flexible
- 03.06.2010: Due to Spring Break, I will not have office hours on Monday but will be available on Tuesday by appointment.
- 03.09.2010: Project Proposals are due on 03.29.2010. Please ensure you do a complete literature survey of the problem you are taking a crack at. How will you get the dataset ? What methods and tools will you use ? Here is a template that you could use
- 03.21.2010: Jigsaw Reading on MSA scheduled for 03.29.2010. Please ensure you attend the class on 03.29.2010 and read the paper assigned to you. If you missed the class on 03.15.2010 send me an email and I can assign a paper to you. Note the reading amounts to 10% of your class grades. Jigsaw PDF here
- 03.23.2010: Sample Mid-Terms: Paper1 and Paper 2
- 03.28.2010: Syllabus for mid-term will include everything till (including) Markov Models. Refer to the Readings Section. The exam will be closed book, closed notes and will be approximately 1hr 30 minutes
- 04.08.2010: I will not be having office hours on Monday 04.12.2010. The plan will be to study protein structure prediction methods. I would recommend you taking a look at the readings before class. Slides have been uploaded as well.
- 04.12.2010: Slides updated.
- 04.18.2010: Project Presentations will be held on 05/03/2010 and 05/07/2010 (Make-up Day as scheduled by the University for the record snow storms). I have selected the groups for presenting on the two days in a random order.
- 05.03.2010: Anveshi, Priyanka & Sridhar, Kshama, Syed
- 05.07.2010: Sneha, Sam B, Zeehasham, Weizi Li, Dan V
Attendance is compulsory for all students on the two days, irrespective of
whether you are presenting that day or have chosen A3.Presentations should be 20 minutes each with 5 minutes for questions. This is a strictly
enforced time limit. Please email me if you have questions. Useful Resource on Presentation . - 05.02.2010: Clarification: A3 is due on 05.10.2010 (11:59 pm EST) via email
