CSE 591 : Computational Molecular Biology

Spring 2003

CSE 591

Day & Time: MW 1:40PM-2:55PM

Room: PSA 113

Instructor: Chitta Baral.

Office: GWC 366

Office hours: M 3:00 pm-5:00pm (in my office), W and F (5 - 6 PM) email only.

Phone: 727-6047 Email: baral-aat-asu-period-edu

Project Demo Schedule. 5/4/03 9:06 AM.
Internship position was available at TGen. 5/1/03 8:15 AM. *** (Position has been filled. 5/13/03 1:45 PM.) ***
Solution for the last homework is posted. See the last 2 pages of the updated slides on Hidden Markov Models. 4/30/03, 9:53 AM
Project due date is changed to May 6th. On May 6th I will meet each group for 20 minutes during 10 to noon, and 1 to 6 PM. Today in the class we will draw lots to decide the meeting times. During the meeting you need to give a demo of your project. (Bring your laptop.) Besides the demo, make some slides to present your project. You also need to bring folder with all your project reports and presentation slides. In addition each student should also bring a folder with all the homeworks, and scribe notes. Before you come to the demo have all your reports uploaded to your website. You may remove it after the graduation day. 4/30/03, 9:34 AM.
For the Home work due on 4/28, please bring it as hard copy to the class. DO NOT put it in your web page, as for this particular HW I donot want any chance of people copying from others. 4/27/03, 11:22 AM.
For the class on 4/27/03, there is a slight possibility that I might be a little late as I have an unavoidable appointment in Phoenix in the morning. Please wait for me. 4/27/03, 11:20 AM.
Hope everyone is making good progress on their project. If you are facing problems please see me the coming week (Monday office hours or Friday afternoon). Don't wait until it is too late. (Also, I am going over your reports and will send you some feedback.) 2:20 PM 4/4/03.
I graded HW 3 and following are some good answers, particularly in terms of using the English-like constructs. 4:35 PM 1/4/03
http://www.public.asu.edu/%7Eamdavis1/.
http://www.public.asu.edu/%7Enhtran/cmb-s03/hw3.txt
http://www.public.asu.edu/%7Ecwen1/cse591/
http://www.public.asu.edu/%7Esgzimme/cse591homework.htm
3/26/03 7:26 PM. Scribe notes page. (I have not reviewed them.)
3/26/03 10:00 AM. A break down for the first test is posted.
3/10/03 11:20 PM. The class test will be postoned by a week because of the student presentations delaying the material that I planned to cover before the test. The date for the next project report will be postponed by two weeks to 3/26/03.
2/24/03 4:00 PM.In regards to the project report, besides the 3+ pages report, you should also have a project summary of 1/2 a page.
2/24/03 1:05 PM. This is a reminder that each group will present their proposal in the class on 2/26/03 and 3/3/03. The order of presentation will be the reverse order of the scribe schedule. The presentation should be about 5-7 minutes. For your proposal, think of writing atleast about 3 single spaced pages without counting figures or data.
2/19/03 1:28 PM. Submission through web links has worked very well. To simplify the process further, I would like every one to designate a particular web page for this class. In that page you need to have a list of pointers to your various homeworks, projects notes, etc. After the due date I will just go there and retrieve the appropriate documents. This makes things convinient to you and me.
2/17/03 4:45 PM. Homework, notes by scribes, etc, should be put in a web page and the URL should be emailed to the TA lctuan@asu.edu.
2/17/03. 4:45 PM. Some students requested to postpone the HW 3 deadline to 2/24. Thats fine with me. So the HW 3 deadline is now 2/24. also, the due date of phase 1 of the project now is 2/26.
2/10/03 11:58 PM. As announced in class: We will not have the Biology Quiz. HW2 deadline is postponed to Feb 17th. HW 3 due date is Feb 19th.
2/10/03 12:16 PM. Is a good pointer for indroction to signal networks.
2/9/03 6:08 PM. You must start forming groups for the project. In case you have not done so yet, on Monday I will finish 10 minutes early so that you can talk to your class mates at that time. Individual projects are fine too. As mentioned earlier, if you have some other project in mind (besides the one that I have been talking about) then feel free to bring it up with me.
2/9/03 6:06 PM. For HW2, Q1 the data that is asked for has to consist of numbers. Pictorial data is not ok.
2/5/03 noon. HW 2 is posted in the Homeworks section. Due: 2/12/03.
2/4/03 12:37 PM Besides the bibliography in my microarray slides the following is also a good paper: Altman & Raychaudhuri: Whole-genome expression analysis: challenges beyond clustering
2/4/03 12:09 PM. On 2/5/03 I will discuss several CMB databases. On 2/10/03 I will discuss Pathways. On 2/12/03 we will discuss all aspects of the projects. Please come prepared that day to ask me questions about projects. You can ask me all kinds of questions about the projects including questions like `If xyz would be a good project or not?' etc.
2/4/03 12:08 PM Tomorrow's class will be in GWC 487.
2/3/03 5 PM. Date for quiz: 2/17/02. Will cover material until and including 2/10/02.
2/3/03 4:15 PM. Change in deadline: First phase of the project due on 2/24 instead of 2/12.
2/3/03 1:35 PM. Scribe schedule is added. Some basic instructions. You are also suggested to look at the scribe instructions for a similar course at Tel Aviv U.
1/23/03, 5 PM: The Homework question is elaborated.
1/22/03, 5 PM: If you missed the class today, familiarize yourself with all the information in this web site. In particular, check out the homework.
1/22/03, 5 PM: Please install the CD-ROM that was distributed in the class and return it to me next class on 1/27/03.
1/22/03, 5 PM: On 1/27/03 we will go over the transcript slides that I made of the relevant portion of the Roche Genetics CD-ROM.
1/22/03, 5 PM: From the class survey it seems that more than 80% of the students in the class do not have Biology background beyond high school. Hence, I am thinking of a quiz worth 10% of the total grade (to come out of the class test portion) first or second week of February. This quiz will focus on the biological aspects.