Nyhetsflöde

The last lecture will be held at SciLifeLab again. We start at 15:15 in "Big", a seminar room on floor 3.

Please let me know if you plan to participate.

In an overwhelming vote, it was decided to have the last lecture on Tuesday. I choose to schedule the lecture to 15-17, and I will get beck to you when I have a room booking.

Dear all,

I have to move the last lecture of the course. Please surf to the doodle and mark what times work for you. 

I have decided to have the two extra lectures at SciLifeLab on the Karolinska campus. Details:

• Monday May 6 at 13, "Kilsbergen" seminar room, floor 4 of the Alpha building at SciLifeLab.
• Wednesday May 8 at 10, "Kinnekulle" seminar room, floor 5 of the Alpha building of SciLifeLab.

Unfortunately, entrance doors are locked, but I (and others) will be able to see you and help you in. Both seminar rooms have a window to the main stairway/elevator hall. If you need to, call my mobile on 076-9418607.

How to get here:

• Map from Google
• The adress is Tomtebodavägen 23A
• Convenient buses are:
  
  • 73 from KTH/Östra station, stop "Tomtebodavägen"
  • 70 from Odenplan, stop "Karolinska vägen"
  • 3 from St Eriksplan, Fridhemsplan, et c, stop "Karolinska vägen"

Dear all,

I have to cancel today's lecture due to a health issue. I am sorry for the late notice.

In the meanwhile, please look at the HW2 assignments and let me know if you need clarifications!

I expect to bring you the graded HW1 on Thursday, and schedule replacement lectures based on your input.

Hej,

Please note that the lecture Thursday April 24 is cancelled. Or, rather it should be rescheduled together with a previous lecture. Therefore, please surf to

http://doodle.com/zr6pecir3ygrupxy

and vote for the times that are good for you!

I have now finalized Homework 1. Go forth and earn points!

A first draft of homework 1 is now posted. More questions (and some data) will be posted tomorrow!

If you have not gotten a confirmation from Hossein regarding the recieval of your submitted homeworks by now, please resend it.

The last lecture will be in room D35 at the main campus tomorrow Wednesday at 13.15!

Dear all,

Last friday, I set up a doodle poll for when have the last AlgBio lecture. I thought I announced here in this forum too, but apparently, that never happened. So, here is belated request for input. I apologize for the lateness.

Please go to the poll and give me your preferences! I will close this poll tonight!

I have extended the deadline for HW3 due to scheduling conflicts with another course. The new target date is May 31. Of course, you are still allowed to hand in solutions on Friday in order to enjoy the weekend better!

I have updated the formulation for HW3:5.

Hej!

I want to remind you that tomorrow, Tuesday May 17, at 10 in D41, Jens will give the next to last lecturein the course. I will speak at the last lecture which I will schedule as soon as possible. Unfortunately, we won't have time for doodling.

HW3 is now posted. The due date is May 27, at 9.00 AM.

Please notice that I have left two questions open, I want to fill them in the next couple of days.

I can tell you that Tuesday's lecture (May 17) will be in D41 and will cover model-based methods for estimating phylogeny. On the last lecture, yet to be scheduled, I will discuss tree reconciliations, which is about how to relate one tree to another.

I want to let you know that I have decided to skip HW4. Or rather, it will be merged into HW3. The size of HW3 will not double, so don't worry, but the due date will be after the last lecture.

Hej alla,

I am starting to realize that I will not be able give a lecture this afternoon due to a cold. I should have recovered by now, but my head is simply not functioning so I think everyone is better off if I postpone today's lecture (Thursday May 12) to next week. Sorry for any inconvenience. I will investigate possible replacement times.

As I announced recently, the lecture on Tuesday May 10 has to be postponed and we have to decide at what time to meet. I have picked several time slots and want to know which one is best for most people. Please goto this Doodle and tell me when you are available! I have not looked at what rooms are available for these times, so we might (but hopefully not) end up in a situation where the majority choice cannot be taken due to lack of room.

I have gotten several questions about 2B in HW2. As a lead, I want to say that there is no simple and perfect solution. Sorry. This is a question about "algorithmics meeting the reality", and I want you to exercise your algorithmic thinking and report a practical solution that you can justify in some way or another.

I want to announce that Jens Lagergren is talking about the EM algorithm on Tuesday's lecture. I will continue with phylogenetics on Thursday.

Clarification time again! I have now rewritten 2B to something that hopefully will be easier to understand. There is even a small example.

One more clarification. In assignment 2A, I want you to look at the SP score with affine gap costs by taking the multialignment and then extracting all pairwise alignments. Then you strip away all indel-only columns before you compute its score. This means that

AAACCC---AAA
AAA------AAA

should be changed to

AAACCCAAA
AAA---AAA

and then have the score computed.

Hope this helps!

I have made a small update to question 4 on homework 2. I am clarifyng that you need to compute NC for all pairs of input sequences.

Dear all,

I want to let you know that I have postponed the deadline for homework 2 one week, to May 3rd.

Homework 2 is now officially posted. Please notice this is a firm deadline and that copying text from a web page is considered cheating.

Dear all,

Hossein has replied to all emails with homeworks that you have sent him. If you have not received such a receipt, please resend your submission with doublechecked email address (farahani@kth.se) and fingers crossed.