Nyhetsflöde
Logga in till din kurswebb
Du är inte inloggad på KTH så innehållet är inte anpassat efter dina val.
I Nyhetsflödet hittar du uppdateringar på sidor, schema och inlägg från lärare (när de även behöver nå tidigare registrerade studenter).
Maj 2016
Mars 2013
Thank you all for your significant efforts with the projects and at the poster session today!
Please remember to email a pdf of your poster to the teachers!
Directions to the venue for the poster session
The poster session takes place at Science for Life Laboratory Stockholm (SciLifeLab), Tomtebodavägen 23A in Solna (at the outskirts of the Karolinska Institutet campus). Specifically, in the Alpha house, floor 4, room "Kilsbergen".
Please see this link: http://www.scilifelab.se/index.php?content=find_us
From AlbaNova, it's easiest to go by bus 73 (get off at "Karolinska vägen"), but bus 3, 70, and 77 will also do the trick.
I suggest we all gather by the Reception at SciLifeLab tomorrow Friday at 13:00. Then we will take you to the room.
Peer review of posters
One important part of the poster session is that you should evaluate your fellow students' posters. Please see the attached pdf document for more instructions (instructions will also be briefed at the poster session).
Poster session instructions incl. peer review.
Clarification - the format of the poster session is like this:
You put up your poster on the wall (and the other 4 groups do the same), then you stand by your poster and anyone interested in it could ask questions, discuss the methods and results on the poster. This "anyone" could be your fellow students, your teachers at this course, and maybe a couple other interested people here at SciLife.
Consequently, you don't stand by your poster all the time, since you also need to look at the other posters. At scientific conferences, a poster session is usually "mingle time" where you walk around and talk science to the poster presenters and other people you meet there.
Thus, there is no specific time allocated to the presentation of your project. There will be no specific time where you get everybody's attention. You should not prepare a powerpoint presentation - only a poster!
Poster printing instructions
Posters can be printed at AlbaNova. Get in touch with the reception desk at AlbaNova, floor 5.
You should bring the poster in pdf format, preferably on a USB memory stick. It might be possible to email your pdf file as well, but that has to be agreed beforehand with the reception at AlbaNova.
Posters are printed between 8.00 and 15.30. It takes about an hour to print a poster. To allow for the waiting time you should provide the poster for printing on Thursday. The earlier the better of course, but the exact turn-around time depends on their total poster printing work load (including potential posters not originating from this course).
You will need the following information:
1. Your name
2. You phone
3. Your school. Which is either Biotechnology (BB2490) or CSC (DD2399).
4. Name of your pdf file
5. Who should pay -- to get this information, get in touch with your project supervisor (i.e., Lars, Lukas, or Olof).
Standard poster formats are A0 (84x118), A1 (half A0), B1 (70x100) cm. Other formats might be available too. You decide yourselves whether you prefer "landscape" or "portrait" orientation of your poster.
Hello,
I would like to express some problems we faced regarding the project. In our project, we need to use UPPMAX and SLURM heavily. We need to run cutadapt, tophat and cufflinks commands and these commands are really time consuming, it takes hours or even days to process our 15 million reads. However, we wait in the SLURM queue for maybe 15-20 hours at best to get our job ran.
So in short, we make progress very slowly, since UPPMAX is involved, and of course the data is huge. When I talked to other groups, they said that they were experiencing the same problems. On the other hand, we also want to present reasonable results in the poster session.
So, is it possible for you to extend the project deadline until March 20th or 21st?
Februari 2013
Lärare
Olof Emanuelsson
korrigerade
12 februari 2013
Here are instructions for the project: BB2490 Project work - general instructions
Dear all,
In order to help some students with a conflict with another course, we will start already at 9:15 tomorrow Tuesday. We are in the same room, FD41, as planned.
I know this is a late notice. Please acknoledge by replying to this message!
Location for the lecture Friday 8 February at 10:15
As you already know, the cancelled lecture from this Monday ("L8" on the schedule) was moved to tomorrow Friday 8 February at 10:15-12:00.
The location is now determined: we will be in the seminar room "Gallerian" at the Biotechnology department at AlbaNova (http://www.kth.se/en/bio/). The entrance to the department is at the 3rd floor at the AlbaNova main building, which means 2 stairs down from the main entrance. When you have descended the stairs (the main stairs in the middle of the building), the entrance is directly to the right of the next stair down.
You need a card to enter, so I'll regularly check at the door (from ca 10:00 to 10:15) to let you in as you come.
The "Gallerian" room is then some 10 meters into the corridor.
Today during the lab, we had an issue about the sbatch options. When we copied sbatch arguments from the PDF file or from sbatch template file to the console and run the following command:
sbatch –A g2012230 –t 2:00:00 –p node –n 8 --res=g2012230_1 –o my_job_name.out sbatch_template.sh
We got an error:
sbatch: error: Unable to open file –A
Then it turned out that, in the Lab manual (and also in the sbatch_template.sh file) en-dash sign (–) precedes the options such as A, t and n instead of the usual hyphen/minus sign (-). Since –A is not same as -A, sbatch thinks that –A is the filename, not an option.
So, it would be nice to raplace all these en-dash characters in the PDF and sbatch template with the hyphen/minus character.
Lärare
Olof Emanuelsson
ändrade rättigheterna
3 februari 2013
Kan därmed läsas av alla och ändras av gokcen eraslan (gokcen@kth.se).
Important! Due to sickness I have to cancel the lecture tomorrow Monday 2013-02-04 at 10:15. I'm very sorry for the inconvenience.
We will reschedule this lecture at a later occassion, including the student presentations.
Dear students, I am unable to supervise at today's lab due to sick child. I am trying to find a replacement, but at any rate that person will be late. Try to get going anyway! Help each other figure things out!
Sorry for the inconvenience.
Januari 2013
Please note that instructions for lab 2 are now available, see "Computer exercises".
Lärare
Olof Emanuelsson
korrigerade
28 januari 2013
Lecture notes for L6 2013-01-28 (genes/transcriptomics/RNA-seq) now available at the Course wiki, https://www.kth.se/social/course/BB2490/page/slides-3/
I have linked to two papers for lecture 5 on read mapping, found under "Literature". We need two presenters for these papers for lecture 6!
The papers (Koehler et al and Trapnell-Salzberg) will be handed out in paper form at today's lecture.
For computer exercises 2-4 (and for the project work later), we will use UPPNEX and SNIC-UPPMAX resources. This means that you'll need an UppMax account to access these computing resources. Please go to http://www.uppmax.uu.se/user-account-application and fill in your application for an account. Use your university email (not gmail, hotmail etc.). Choose project g2012230:BB2490_vt2013 from the Project list. Choose the Kalkyl computer system (thanks to Gokcen for pointing this out). Note: if you already have an Uppmax account, do not apply for another account.
Lärare
Olof Emanuelsson
korrigerade
23 januari 2013
For computer exercises 2-4 you'll need an Uppmax account. Please go to http://www.uppmax.uu.se/user-account-application and fill in your application for an account. Use your university email (not gmail, hotmail etc.). Choose project g2012230:BB2490_vt2013 from the Project list. Choose the Kalkyl computer system (thanks to Gokcen for pointing this out). Note: if you already have an Uppmax account, do not apply for another account.
Lärare
Olof Emanuelsson
korrigerade
23 januari 2013
For computer exercises 2-4 (and for the project work later), we will use UPPNEX and SNIC-UPPMAX resources. This means that you'll need an UppmMax account to access these computing resources. Please go to http://www.uppmax.uu.se/user-account-application and fill in your application for an account. Use your university email (not gmail, hotmail etc.). Choose project g2012230:BB2490_vt2013 from the Project list. Choose the Kalkyl computer system (thanks to Gokcen for pointing this out). Note: if you already have an Uppmax account, do not apply for another account.
Instructions for the project work is now available here.
If you don't find the link to the information on student presentations (under "wiki" in the right margin), follow this link!.
Augusti 2011
Please note that they are closed for lunch between 12 and 13 every day.