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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!

Anmäl missbruk

Lärare Olof Emanuelsson skrev inlägget 15 mars 2013

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.

Anmäl missbruk

Lärare Olof Emanuelsson skrev inlägget 14 mars 2013

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.

Anmäl missbruk

Lärare Olof Emanuelsson skrev inlägget 14 mars 2013

Olof Emanuelsson taggade med poster. 14 mars 2013

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!

Anmäl missbruk

Lärare Olof Emanuelsson skrev inlägget 14 mars 2013

Olof Emanuelsson taggade med poster. 14 mars 2013

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.

Anmäl missbruk

Lärare Olof Emanuelsson skrev inlägget 11 mars 2013

Olof Emanuelsson taggade med poster. 11 mars 2013

Lärare

Olof Emanuelsson kommenterade 13 mars 2013

Please note that they are closed for lunch between 12 and 13 every day.

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?

Anmäl missbruk

Gökcen Eraslan skrev inlägget 8 mars 2013

Gökcen Eraslan taggade med UPPMAX project deadline. 8 mars 2013

Son Hoang Nguyen kommenterade 8 mars 2013

The same thing happened with our project as well. We want to do some experiments with feature extraction and feature selection with our peptide sequences. When it comes to 2mer or 3mer feature set, the experiments usually take days to complete, in addition the waiting time for the submitted job to be executed is also too looong. I don't know if we could cover all of our expected experiments or not with this slow progress. So deadline extension would be great.

I also have problem trying install package FSelector in UPPMAX (something related to JVM when install dependency packages), both from source and from interactive mode. Can anybody help me out of this?

Gökcen Eraslan kommenterade 8 mars 2013

If you get this error when you run java command:

[gokcen@kalkyl1 tophat]$ java
Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.

you may try:

module unload java ; module load java

It worked for me.

Son Hoang Nguyen kommenterade 8 mars 2013

EPIC! It work now, thanks a lot :)

Gökcen Eraslan taggade med project, deadline och UPPMAX. 8 mars 2013

Ha Anh Tuan Nguyen kommenterade 9 mars 2013

Yeah, I totally agree with Gokcen. I think our group need more time to get a resonable result for the poster.

Elias Friman kommenterade 9 mars 2013

An extension would definitely be of benefit.

Daniel Berglund kommenterade 10 mars 2013

We are having similair problems. We only have one program that takes time to run but we have had a lot of problems getting things running. And our first runs have ran out of time so didn't complete.

Gökcen Eraslan kommenterade 10 mars 2013

Our jobs are not scheduled anymore, since we exceeded 5000 h/month limit, I suppose.

Daniel Berglund kommenterade 11 mars 2013

Thats odd, I started some jobs today, they are scheduled and just started running.

Gökcen Eraslan kommenterade 11 mars 2013

Yes, mine too. However, when I try to start an interactive session I get this warning:

[gokcen@kalkyl3 ~]$ interactive -A g2012230 -t 10:00:00
Your project g2012230 has overdrafted its monthly core hour allocation, but you may still run jobs.
Waiting for job 3016392 to start...

Lärare

Lars Arvestad kommenterade 11 mars 2013

Hej,

We want you to present what you have, as scheduled, on Friday. We do not expect you to have publishable results on Friday. You will be assessed on what you have done with the time available.

Olof is now asking for an even higher allocation.

En användare har tagit bort sin kommentar

Februari 2013

Here are instructions for the project: BB2490 Project work - general instructions

Anmäl missbruk

Lärare Olof Emanuelsson skrev inlägget 12 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!

Anmäl missbruk

Lärare Lars Arvestad skrev inlägget 11 februari 2013

Nicolas Girault kommenterade 11 februari 2013

OK!

Gökcen Eraslan kommenterade 11 februari 2013

Son Hoang Nguyen kommenterade 11 februari 2013

The change of time is not a problem for me also, but I got sick so I don't know if I can attend the class tomorrow.

Javeria Ali kommenterade 11 februari 2013

Ok!

En användare har tagit bort sin kommentar

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