My personal and professional adventure into Science

Archives for January 2014

My debut as an external censor

About a month ago I was contacted by Michael Poulsen from Copenhagen University, asking if I wanted to help as external censor at his course Genomic Approaches for Non-Model Organisms. First of all I was surprised that he still remembered me as it was two years ago he gave a talk at CBS about Termite Gut Metagenomes, very interesting talk. I thought the idea sounded fun as I have never tried that before, so of course I said yes. I have been internal censor before at our own courses, and I have had many of my own students for exam, but the external part was new to me.

The exam idea in the course is very interesting, as the students have to pick a topic and prepare a grant proposal with abstract, project description, timeplan and budget. They have a limited space of three pages for the project description, so they really have to think about what they write. For the exam itself, the student give a pitch for 5-6 minutes about the grant proposal and then there is about 20 minutes of digging into the proposal and ask questions in everything they learned in the course.

I think the exams went pretty well, it was a nice début and I am looking forward for the next time as I also learned a lot of new things during the exam. One other bonus is also, that I got in contact with Michael again and we talked about keeping in touch regarding future collaborations 🙂

If you are interested in the course, you can find a description of it here.

Content
The specific goal of this course is to give students a thorough introduction to the types and applications of the different genomic tools available, including understanding their limitations. We will introduce students to the concepts of genomic, metagenomic, and transcriptomic data acquisition and analyses, primarily during lectures and seminars, but supplemented with some computer exercises. In addition, the course will bring in guest lectures, who are specialists in their field and who use genomic tools to answer questions that are primarily driven by ecology, organisma, or evolutionary biology. In the theoretical seminars the students will present, discuss, and critically evaluate studies from the literature that incorporate genomic data to address questions in ecology, behaviour and evolutionary biology.
Learning Outcome
The increasing availability of genome data for non-model organisms creates new opportunities for research in ecology, behaviour and evolutionary biology. Such studies were previously restricted to sequencing single genes for phylogenetic reconstructions and to the use of neutral genetic markers for estimating genetic structure of populations. However, the application of second-generation genome sequencing technology means that non-model organisms will increasingly have sequenced genomes, allowing research that addresses the genetics of adaptations at unprecedented levels of detail. This will not only apply to individual study organisms, but also the communities of microbes that have important ecological functions and coevolutionary relationships with multicellular host organisms.
This course will identify and discuss the main applications of genomic data in ecology, behaviour and evolutionary biology, including various ways to identify single genes, genome annotation, pathway reconstruction, population genomics as natural extension of population genetics, community metagenomics, and the use of genomic data for the study of disease and symbiosis. By the end of the course, students will be able to critically evaluate the use and choice of genomic methods for hypothesis testing in biology.
The course is directed at biology students who want to become familiar with the use of genomic data for hypothesis development and testing, and for bioinformatics and biochemistry students with an interest in applying their skills outside classic model systems for which genomes were already sequenced many years ago.

Illumina announces new sequencers – NextSeq 500 and HiSeq X

Today the battle for the sequencing market has just stepped up as Illumina announced two new sequencing systems, the NextSeq 500 Desktop Sequencer and HiSeq X Ten Sequencing System. Technical specs can be found here for NextSeq 500 and HiSeq X.

 

 

Further reading can be found here:

Illumina Announces New Sequencers: HiSeq X Ten and NextSeq 500 at JPM 2014

Illumina ‘s HiSeq X Ten and NextSeq Press Release

How Does NextSeq 500 Compare With MiSeq and HiSeq?

How Does a Single HiSeq X Compares With HiSeq 2500?

A First Look at Illumina HiSeq X Ten and NextSeq 500

What is the Price of NextSeq 500 and HiSeq X Ten?

Illumina destroy the opposition again – almost….

 

Happy New Year 2013/2014

Happy New Year everyone. I know it’s a bit late, but I hope that you all came safely into 2014, and that 2013 brought you everything you wanted. If not, 2014 will be a new year to try reaching your goals. I  expect 2014 to be a very exciting year, as there are many cool projects and publications in the pipeline for the scientific part. I also expect the private side of my life to be a great year, can’t wait to get started.

Monday I went back to work after five extra vacation days in Berlin. I flew down there on the first of January and flew back home Monday evening. It was a nice vacation where I was lucky to find a good deal for the four star Sana Hotel Berlin, which is very nicely located next to the big shopping street Kurfürstendam. The hotel can be recommended, but think twice about sharing a room if you are travelling with a colleague and wants to have a little privacy… From the bedroom to the bathroom the only cover is a glass wall, and if you book a room with a bathtub like I did, you can see directly from the bed to the shower. A bit weird 🙂 Besides that the hotel was very nice with a sauna, steam bath, pool and fitness, and the staff is very friendly.

Sunday I went outside Berlin to a huge water amusement park called Tropical Islands. It’s an amazing 66.000 m2 water world with a Blue Lagoon, sand beach, a small rain forest and  a 10.000 m2 Spa complex. They also have water slides, where the fastest one you reach the speed of 77 km/t, that was something. All in all a very nice place! If you find yourself close to Berlin at some point, take your time and go there for some nice relaxation 🙂

Tropical Islands

This year I hope to have more time writing here about everything that is going on at work and in my life, I guess the lack of posts is just showing that a lot of things is happening.

What is your New Year resolutions for 2014? I don’t really have any New Year resolutions, but I will try to be more organised, more efficient at work and go more regularly to the gym 🙂

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