My personal and professional adventure into Science

5 good reasons to take your MSc degree in China

For the last two years I have been member of a teaching team that went to Beijing, China to teach danish and Chinese students. From my side they were taught in Introduction to Bioinformatics and Next Generation Sequencing.

Now the school is looking for more brave students who wants to pull up their plugs, jump into something new and go to Beijing for their master. If you are interested please take a look at the post below and then I hope to see you in China ūüôā

5 good reasons to take your MSc degree in China

  • Get a head start on your future career
  • Study at a top University in China
  • Researched based teaching
  • Professional service and guidance
  • An unique intercultural experience

Dear student,

In this mail you will find some information about SDC, the different programmes and also studying and living in China. If you have any further questions, please do not hesitate to contact us Рthere are only good questions! Contact information is below.

SDC (Sino-Danish Center for Education and Research) is a partnership between all eight Danish Universities and University of Chinese Academy of Science (UCAS) in Beijing. The overall aim of SDC is to promote and strengthen cooperation between Danish and Chinese learning environments, and increase the mobility of students and scholars between the two countries. SDC offers seven unique MSc programs in Beijing. All programs are 120 ECTS and when you finish you will obtain a double MSc degree Рi.e. a MSc degree from the Danish University and an MSc degree from the Chinese University. All programmes qualify for the Danish state educational support (SU). To read more about the programmes Master Programmes.

All courses are taught in English by Danish and Chinese teachers/researchers. Your classmates will also be a mixture of Danish and Chinese students and in some cases also other nationalities. Professional help and service РSDC helps you both before and during your stay in Beijing with all practical matters. Before departure to Beijing we host an introduction seminar in Denmark and upon arrival in China you will have 2 whole introduction weeks before classes start. First you will have one week just with the other candidates from Denmark and then following that, a week also with all the Chinese students. We also have an office in Beijing with both Danish and Chinese staff that can help and guide you in terms of both academic and practical matters.

Living in Beijing РBeijing offers adventures of all kinds Рso pack your bags and get an experience of a lifetime! Although prices in China are rising, it is still very cheap in relation to most countries in the EU. You can easily live and eat for your SU. SDC offers accommodation on campus at a very favorable price, but it is also possible to find a flat if you want. For more information on living in Beijing Living in Beijing.

If you have any questions (academic, practical or other) please send an e-mail to contact@sinodansihcenter.dk and we will make sure you get a quick response.

 

 

Making your research (and yourself) visible…

Whaoo, It has been over a month since I last posted something on the blog. So much have happened – and time just disappeared. Right now I am preparing a talk for tomorrow with the title “Making your research (and yourself) visible‚Ķ”, which I will give in the PhD club. Here I will present my way of marketing myself online, and I do have a few good case stories to tell. First of all my very first publication, published in a journal with an Impact factor of 2.22 in 2009, and now it has more than 200 citations. The web server itself has analyzed more than a million sequences !!! So yeah, it did help to spread the news when I got the paper out ūüėČ

Making your research (and yourself) visibleBesides that I will also talk about my recent journey to the Salterns in Mossoro and the start of my company Bison-Seqtech ūüôā

 

CEBio Metagenomics course February 2015

A great course has now come to an end, and I have finally gotten some sleep again. It was well needed. Unfortunately the calendar now says rain, rain, rain, now when I was hoping that I could get out to get a little tanned…

The course was a free course, organized by Guilherme Oliveira, on the topic of Metagenomics.

The course is aimed towards students, post-docs and researchers novice to metagenomics. The course will provide training in: data generation, experimental design, statistical considerations, sampling methods, data generation for 16S, shotgun and transcriptome, data analysis for diversity and functional studies, metadata analysis, single cell genomics.

Speakers included teachers from CEBio, Colombia, Egypt, USA and Denmark, a fantastic team that Guilherme once again had gathered. The list of instructors can be found here: Metagenomics Course 2015 _ instructors.cebio and the course schedule can be found here: Course Program _ metagenome.cebio.

Below are some pictures from throughout the course.

First talk at CEBio Metagenomics course 2015

Today I gave my first talk titled “General data production considerations, public tools and computational resources” at the CEBio Metagenomics course 2015. It was a more general talk with introduction to our Metagenomics group at CBS, followed by an introduction to Computerome which I got a really nice response to. Then I followed up by presenting some CBS tools that I thought would be relevant for the students during their studies, and then I gave some guidelines for using online prediction tools generally in a critical way ūüôā Tomorrow I will give a talk in “Preprocessing, quality, error correction, assembly” which I am really looking forward to ūüôā

Exam in Introduction to Bioinformatics

Last night I most likely had a student or two that had difficulties sleeping, hopefully many was looking forward to this day, as today was the exam day for the course I am co-responsible for: “Introduction to Bioinformatics”.¬†

109 students was this year signed up for the course and 99 had registered for the exam. The examination setup is a 4 hour written exam, where the students will touch upon the tools and subjects that they have been taught during the course. This is among others databases like GenBank¬†,¬†UniProt¬†and PDB, Pairwise and multiple alignment, Phylogenetic trees, BLAST, LOGO-plots, Weight-matrices, Prediction methods and other interesting and fun stuff ūüôā

Now the exam is closed, 89 students handed in, and I now have three weeks to correct all the exam sets. The students might have been sweating today, but now it’s my turn to sweat while correcting them all. I’m looking forward to see how they all performed ūüôā

 

Cebio Metagenomics Workshop 2014

Yesterday the workshop started and so far its really cool, full of amazing people. We started with a talk by David Holmes РAstrobiology: emerging opportunities for environmental microbiologists, followed up by Francisco Rodriguez-Valera РPostgenomic Microbiology and then we had a talk about the Brazilian Microbiome Project.

This morning of the second day we had a fantastic Bacterial Metagenomics mini-course by Carolina Megumi Mizuno, Rohit Ghai and Francisco Rodriguez-Valera.

After the course, it was time for my talk, and I think it went fantastic. I had students approaching me afterwards and there might be a few collaborations on the way. Plus, invitations to come back to Brzail to do some teaching and talk about projects, couldn’t be better ūüôā

Last talk was from Ramy Aziz talking about Genes Without Borders: Mobile Genetic Elements in Genomes.

Good links from Ramy:
http://theseed.org РHome of the SEED
http://kbase.us РTake a look at the Iris section (IRIS РThe web-based terminal to give you access to the full KBase command line.)
http://www.phantome.org РPhage annotation tool

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 d√©but 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 ūüôā

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.

Are you a good teacher?

Every Friday we have a CBS group meeting where all staff is suppose to attend. Each week it will be a different group presenting exciting new discoveries, tips & tricks or whatever they choose to talk about. Once per month the subject is teaching, and today Irene presented a bit differently than usual, she showed us three small videos ūüôā

During my Teaching & Learning course at DTU we used a book by Professor John B Biggs on the subject of Constructive Alignment. The book is titled Teaching for Quality Learning at University: What the Student does (Society for Research Into Higher Education).

Constructive Alignment is a principle used in teaching and learning, which is not typically used in traditional lectures and examinations. Often, you unfortunately see, that the learning objectives are not aligned with the examination method, which means that students who does not get into the deeper learning can be lost in the process. If the student is only interested in passing the course, he/she will typically look on what is required to pass the course. You have probably all heard questions like “Will this be in the exam?“, “Do we really need to remember this to pass the course?” etc. If the learning objectives are not well aligned with the requirements for the assessment method, these students will typically only read up on what is required to pass the exam and not get into the deeper learning.

Using constructive alignment will force these students to actually learn the subject the teacher intended the student to learn.

√Örhus University created three award-winning movies illustrating this, which I can only encourage you to watch if you want to improve your teaching.

Check out the videos below, they are short and to the point!
Also, feel free to give me your opinion in the comment box ūüôā

Video 1/3

 

Video 2/3

 

Video 3/3

 

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