My personal and professional adventure into Science

Invitation to the 2nd Annual Danish Bioinformatics Conference, Aug 25-26, 2016

ELIXIR Denmark is sponsoring and organising the 2nd Annual Danish Bioinformatics Conference, to be held on August 25-26, 2016, in Odense, Denmark.

The two-day meeting provides attendees with opportunities to share and discuss their latest findings, and learn about the newest national and international developments within computational proteomics, machine learning in bioinformatics, network biology in disease, non-coding RNA bioinformatics, population genetics and evolution, and transcriptomics and transcriptional regulation.

The following speakers already confirmed their participation:

Anaïs Baudot, CNRS, France
Anders Krogh, University of Copenhagen (UCPH), Denmark (DK)
Anton Petrov,  EMBL-EBI, United Kingdom
Bruce Shapiro, NIH/NCI, USA
Robert Young, University of Edinburgh, United Kingdom
Jürgen Cox, Max Planck Society, Germany
Lennart Martens, University of Gent, Belgium
Martin Simonsen, QIAGEN, DK
Peter Løngreen, Technical University of Denmark (DTU), DK
Rute Fonseca,  UCPH, DK
Søren Brunak, DTU, UCPH, and RegionH, DK
Jon Ison, DTU, DK
Mikkel H. Schierup, Aarhus University, DK

Relevant information and key deadlines:

  • Details regarding registration and accommodation—and conference programme, still not final—may be accessed via the ELIXIR Denmark website (http://www.elixir-denmark.org/)
  • Students (incl. PhD studens), members of the programme comittee, invited key note speakers and ELIXIR Steering Group members may register free of charge, while for non-students the registration fee is 1,200.00 DKK (excl. VAT). The fee covers catering, dinner and social activities;
  • Please note that the registration fee is non-refundable;
  • Registration deadline: August 10, 2016;
  • You are invited to submit an abstract for the poster sessions. All abstract submissions must be received on or before August 10, 2016;
  • However, among the abstracts received on or before May 1, 2016, some will be selected for 15-minutes oral presentations;
  • The winner of the best poster will be announced during the meeting closure;
  • Poster board size: 95 x 240 cm;
  • To ensure that you have a hotel near the event, please register and book your accommodation via the registration site by 1 May 2016, as there is a limited number of pre-booked hotels: Hotel Ansgar, City Hotel Odense, Radisson Blue HC and Hotel Windsor.

For any questions about the event, please do not hesitate to contact:

Myhanh Nguyen (myng@bio.dtu.dk).

 

Kind regards,

ELIXIR Denmark Steering Group:

Anders Krogh, Professor, UCPH, DK
Bernt Guldbrandtsen, Aarhus University (AU), DK
Jan Gorodkin, Professor, UCPH, DK
Mikkel Heide Schierup, Professor, AU, DK
Ole Nørregaard Jensen, Professor, University of Southern Denmark (SDU), DK
Søren Brunak, Professor, Head of ELIXIR Denmark, DTU, UCPH, and RegionH, DK

Conference Programme Committee:
Bent Petersen, Associate professor, DTU, DK
Ida Moltke, Assistant professor, UCPH, DK
Kasper Munch Terkelsen, Assistant professor, AU, DK
Kirstine Belling, Associate professor, UCPH, DK
Robin Andersson, Assistant professor, UCPH, DK
Stefan Seemann, Assistant professor, UCPH, DK
Søren Besenbacher, Postdoc, AU, DK
Veit Schwämmle, Assistant professor, SDU, DK
Vivi Gregersen, Postdoc, AU, DK

 

Sponsored by:

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 🙂

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 – there 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 – i.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 – SDC 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 – Beijing offers adventures of all kinds – so 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.

 

 

ICG10 – The 10th International Conference on Genomics #DTUicg10

On Tuesday I will finally get some air under my wings again (It’s been almost 2 months since my last flight !!), as I will be heading towards Shenzhen, China. The occasion is the 10th International Conference on Genomics held by BGIGigaScience and China National Genebank. The aim of the conference is to:

… gather leaders, researchers and professionals in ‘omics’ research focusing on human health, animal and plant science, including agriculture and related fields, to share their thoughts and discuss the implications of the latest developments in genomics.

ICG-10

The conference is from October 22-25, 2015. With more than 80 speaker split over 16 sessions I am sure that it will be very interesting. The program can be found here: Sessions and workshops. Note that on Sunday we have a session, S16 AI, Big Data and Health. This session is chaired by Ramneek Gupta from CBS and consist of speakers from CBS, DTU and KU (see below).

If you have not signed up for the conference, I will do my best to Tweet using the hashtag #DTUicg10, and if the internet connection allows it I will also write a few blog posts, so make sure to signup for notifications from my blog as well. You can do that on the right side of this page.

If you are attending the conference, then send me a tweet, Twitter, so we can meet for a beer at the banquet 🙂

Below is the session Chaired by DTU which I can only recommend you to attend!

S16 AI, Big Data and Health (15:45-18:20)

Chair: Ramneek Gupta, Technical University of Denmark, Denmark
Introduction:

Life Sciences today easily fulfils the major tenets of the need for Big Data thinking: Volume of Data, Velocity of data accrual and Variability of data. Indeed, all of these offer opportunities in gathering unprecedented insights into living systems. However, how far up the Hype Curve is current Big Data thinking in Life Sciences? How do we translate insights to value in the life sciences domain ? For example, when big data approaches are mentioned for precision medicine, what kind of approaches will get closer to clinical implementation ? What kind of infrastructural developments are needed in software or hardware or organisationally to accomplish this ? How does artificial intelligence help ? What are some of the basic challenges faced by the hugely increased Volume, Velocity and Variability of data ?

This track aims to present case stories or ideas in this direction.

Speakers:

Ramneek Gupta15:45 – 15:55
Ramneek Gupta
Technical University of Denmark, Denmark
Track Introduction: What is Big Data, and Why is it Relevant to Life Sciences?
Søren Brunak15:55-16:20
Søren Brunak
Technical University of Denmark, Denmark
Topic: Creating Disease Trajectories from Big Biomedical Data Covering Millions of Patients
Laurent Gautier16:20-16:40
Laurent Gautier
Novartis Institute for Biomedical Research, USA
Topic: Handle Big Data in Drug Discovery and Health Care with Software Prototyping
Line Clemmensen16:40-17:00
Line Clemmensen
Technical University of Denmark, Denmark
Topic: Slimming Big Data
Thomas Sicheritz-Ponten17:00-17:20
Thomas Sicheritz-Ponten
Technical University of Denmark, Denmark
Topic: Big Planes, Big Risks and Big Data
Helle Krogh Pedersen17:20-17:40
Helle Krogh Pedersen
Technical University of Denmark, Denmark
Topic: Ranking Factors Involved in Diabetes Resolution after Bariatric Surgery: A Neural Network Approach for Integrating Clinical and Genomic Data
Ole Lund17:40-18:00
Ole Lund
Technical University of Denmark, Denmark
Topic: Genomic Epidemiology
Peter Løngreen18:00-18:20
Peter Løngreen
Technical University of Denmark, Denmark
Topic: Supercomputing and Cloud: Converging Technologies in Life Science

 

Resumé of the Elixir Conference 27-28 august 2015

Remember to follow the Elixir conference on Twitter

The first annual danish Bioinformatics conference, arranged by the danish Elixir hub, is now ongoing in the old docks in Odense. If you are not already attending the conference, you can still follow it on Twitter by following the hashtag #elixirdk.

The program is very exciting and until now we have had talks in the subject of Systems Biology and Medical Informatics, Proteomics Informatics and RNA Bioinformatics.

Tomorrow the talks will be within the areas of Population Genetics, Medical Genomics and Industrial view on Danish Bioinformatics: Challenges and Opportunities. In the end of the conference there will also be a presentation about Computerome and Cloud computing which I am really looking forward to.

Elixir Denmark – First Danish Bioinformatics Conference in Odense on August 27-28, 2015

I have just signed up for the First Danish Bioinformatics Conference, which will be kicking off in Odense, Denmark on August 27-28, 2015, and I can only urge you to do the same. The conference is organized by ELIXIR Denmark Denmark.

Who should join?
Well, everyone interested in bioinformatics as the conference is relevant to all bioinformaticians who wants to be updated on the latest developments within the fields of Protein-, RNA-, and DNA- Bioinformatics, Medical Genomics, Population Genetics, and Systems Biology.

When is the deadline for registering?
The deadline for joining is 10 August, but if you register before 15 July, the registration fee is a bit lower (DKK 1250 | approx. EUR 167) compared to after 15 July (DKK 1687 | approx. EUR 226). Students (Including PhD students) are free of charge !

If you want to present a poster the deadline is June 28. All the details, including program, can be found here: DKBiC-2015-leaflet4.pdf

So go to the website to register and then I’ll see you there 🙂

 

PRACE Summer of HPC 2015

Would you like to work with SuperComputers? I am posting the ad below for DEIC who founded a great part of our supercomputer. Deadline for signing up is ending soon!

Would you like to spend the summer working abroad at an European High Performance Computing (HPC) Centre?

Are you interested in programming and are eager to improve your skills?

Have you a passion for visualising scientific data in novel ways to grab the attention of the general public?

Summer of HPC

If you have answered yes to any of these questions the Summer of HPC is for you! Read on tofind out more information about the programme.

PRACE opened applications for Summer of HPC in 20 February 2015. Twenty students will go to 10 PRACE member centres around Europe (2 to each centre), where they will work on PRACE related projects for 2 months during the summer (July / August). Students are invited to revise 2015 projects and apply before the deadline!

https://summerofhpc.prace-ri.eu/

About the PRACE Summer of HPC

Summer of HPC is a PRACE programme that offers summer placements at HPC centres across Europe to late stage undergraduates and early stage postgraduate students. Up to  20 top applicants from across Europe will be selected to participate. Participants will spend two monthsworking on projects related to PRACE scientific or industrial work and ideally produce a visualisation or video of their results.

At the end of the programme, two best participants will be awarded for their contribution – there are awards for Best Visualisation and for HPC Ambassador.

The programme will run from 1 July to 31 August 2015. Flights, accommodation and a stipend will be provided to all successful applicants; all participants need to bring is an interest in computing and some enthusiasm!

https://summerofhpc.prace-ri.eu/

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 🙂 Tomorrow I will give a talk in “Preprocessing, quality, error correction, assembly” which I am really looking forward to 🙂

NGS Conferences 2014

Recently I stumbled upon the blog of NextGenSeek. It’s an excellent blog to follow covering the latest happenings in NGS and NGS data.

NextGenSeek is maintaining a list of all Next-Generation-Sequencing conferences in 2014 from all around the world. It is worth checking out if you are interested in NGS. You can find the list here.

Benzopyrene_DNA_adduct_1JDG

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