My personal and professional adventure into Science

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

 

Impute.me – Get four times as much information from your genome

Are you one of the people who bought a 23andme kit, and then ever since “wanted more”? Lasse Folkersen, one of my colleagues from CBS, is one of those people, but instead of just thinking about it, he actually did something about, and now he needs help on his recent Kickstarter project to back his imputation server.

impute

Get four times as much information from your genome

Imputation is the name of a technology that is used in almost all major genetic studies today. Simply put it is a well-validated method of ‘guessing’ or imputing large parts of a non-measured genome, based on existing measurements from genotyping microarrays, as well as large reference databases such as the 1000 genomes project. From an input of 0.7M genotyped genetic variants, one typically gets knowledge of more than 4M new genetic variants.

However, the required command-line handling can be daunting to do this on a personal scale. That’s why an interesting new service called www.impute.me offers an easy interface to this technology. Upload your genome-data and get four times as much information back.That’s going from a large data file to an even larger data file.

But what can it then be used for? — the answer is broadly to get up-to-date with modern genetics research. Since most modern genetics studies use this technology, the majority of new findings are not available on basic direct-to-consumer microarrays, such as the ones offered by 23andme. So the second extension of the site is of course also to provide a selection of these novel analysis. A few basic analysis modes have already been implemented to show the added, benefit – such as for example a height-predictor, using the recent GIANT-consortiums findings on genetic variation of human height, as well as the ability to actually get the imputed data for this variation. However, the future idea is to provide many more of these modules – which are easily implementable, once the general imputation framework is in place.

Or – you could of course just enjoy your own personal 4 million extra data points in excel: the choice is yours, but there is no doubt that imputation is the way forward also for personal genomics.

You can see Lasses Impute.me kickstarter project here.

The last wild horses on Earth – Przewalski

Yesterday we got our story about the Przewalski horses published in Cell Current Biology. The article describes the world’s last remaining truly wild horses, which only comprises around 2,100 individuals worldwide. Eleven Przewalski horses were sequenced and compared to the genomes of 28 domesticated horses to provide a more detailed look at the endangered species which is shown to have diverged from Domesticated horses ~45.000 years ago. Finally the genomic impact of ∼110 years of captivity is also monitored, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%.

For a great Photo story check out the Discovery news website.

https://www.genomeweb.com/genetic-research/comparative-genomics-offers-clues-przewalskis-horse-conservation-efforts

http://horsetalk.co.nz/2015/09/25/study-reveals-genetic-ties-between-przewalskis-and-domesticated-horses/#axzz3mk41voq5

http://videnskab.dk/miljo-naturvidenskab/przewalski-heste-har-klaret-100-ars-fangenskab-overraskende-godt

 

 

Copyright: Ludovic Orlando

Copyright: Museum of domesticated animals, “Julius Kühn” at University of Halle-Wittenberg

Copyright: Ludovic Orlando

Copyright: Museum of domesticated animals, “Julius Kühn” at University of Halle-Wittenberg

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

DerSarkissian_media3

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

Copyright: Ludovic Orlando

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.

Stephen Hawking – ’Quantum Black Holes’

A few months ago I won a ticket through DTU Alumni to Stephen Hawking‘s Stephen Hawking public lecture – ’Quantum Black Holes’. So now I took and extra vacation day and flew to Stockholm to see his lecture. I know nothing about Quantum Black Holes, but it will be interesting to see Stephen Hawking live giving a lecture 🙂

 

Stephen Hawking

Stephen Hawking

Stephen Hawking, one of the greatest minds of the modern age and a cultural icon admired by millions worldwide, will present the public lecture “Quantum Black Holes” at the Stockholm Waterfront Congress Centre. Carol L. Folt, chancellor of the University of North Carolina at Chapel Hill, will provide opening remarks.

Hawking has dedicated his career to studying the basic laws that govern the universe. With Roger Penrose, he showed that Einstein’s General Theory of Relativity implied space and time would begin with a singularity at the Big Bang and end in a singularity in the center of black holes.

I will stay overnight as his lecture is at 19.00 and then fly home tomorrow morning and go straight to work. There will be a lot of work waiting 🙂 In the meantime I found a hotel at an old castle, Ulfsunda Slott. Very nice and beautiful inside, they have really done an effort to preserve the old style and details. Very cool.

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 🙂

 

Read the Interview with me in DeIC annual report 2014

The DeIC annual report 2014 is out, including an interview with me about my Computerome HPC usage. You can find the full report DeIC annual report 2014 (DeIC website) or here DeIC_aarsrapport_2014 (PDF). The interview with me is at page 22-23 and can also be found here: DeIC_aarsrapport_2014_Bent (PDF), note that it is only in danish.

DeIC – Danish e-Infrastructure Cooperation was established  on April 19 2012, with the purpose to support Denmark as an e-Science nation through delivery of e-infrastructures (computing, storage and network) to research and researchbased teaching.

P1080659

VBB Berlin fail – What a way to treat your customers…

Sunday I arrived in Berlin for one last vacation day before I head home. I go to the ticket machine to buy a ticket for the Ubahn, and I’m met with so many options. What I really wanted was a 24 hour ticket… Couldn’t easily find it, and then I was also met with the options to buy for “A”, “AB”, “BC” etc. Having no idea what to buy as the is no explanation next to the machine, I may have spent some time in the queue, when suddenly a friendly looking official VBB guy approaches me. “Can I help you?”. “Yes please” I reply and explain that I would for now just like to buy a ticket to go for Alexanderplatz where my hotel is. He clicks an option, I pay and thank him for the help.

The Ubahn arrived shortly after and very quickly I am greeted by a civil dressed inspector who wants to see my ticket. He tells me right away that I bought a ticket for the wrong zone so now I have to pay a fine of 40€. I try to explain what happened, but he doesn’t care and asks me for the money. I show him the last 5€ I have, he pads me on the jeans and says, “You have a credit card so we will follow you to an ATM.” Then three guys follows me to the machine, takes my suitcase so I can’t run – as I would even try that? – and waits for my money. After that he tells me that it’s my responsibility to check and pay the right ticket, no matter if it’s an official person who helps me …

VBB Fine

My €40 fine after following the advice from a VBB employed person

 

It’s your own fault you followed another persons advice – even if it was a VBB employee. You have to check yourself. VBB civil ticket inspector

Today I checked out the station on my way to the airport. There is no explanation of zones next to any of the four ticket machines. The machines are placed in the beginning and end of the station and the transportation map is located in the middle. The station is quite big and when you get down to the station, it not at all obvious that the map will be located far away from the ticket machines..

Furthermore, the ticket I bought was actually more expensive than the one I was suppose to buy. The one I bought costed 3€, but the correct one only 2.70€. So in principle I got a fine of 40€, because I bought a ticket that costed 0.30€ too much.

So VBB, how was it I cheated you? Yes, I bought a ticket after the advice from one of your employees for the wrong zone. But, I did not pay less than I was suppose to and cheated you in that sense… I actually paid more and cheated myself. How did this harm your business (or other people) in any way? How can you treat people like this? Is this your way of getting easy money out of stupid tourists, to me it seems like that.

I have never in my entire life cheated on public transportation, not even when I was a poor student, and I don’t plan to. And this, this is simply ridiculous VBB, I want my money back!

Please share this post if you have ever felt cheated by VBB like I do.

Dear grandfather – today you would have become a Centenarian

A Centenarian is a person who lives to or beyond the age of 100 years – Wikipedia

For the last 10 years, you always told us that you would never turn a 100 years and we didn’t believe you, because you kept strong all the time, except for the last 6-8 months. Unfortunately you were right, and on the 29th January 2015 you took your last breath, 2 months and two days before your 100 years birthday. Now you are laying peacefully next to Grandmother.

Approximately 15 years ago we asked you to write down your memoirs and reading them is simply amazing. What a life you have had !! I wanna share a bit of that with you all.

At the age of 23 you were already a trusted employee in the company you were working in and your Jewish boss sent you to Germany to finish some deals that he for good reasons couldn’t do himself. Hitler was already on his way forward at that time, but you refused to “Heil Hitler” when you entered cafe’s or bars, which people around you found weird, because they were afraid of Hitler, but you didn’t care. During many of your trips to Germany you among others introduced the danish bread industry for the concept of Whole Grain bread, previously not known in Denmark. At that time you were not satisfied with just being an employee and your entrepreneur genes took over and gave you quite some adventures, we can read that in your memoirs and I don’t even think that the list is complete.

P1030102

 

During the war it was very difficult to get all products so people had to live with replacements, and you sold a lot of those. For your company it was not difficult to make your own recipe for Rum and Almond essence, you even made tobacco replacement, found out that lead could be extracted from old toothpaste holders, silver could get extracted from old camera and movie rolls (we have a big lump of silver from that production) and you even created essential oils for perfume production. You and co-workers had a toy shop – which was later sold to the big danish toy chain, BR. At some point during the war, the resistance group Holger Danske contacted you. Their leader Egil Barfod asked you to keep some money for them. It started with 30.000 DKK (That was a lot during in that period), and later it turned out to be larger and larger amounts. Fortunately you were never caught. Today we have a gratitude plate from the Copenhagen Management for your deeds during the war.

In the early days of Insulin production you helped Novo Nordisk to grind pancreases for the extraction of Insulin. You got the pancreases from Pigs in big frozen blocks, grinded them using colloid mills and in the end sold your custom designed hole discs to Novo when you had to move on. You put together your own Vitamins for pigs, named Biotom, produced chewing gum gold coins,  sold Vanilla mixture for ice cream factories, sold Beech sawdust you bought from Junckers wood factory to soap producers and at some point you and dad also dealt with mustard milling. You and your companion extracted the aluminum from old pots and pans using HCL, mixed it to get the right solution of aluminium chloride and water and sold it to barbers and haircutters to stop the bleeding. The product was called “Det standser blodet, DSB” (It stops the blood) and it is still sold today. In the early days of Cola Cola’s entry to Denmark, you were also producing and selling cola extract for the danish breweries, and the name of the soda was O’Cola, amazing…

You had an amazing life, and I am so happy to have been a part of it.

Where ever I have been travelling, I have always given you a short call to tell you where I were and what I was doing. I know you enjoyed receiving these calls, and it didn’t matter if I was in Australia, USA, China, Brazil, Latvia, Austria etc. I did it to show you that I was thinking of you no matter where I was. Now I can’t call you anymore, but it doesn’t mean that we will stop thinking of you. You will always be in our hearts, and we will always love you. May you rest in Peace, Farfar.

 

%d bloggers like this: