Job: Bioinformatics position in new informatics cluster

Bioinformatics position in the new informatics cluster supporting the Novo Nordisk Foundation Centers for Stem Cell Biology and Protein Research.

The NNF Centers for Protein Research (CPR) and Stem Cell Biology (DanStem) at Faculty of Health & Medical Sciences at the University of Copenhagen are establishing a new integrated informatics core that will cover a range of technologies. This new core was recently expanded to include bioinformatics as a result of our establishing a new platform for single cell sequencing. We are currently looking for an ambitious bioinformatician who will assist with NGS analysis with in this core and provide new bioinformatics pipelines to individual scientists with in both centers. The individual will be imbedded in a bioinformatics core with expertise that will include NGS, proteomics, and image data analysis. The bioinformatician will join the centers starting from November 2017 or upon specific agreement.

Job description

The job will sit at the nexus of the two centers and astride several existing joint efforts to bridge computational technologies including image analysis and single cell sequencing. The tasks associated with this position will include providing bioinformatics support to our scientists, constructing pipelines for their analyses, and running courses that will help them acquire bioinformatics literacy. In particular this position will be responsible for developing and executing projects with other center scientists and helping them to make the best use of their own data and that already in the public domain.

The application deadline October 15th, 2017. For further details, please refer to http://employment.ku.dk/staff/?show=145792the official job ad.

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Tip: How I minimize jet lag

People who know me can attest: I travel a lot. Over the past 12 months, I have done one return trip to Australia, two to Asia, five to the US, and more than ten within Europe.

By now, I manage to do this with minimal jet lag almost every time. Several people have suggested to me that should write a blog post about my tricks, so here are my thoughts on how to avoid jet lag. Take them for what they are — one person’s personal experience.

Plan to hit the destination timezone

The most fundamental mistake that I see people make is that either they just let things happen and hope for the best, or they plan how to keep themselves entertained during the long flights and layovers in airports. I am not at all concerned with how to make time pass. I have a laptop, plenty of work that needs doing, and noise-cancelling headphones to block out my surroundings while doing it.

My only concern is how to make my body and mind hit the target timezone and be able sleep well already the first night after arriving. I always have a plan for how to make that happen and the plan starts at the latest in the morning of the day that I will be leaving for my trip.

The half night of sleep

By far the most important factor in avoiding jet lag is, unsurprisingly, sleep. When flying to a faraway timezone, the fundamental problem is this: you cannot stay awake until the evening but if you sleep on the trip, you cannot sleep the next night and will suffer jet lag the next day. This is particularly true when flying east.

My solution to that is to get half a night’s sleep on the trip. It is enough that I can make it through the following day feeling mostly fine, but not so much that I cannot sleep the following night. If flight schedules permit, I try to time my 3–4 hours sleep so that I wake up around 6am in my destination timezone. This plan will very often not coincide with when the airline thinks it should be night; I frankly could not care less.

If you wonder how this can possibly work, I suggest reading some of the literature on bi-/poly-phasic sleep.

Skipping a meal

I often find myself on eastbound, overnight flights that leave in the early evening and arrive at the destination in the morning. Invariably, the cabin crew will serve dinner an hour or two into the flight, by when it will be after midnight at my destination. Eating a main meal is not how you tell your body that it is nighttime. Also, flying east compresses the day, resulting in too many meals too shortly after each other.

My solution to this is to usually skip the dinner served by the airline on an overnight flight. For example, when I from the East Coast of the US to Europe, I will usually eat a big breakfast, eat nothing at lunchtime, and have a meal in the late afternoon at the airport. The latter meal will be roughly around dinnertime in Europe, and my next meal will be the breakfast, which is served by the airline shortly before landing. I have thereby already hit the destination mealtimes before even boarding the first flight; that is what I meant by having a plan.

Let there be light

Another important factor that regulates the circadian clock is light, in particular blue light. The latter is why many people who work with computers, myself included, use so-called redshift software to turn down the blue light emitted by our monitors in the evening. Airlines generally make the cabin dark for an extended period of time, which is far longer than the 3–4 hours of sleep in my plan, and sometimes on flights when I plan no sleep at all.

My solution to that is to work on my laptop, keeping the screen brightness reasonably high. Do not forget to change the geographic location data of your redshift software to the destination. That way I get enough (blue) light to convince my body that it is daytime when I want it to be daytime; I stick to my plan whether it agrees with that of the airline or not.

When I arrive somewhere during daytime and my work schedule permits, I always try to get outside for a walk. Strong sunlight and physical activity does wonders to reset the circadian clock and thus minimize jet lag.

Summary

You need to have a plan for how to hit the destination timezone, it starts before you even head to the airport, and you should stick to it even if the airline has other plans. The plan should factor in both the timing and the amount of sleep, of food, and of light.

Don’t wing it when you fly.

Announcement: Microbiome data interpretation workshop

Microbiome_workshop

Manimozhiyan Arumugam from the NNF Center for Basic Metabolic Research and I will be organizing a hands-on workshop on microbiome data interpretation in Copenhagen on October 25-26, 2017.

Together with Luis Pedro Coelho from the European Molecular Biology Laboratory and Evangelos Pafilis from the Hellenic Center for Marine Research, we will cover text mining and other useful methods for interpreting microbiome data in the context of the literature.

To apply, register here before August 1, 2017.

Job: Data mining of health record data

A postdoc position is available in the Cellular Network Biology group at the Novo Nordisk Foundation Center for Protein Research (CPR). The group focuses on network-based analysis of proteins and their posttranslational modifications in the context of cellular signaling and disease. The postdoc will work on analysis of data from electronic health records combined with molecular-level data in the context of alcoholic liver fibrosis and be part of the GALAXY consortium.

Candidates for the postdoctoral positions must hold a PhD degree (or equivalent) within a relevant discipline and have experience with programming and large-scale data analysis. The successful candidates will have strong qualifications or experience within several of the following areas:

  • Bioinformatics / computational biology
  • Experience with medical data
  • Statistical data analysis
  • Programming in Python and/or R

For further details please see the official job advert.

Update: The BuzzCloud for 2016

A new year has begun, so it is time for an update of the BuzzCloud.

buzzcloud2016

Comparing it to the cloud from 2015 year, it is clear that not much has happened in terms of new scientific buzzwords. However, readers of this blog will likely be pleased to see that the terms “data analytics”, “data science”, “data technology”, and not least “citizen science” and “open science” are all trending.

Job: Postdoc position on computational proteomics

A postdoc position is available in the Cellular Network Biology group at the Novo Nordisk Foundation Center for Protein Research (CPR). The group focuses on network-based analysis of proteins and their posttranslational modifications in the context of cellular signaling and disease. The postdoc will work on developing novel computational methods for analysis of proteomics data and apply them to unpublished state-of-the-art mass-spectrometry data in close collaboration with the proteomics groups at CPR.

Candidates for the postdoctoral positions must hold a PhD degree (or equivalent) within a relevant discipline and have experience with programming and large-scale data analysis. The successful candidates will have strong qualifications or experience within several of the following areas:

  • Bioinformatics / computational biology
  • Statistical data analysis
  • Mass spectrometry / proteomics
  • Programming in Python and/or R

For further details please see the official job advert.