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An enormous step forward in whole genome sequencing

The idea might not be new – we already diluted DNA already a decade ago ( see this 2003 paper ). A new Nature paper by Peters ( Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells… ) now shows that diluting DNA into 384 wells, adding unique tags, and pooling again before sequencing everything on a Hiseq, will result in an enormous reduction of sequencing errors – a problem that we are fighting now for a year. IMHO the paper isn’t primarily about the low number of cells that can be sequenced, but also about error reduction in WGS. The two key facts are certainly

To ensure complete representation of the genome we maximized the input of DNA fragments for a given read coverage and number of aliquots. Unlike other experimental approaches this resulted in low- coverage read data for each fragment in each of the wells a fragment is found in.

plus an intelligent phasing algorithm Continue reading An enormous step forward in whole genome sequencing

 

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Add geolocation barcodes to travel guides, conference leaflets, etc please

There are so cute little files while I am constantly looking up addresses in travel guides, madly identifying them at google earth before transferring location bookmarks to my mobile devices.

Why can’t publishers produce just some small geo.kml or geo.rdf files, deposit them somewhere on their web server and link them with barcodes that are printed each time a geolocation is referred too (example link Groebenzell)?

The iPhone needs a slightly different form (without kml) as well as an app like i-nigma that is pointed by this barcode

QRCode

to maps://?geocode=&q=gr%C3%B6benzell&ie=UTF8&client=safari&oe=UTF-8&hnear=Gr%C3%B6benzell,+Oberbayern,+Bayern&gl=de&t=m&z=14”>Groebenzell.

 

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Warning: Reply to all

Nature 486, 157 (14 June 2012) warns:

Scientists discussing their work through written media, including e-mail, should be aware that they could at any time be asked to reveal their conversations.”You are commanded to produce…any and all documents, data, and/or communications.” Towards the end of last year, those orders appeared in a subpoena that landed at the Woods Hole Oceanographic Institution in Massachusetts.

so please write me private things only in a closed letter. Maybe it’s not such a problem Continue reading Warning: Reply to all

 

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A broken contract

Erika Check Hayden ( who asked me by email before she wrote that piece ) has a new article about “A broken contract – as researchers find more uses for data, informed consent has become a source of confusion. Something has to change“. While I largely agree with her analysis of the current situation, her points for change are somewhat weakly described ( BTW that paper already generated a heated discussion at The Mermaid’s Tale: “Informed consent — who’s it supposed to protect, anyway?” ). Continue reading A broken contract

 

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A Word file that crashes the Macbook hard disk

Believe it or not, I was editing this week a document that I received by email. After 3 minutes Word Mac 2011, Version 14 crashed, leaving only a temporary file back on my OSX 10.7.4 desktop.

As restarting Word did not work, I used disk utility, that recommended to be started from another disk.

When doing so, it recommended to reformat my hard disk (which I did). Continue reading A Word file that crashes the Macbook hard disk

 

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What is life?

There is an interesting discussion going on starting with Trifinov’s ( whom I met here last year ) seminal paper in J Biomol Struct Dyn 2011

Analysis of the vocabulary of 123 tabulated definitions of life reveals nine groups of defining terms of which the groups (self-)reproduction and evolution (variation) appear as the minimal set for a concise and inclusive definition: Life is self-reproduction with variations… Over 100 of definitions of life exist today– learned opinions each one of which is, or has been in the past, defended not without a reason though generally met with skepticism. Continue reading What is life?

 

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Prevision

In my recent review on vitamin D and allergy I introduced the rather new concept of epigenetic priming of the offspring’s vitamin D system. I could find only a limited number of studies supporting this view. Fortunately, there is a new study published today that gives me some support. Using a twin design the authors (AJCN. First published ahead of print May 30, 2012 as doi: 10.3945/ajcn.112.035683) find

Our results suggest that maternal circulating 25(OH)D is the most significant regulator of neonatal circulating 25(OH)D concentrations, with underlying genetic factors playing a limited role.

 

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Science is not about certainity. But also not objective at all?

Re-post of a conversation with Carlo Rovelli 30/5/2012

I seem to be saying two things that contradict each other. On the one hand, we trust scientific knowledge, on the other hand, we are always ready to modify in-depth part of our conceptual structure about the world. But there is no contradiction, because the idea of a contradiction comes from what I see as the deepest misunderstanding about science: the idea that science is about certainty.”

which is in line Continue reading Science is not about certainity. But also not objective at all?

 

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Intellektuelle Zerstörer

“Auf den ersten Blick scheint er [der Intellektuelle] ein Zerstörer, man sieht ihn, einem Metzger vergleichbar, stets die Hände voll von Eingeweiden der Dinge. Aber das Gegenteil ist der Fall. Der Intellektuelle kann nicht, auch wenn er es wollte, im Hinblick auf die Dinge Egoist sein. Er macht aus ihnen ein Problem. Das ist das höchste Kennzeichen der Liebe.” (Der Intellektuelle und der Andere, 1940)

zitiert nach der “der Freitag

 

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