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Comment Re:those were the days (Score 1) 117

After entering page after page of code only to have it not work, we found, the back of the book, a small note about how the authors intentionally left errors in the code that you had to troubleshoot.

'Hey Bob, this doesn't even compile! You know the print deadline is tonight, right?'

'Sorry, I'm going bowling at 6. Just stick a note in the back saying we made some deliberate errors. Nobody will ever type the whole thing in anyway.'

Comment Re:This breaks my brain. (Score 2) 33

Though it hasn't yet lived up to its potential (Nanopore sequencing has been Next Year's Big Thing for several years now) it is rather incredible what can be done with such a small and cheap piece of kit. It still has major problems with accuracy, but is starting to find a niche in applications where speed, portability and long sequence reads are required. Here's a nice piece from a fan of the technology that has a bit of history and an appraisal of where it stands in 2016:

Comment Re:Where did they find the changes? (Score 1) 75

30x is generally considered adequate for variant calling from routine whole genome sequencing using standard Illumina technology, which has a reasonable error rate. But this figure (30 reads covering each base) is just the average of a Poisson distribution - according to Illumina 'the data would be expected to fall to 15x or below about 0.2% of the time', so there will always be some poorly covered bases where we can't confidently call variants.

The biology can also make things interesting - e.g. mosaicism and copy number variations can mean that there are interesting variants at low allelic ratios (i.e., much lower than the 50% you'd expect from a heterozygous change). Cancer is a major challenge, partly because the tumour may be mixed (effectively diluted) with normal tissue (e.g. from blood) reducing our ability to detect purely somatic changes confined to the cancer, and also because of heterogeneity (many, even most, somatic mutations are not in every cell of the tumour). Because of this, tumours are routinely sequenced at higher depth than normal 'germline' DNA by the UK 100k genome project (and others).

Comment Re:Neither (Score 4, Funny) 329

Once upon a time you might have written you prefer quality British-made tools, but they must be pretty thin on the ground now. I have an excellent Norbar torque wrench (Norbar apparently dates back to World War 2, when they made tools for the Merlin aero engine). A bit of Googling suggests that the wonderfully named 'King Dick Tools' are still making stuff here. I now have to go out and buy one of their products, partly to support British industry, but mainly so I can brandish a tool with 'King Dick' written on it.

Comment Re:Where did they find the changes? (Score 1) 75

This project does whole genomes. Even at commercial rates, a 30x depth whole genome is only 2-3x more expensive than an equivalent exome (the difference may be smaller on the scale they are doing this, and sequencing is probably getting cheaper more quickly than target capture, narrowing the gap further). Genomes also give more even coverage at similar depth (capture bias means that some regions are never represented well in exomes, and it's possible to miss exonic mutations that are supposedly covered by the probe set). They are also looking to the future - the aim is to put the infrastructure in place so that genome sequencing can be used routinely by the NHS, they want to boost the UK genomics industry, and they'll have a very large well-documented data set that can be mined in the future.

Comment Re:Good luck ... (Score 1) 75

And now a company will patent her genes, and every insurance company will call this a pre-existing condition and deny treatment for anything related to this or its treatment.

This is a publicly funded project in the UK, which has universal healthcare free at the point of delivery (the NHS). Any IP will be owned by Genomics England, a company owned by the UK Government. They intend to set up licensing agreements with the commercial sector on 'favourable terms'. These terms aren't precisely defined, at least publicly, and I imagine the drug and medical testing companies (who must pay to join a consortium with Genomics England if they want to work with them) may have a different definition of 'favourable' to the IP holders! The intention is presumably to make sure that the NHS doesn't get screwed in the process, but we'll see how this works out in practice. The Conservative Government has something of a conflict of interest between wanting to spend as little as possible on the NHS, while also promoting the UK pharma and genomics industry.

Comment Re:So that most of the world gets an idea... (Score 1) 274

I think the summary could do a better job at reporting news and use SI units -- avoiding such odd ones like a "pint", which are different in the various English-speaking countries to start with.

1 Unit = 10 ml pure alcohol. The smallest spirit measure used in the UK is a 25 ml single shot, equivalent to 1 Unit of a 40% v/v spirit. A 175ml medium glass of a 12% wine will give you just over 2 Units, and a 568 ml UK pint of a 3.5% beer nearly as much. A lot of beer is stronger than this, though - a 5.5% brew will give you over 3 Units per pint.

Comment Oh what times we live in! (Score 2) 174

This must be the most momentous, earth-shattering event since Instagram allowed rectangular photos! My predictions for 2016:

- Snapchat snaps to be viewable for 6 months after opening.
- Vine clip limit extended to 90 minutes.
- Dice completes gradual 'stealth beta' transformation of Slashdot.
- Civilization altering asteroid strike leaves Usenet newsgroups as most important social media.

Comment Re:Great event! (Score 1) 420

One exception may be certain parts of the diary that have been published in 1986. Back then, copyright law in several European countries protected a work for 50 years after its first publication instead of until 70 years after the author's death.

That's interesting. I'd assumed that, since the 80s Critical Edition made available Anne Frank's original versions (her diary and her own later edit), they could be extracted and re-published even if there were some merit in the Foundation's case about Otto Frank's contribution to the standard edition. But of course this wouldn't be the case where publication + 50 applies (in which countries?). The other thing worth noting is that under death of author + 70 rules, no current English translation is out of copyright, and won't be for a long time:

Comment Re:Is that the new Netiquette? (Score 3, Informative) 216

Get a job offer, respond angrily for no reason in particular and start harrassing the company who offered the job?

There was no job offer - 'join the team' is poor phrasing from Tim Cushing at Techdirt, in an article that's more distorted and melodramatic than the piece he's complaining about (which doesn't seem particularly angry). The publisher was approached by Google about selling their books via Play. The publisher declined, and pointed out that Google was at the same time making a profit from linking to pirated copies of the publisher's books in its search results. The publisher doesn't seem terribly well informed about how this whole Internet thing operates, but Techdirt's hyperventilating clickbait isn't exactly a model of clarity and accuracy either.

Comment Last Christmas (Score 1) 90

It's all fun and games until someone has a few too many at the NORAD Christmas party, loads the Santa data into the wrong terminal, and the WOPR identifies Dasher, Dancer, Prancer, Vixen, Comet, Cupid, Donner, and Blitzen as an incoming salvo of ICBMs from Murmansk.

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