Is it even possible to retroactively change the terms of a software license like that? Or did the new license only apply to new versions of the software?
Even before he went completely off the rails, the author had this weird thing where the user had to click to agree with the CURRENT version of the licence (which he could change at any time) every time the package was run, or else create a text file in a specified format (which the software would check on startup) where they promised always to abide by the latest licence and basically be his bitch. Whether this sort of nonsense is actually legal is another thing, of course.
It's a BMC journal, born in the Web age - it didn't exist in the 70s. But there may well be other software that's no longer available even in the lifetime of the journal just through link rot (which is why they encourage authors include a copy of the software and ideally the source as supplementary material).
That was my first, second and third thought. I don't generally bother with themes as such, but Classic Theme Restorer is what has kept me from switching to Palemoon or Seamonkey as it currently provides the best of both worlds - access to the huge library of Firefox plugins and the occasional useful innovation in the core browser, with an interface I can make look like a subtly updated 3.x (for me the high point of FF interface design). CTR is an extension rather than a theme, but I assume it hooks into the same code as 'Complete Themes' to do its magic (does anyone know for sure?) If it's unaffected by the changes, or if the same thing can be done by whatever new mechanisms the Mozilla developers put in place, then I'm likely to stay with FF. But if it's permanently broken and nothing takes its place, then the alternatives are going to look pretty attractive. CTR has been downloaded a couple of million times, and has over 400,000 active users, so I'm not likely to be the only one making a switch. The range of plugins and the ability to customise are what make Firefox still relevant in the age of Chrome - developers mess with these features at their peril!
SNP genotyping can still be useful for detecting losses or duplications of large parts of a chromosome ("structural" variations)
Maybe you are just being lazy with your terminology, but SNP genotyping, by definition, does not look for structural variations. SNP == single nucleotide polymorphism. There are separate arrays to look for these variations, but they are not SNP arrays.
You can certainly use SNP arrays to look at losses, duplications, and copy number changes in general - this is done routinely. Full SNP array data gives you not just variant calls, but also signal intensity etc. for each probe. You can't look directly at other forms of structural variation like translocations and inversions, although it may be possible to pick up focal copy number changes at the breakpoints.
That was really just a comment for biology geeks about the kind of data they provide. With a true raw file, you can get more out of SNP array data (e.g. genomic copy number). The 23andMe pricing is pretty keen, though, perhaps only about double what what you'd pay an academic service provider to run a SNP array of similar size (you'd get full raw data, but would have to do the DNA extraction and data interpretation yourself). An exome costs about 10x the price of the cheapest SNP array, and a whole genome maybe double the exome price (more if you want high depth of coverage), so I agree that SNP arrays still look good for some applications. There's more than enough data on the 600k 23andMe array to run into the multiple testing problem if you aren't careful with the stats! 23andMe themselves only report on a very small fraction of the variants, but the rest of the calls are available in the 'raw' output.
23andMe use SNP arrays (custom Illumina BeadChips) rather than NGS at the moment. The 'raw' data they supply isn't really raw at all, but a processed list of several hundred thousand variant calls:
There's the small chance the BBC could cease to exist, of course, but then the world would have way bigger problems than a few of us Brits not being able to rewatch Doctor Who box sets.
There's a rather larger chance the BBC will not exist in its current form in the medium term, especially given some of the noises the Tory government are making. But that's not the only issue. From the T&Cs:
'We cannot guarantee that you will be able to stream or re-download Content that's in your BBC Store account forever. Where our right to make content available has expired, you will no longer be able to stream or download that content from your BBC Store account. We'll try not to take down expired content without first notifying you that it is due to expire, so that you have the opportunity to download and playback the content through the Store Download Manager.'
If your 'purchase' is no longer available from the store, downloaded content presumably only lasts as long as the device does.
Good Lord, is that the first useful addition to the core browser in the last 5 years? Looks like I'll be less well-informed about the world from now on, though: https://xkcd.com/1280/
Recognizing that a particular genome contains sequences related to heart disease or lung cancer in no way makes it identifiable or linked to a particular person.
It's the other way around. Here you already know the identity of the person and their genome sequence, and are trying to work out if that genome is present in a database of genomes devoted to, say, heart disease, implying that this person (or perhaps a family member) has the condition. Although the 'beacon' databases that the attack targets release only small pieces of anonymous data, the results of multiple queries can be combined to figure out if the database contains the genome of interest.
This is just another scare mongering story, probably clickbait... nothing to see here, please move along.
I guess the idea is you don't have to wait for a response from the author, who might now be working in a top secret underground facility with no contact with the outside world / driven insane by the terrible implications of their latest discovery / not inclined to honour requests from ignorant fools without journal subscriptions / abducted by North Korea to work on the Dear Leader's superweapon / chained to the bench by their psychotic head of department with orders to produce another Nature manuscript if they ever want to see daylight again (this is quite likely) / working in Starbucks after the grant ran out (this is also quite likely) / doing a postdoc...in Belgium / used to regarding all unsolicited email from strangers as spam (this is almost certain) / on holiday (well, maybe not the last one). This way anyone who subscribes can 'sort you out' with an illegal black market pdf, possibly within minutes if this ever catches on.
No, it's whole genome (though most of the 'actionable' variants will be exonic and coding). If you have sequencing and computational capacity to burn, then whole genome can be very fast (and no need to mess around with an exome enrichment hybridisation). For centres without this capacity, it probably makes sense to do an exome and/or a targeted NGS panel containing only the genes where variants are diagnostically or prognostically valuable, or are actionable drug targets. Exomes on their own aren't always ideal if you're interested in specific genes rather than discovery, since coverage can be uneven, so some centres do both exomes and targeted panels. Whole genomes at reasonable depth have more even coverage.
Always interesting to hear Freeman Dyson, but can't help thinking The Register asked for an interview just for the climate quotes - both the interviewer and the current editor are climate change deniers, and The Reg is shamelessly used to push these views.
I always assume I am always logged by some alphabet agency and added to some bad-list for checking out the very cool stuff at cryptome.org throughout the years...
Good luck TLA, I'm behind SEVEN PROXIES whenever I access Cryptome.
Yes, it was used for the very first (British) edition, as were his black and white illustrations (the paintings were added in later printings) and his dragon motif on the board underneath the dust cover. In the UK there were only minor issues - in one of his letters from 1937 Tolkien is concerned about whether the original dust jacket illustration was too complex and had too many colours to print - the publisher went with his suggestion to replace the red sun with a white circle (restored in more recent editions). Tolkien certainly had problems with jackets and covers in other countries, including the US - some had random fantasy designs with no connection to the book (the first official US paperback's infamous 'emu and bulbous fruit' cover was especially bad).
He also did the maps, endpapers and what I think are still by far the best illustrations for The Hobbit. These were in the edition I first read as a child, and it's always disappointing to pick up a version that doesn't have the painting of Smaug on the hoard, or the drawings of the mountain path, Laketown and Beorn's hall. There's a nice selection of Tolkien's art, including the Hobbit illustrations, here:
Slashdot Mirror
I suffer this problem have having books topple. Where would I find an infinite shelf? Is that something they sell at Ikea?
You'll probably find it somewhere on here, which is my new favourite web page:
http://bookshelfporn.com/
Thank me later.
Why does anyone require 'due diligence' and fact-checking against insane violent assholes
This is why: https://en.wikipedia.org/wiki/...
I just did. Alas, I do not wish to download anything that only offers a so-called "web installer".
You don't have to. The offline installers are linked from the 'Download' dropdown menu right there on their home page.
Is it even possible to retroactively change the terms of a software license like that?
Or did the new license only apply to new versions of the software?
Even before he went completely off the rails, the author had this weird thing where the user had to click to agree with the CURRENT version of the licence (which he could change at any time) every time the package was run, or else create a text file in a specified format (which the software would check on startup) where they promised always to abide by the latest licence and basically be his bitch. Whether this sort of nonsense is actually legal is another thing, of course.
It's a BMC journal, born in the Web age - it didn't exist in the 70s. But there may well be other software that's no longer available even in the lifetime of the journal just through link rot (which is why they encourage authors include a copy of the software and ideally the source as supplementary material).
That was my first, second and third thought. I don't generally bother with themes as such, but Classic Theme Restorer is what has kept me from switching to Palemoon or Seamonkey as it currently provides the best of both worlds - access to the huge library of Firefox plugins and the occasional useful innovation in the core browser, with an interface I can make look like a subtly updated 3.x (for me the high point of FF interface design). CTR is an extension rather than a theme, but I assume it hooks into the same code as 'Complete Themes' to do its magic (does anyone know for sure?) If it's unaffected by the changes, or if the same thing can be done by whatever new mechanisms the Mozilla developers put in place, then I'm likely to stay with FF. But if it's permanently broken and nothing takes its place, then the alternatives are going to look pretty attractive. CTR has been downloaded a couple of million times, and has over 400,000 active users, so I'm not likely to be the only one making a switch. The range of plugins and the ability to customise are what make Firefox still relevant in the age of Chrome - developers mess with these features at their peril!
'Meet hot singles with compatible MHC haplotypes in your area!'
'Want to make those brown eyes blue? Visit airoptix.com today!'
'With perfect matches to sample profiles from seven different crime scenes on file at the FBI, Better Call Saul!'
SNP genotyping can still be useful for detecting losses or duplications of large parts of a chromosome ("structural" variations)
Maybe you are just being lazy with your terminology, but SNP genotyping, by definition, does not look for structural variations. SNP == single nucleotide polymorphism. There are separate arrays to look for these variations, but they are not SNP arrays.
You can certainly use SNP arrays to look at losses, duplications, and copy number changes in general - this is done routinely. Full SNP array data gives you not just variant calls, but also signal intensity etc. for each probe. You can't look directly at other forms of structural variation like translocations and inversions, although it may be possible to pick up focal copy number changes at the breakpoints.
That was really just a comment for biology geeks about the kind of data they provide. With a true raw file, you can get more out of SNP array data (e.g. genomic copy number). The 23andMe pricing is pretty keen, though, perhaps only about double what what you'd pay an academic service provider to run a SNP array of similar size (you'd get full raw data, but would have to do the DNA extraction and data interpretation yourself). An exome costs about 10x the price of the cheapest SNP array, and a whole genome maybe double the exome price (more if you want high depth of coverage), so I agree that SNP arrays still look good for some applications. There's more than enough data on the 600k 23andMe array to run into the multiple testing problem if you aren't careful with the stats! 23andMe themselves only report on a very small fraction of the variants, but the rest of the calls are available in the 'raw' output.
23andMe use SNP arrays (custom Illumina BeadChips) rather than NGS at the moment. The 'raw' data they supply isn't really raw at all, but a processed list of several hundred thousand variant calls:
http://www.snpedia.com/index.p...
You can convert this into something standard like VCF, which most tools that deal with variants will read.
There's the small chance the BBC could cease to exist, of course, but then the world would have way bigger problems than a few of us Brits not being able to rewatch Doctor Who box sets.
There's a rather larger chance the BBC will not exist in its current form in the medium term, especially given some of the noises the Tory government are making. But that's not the only issue. From the T&Cs:
https://store.bbc.com/terms
'We cannot guarantee that you will be able to stream or re-download Content that's in your BBC Store account forever. Where our right to make content available has expired, you will no longer be able to stream or download that content from your BBC Store account. We'll try not to take down expired content without first notifying you that it is due to expire, so that you have the opportunity to download and playback the content through the Store Download Manager.'
If your 'purchase' is no longer available from the store, downloaded content presumably only lasts as long as the device does.
Good Lord, is that the first useful addition to the core browser in the last 5 years? Looks like I'll be less well-informed about the world from now on, though: https://xkcd.com/1280/
Recognizing that a particular genome contains sequences related to heart disease or lung cancer in no way makes it identifiable or linked to a particular person.
It's the other way around. Here you already know the identity of the person and their genome sequence, and are trying to work out if that genome is present in a database of genomes devoted to, say, heart disease, implying that this person (or perhaps a family member) has the condition. Although the 'beacon' databases that the attack targets release only small pieces of anonymous data, the results of multiple queries can be combined to figure out if the database contains the genome of interest.
This is just another scare mongering story, probably clickbait ... nothing to see here, please move along.
Judge for yourself - here's the original paper:
http://www.cell.com/ajhg/fullt...
Some flaws the audits missed were discovered a month ago, at least on Windows:
http://www.zdnet.com/article/t...
https://www.youtube.com/watch?...
I guess the idea is you don't have to wait for a response from the author, who might now be working in a top secret underground facility with no contact with the outside world / driven insane by the terrible implications of their latest discovery / not inclined to honour requests from ignorant fools without journal subscriptions / abducted by North Korea to work on the Dear Leader's superweapon / chained to the bench by their psychotic head of department with orders to produce another Nature manuscript if they ever want to see daylight again (this is quite likely) / working in Starbucks after the grant ran out (this is also quite likely) / doing a postdoc...in Belgium / used to regarding all unsolicited email from strangers as spam (this is almost certain) / on holiday (well, maybe not the last one). This way anyone who subscribes can 'sort you out' with an illegal black market pdf, possibly within minutes if this ever catches on.
Yes, he did invent the vacuum cleaner. You know, the one that makes that WHOOSHING noise.
No, it's whole genome (though most of the 'actionable' variants will be exonic and coding). If you have sequencing and computational capacity to burn, then whole genome can be very fast (and no need to mess around with an exome enrichment hybridisation). For centres without this capacity, it probably makes sense to do an exome and/or a targeted NGS panel containing only the genes where variants are diagnostically or prognostically valuable, or are actionable drug targets. Exomes on their own aren't always ideal if you're interested in specific genes rather than discovery, since coverage can be uneven, so some centres do both exomes and targeted panels. Whole genomes at reasonable depth have more even coverage.
Always interesting to hear Freeman Dyson, but can't help thinking The Register asked for an interview just for the climate quotes - both the interviewer and the current editor are climate change deniers, and The Reg is shamelessly used to push these views.
And as a gesture of goodwill, they've also left him a large wooden horse with a bow tied around it outside the embassy.
I always assume I am always logged by some alphabet agency and added to some bad-list for checking out the very cool stuff at cryptome.org throughout the years...
Good luck TLA, I'm behind SEVEN PROXIES whenever I access Cryptome.
http://www.apex-magazine.com/i...
I know this story pissed off those guys who tried to rig the Hugo awards, but banning the whole genre seems a bit extreme.
Yes, it was used for the very first (British) edition, as were his black and white illustrations (the paintings were added in later printings) and his dragon motif on the board underneath the dust cover. In the UK there were only minor issues - in one of his letters from 1937 Tolkien is concerned about whether the original dust jacket illustration was too complex and had too many colours to print - the publisher went with his suggestion to replace the red sun with a white circle (restored in more recent editions). Tolkien certainly had problems with jackets and covers in other countries, including the US - some had random fantasy designs with no connection to the book (the first official US paperback's infamous 'emu and bulbous fruit' cover was especially bad).
Tolkien's cover for the Hobbit was used in the original and many more recent editions:
http://tolkiengateway.net/wiki...
He also did the maps, endpapers and what I think are still by far the best illustrations for The Hobbit. These were in the edition I first read as a child, and it's always disappointing to pick up a version that doesn't have the painting of Smaug on the hoard, or the drawings of the mountain path, Laketown and Beorn's hall. There's a nice selection of Tolkien's art, including the Hobbit illustrations, here:
http://tolkiengateway.net/wiki...
TFS only has one image
It's one of these magic new interweb things. You click the arrows at the sides and different pictures appear, like in the Mirror of Galadriel.