If Oxford Nanopore lives up to their hype, we can expect the price of instruments to fall dramatically. Their technology is supposedly very scalable, with the cheapest gadget packaged as a self-contained disposable $900 (!) USB stick sequencer:
This isn't genome level, as it will 'only' do a few hundred megabases before it burns out, but the workhorse instruments will use many more replaceable nanopores in parallel, packaged in rackable server-like enclosures.
We may well reach a point where it becomes cheaper and easier to run off a whole genome than to do more than a handful of gene-specific assays.
For the human genome, where the reference sequence is already known, the shorts reads can simply be aligned to the genome with free software in a relatively short time on a decent PC, so the cost of the basic analysis is currently less than that of the sequencing (though on an average workstation class computer the time required for alignment, finishing and variant calling may well be longer than the sequencing run!). The linked article is talking about the more nebulous but obviously greater cost of doing a bunch of research on large genomic data sets to look for disease associations and drug targets.
Why should a coal miner, or perpetual student, subsidise the education of some city lawyers and bankers?
I'm descended from coal miners. They were people who cared about education; they built libraries in their working men's halls, organised festivals of music and culture, and wanted the best for their children. I think they would have been delighted to know that free university education was, for a few decades at least, available to any of their descendents who were able to take advantage of it. I think they would have been deeply disappointed that the idea of higher education as a public good, which allowed young people to develop their full potential without fear of debt, would soon be replaced by a system of career mortgages (to add to the huge housing mortgages that graduates will now also be paying).
We've played a pretty nasty trick on the current generation. Those of us who received free higher education did so in the expectation that our taxes would fund the next generation of students (and since we had degrees, we'd probably be earning higher salaries and paying more taxes). But it turns out we'll (supposedly) be able to get away with not paying for them after all, since they'll now have to cover their fees themselves. Hurrah for us!
'One change will immediately be instituted by Microsoft. "Currently students attend English universities yet they do not pay tuition. This is ridiculous. If students in the U.S. pay $50,000 to attend Harvard, Yale or Stanford, British students should do the same to attend Oxbridge." What about those students who cannot afford to pay such a high level of tuition? Gates responded, "Look, I am not totally heartless. Microsoft will be introducing its lifetime earnings program. They can attend any British university for free as long as they agree to pay us 20 percent of their annual earnings for the rest of their lives. I'm even willing to offer a one year moratorium after graduation."'
Their concern over the totally inflated number of $500K/year in administrative costs is sickening.
If anything, translating this to a $500k admin cost grossly underestimates the impact on research. Many types of work will become completely unworkable in California, if TFA is accurate:
"Under the newly proposed bill, a person's genetic information may only be accessed by individuals specifically named on a consent form, and only for purposes written on the form. Genetic information along with the original samples must be destroyed once their specified purposes are fulfilled."
We routinely run genetic tests, all the way up to whole exomes, on tumour and normal samples from a collection donated by thousands of different patients (anonymous to us). Most ot the people curently working in our lab (not to mention collaborators in other labs) had not even joined when the bulk of the samples were collected. It would be completely impractical to seek fresh consent from every relevant patient whenever a new researcher needed to run a test or access a piece of data. It would be a tragic waste to destroy data and precious samples prematurely (and usually against the wishes of the donors, who typically want us to do all we can with the material).
Far from being worried about 'lost profits', many researchers share your concern about gene patents (and very few profit from them directly!). But this is not the way to the address the problem - we need reform of the patent system, not unduly restrictive 'DNA privacy' laws.
It just kills me that I wont get a copy of my data.
Usually you'll be anonymous to the people with access to the raw exome data, and there's probably no mechanism for feeding it back to a named donor. This type of research will also be subject to a strict legal and ethical framework which will not permit the researchers to act as providers of genetic tests to named individuals. If you want an exome you'll probably have to get it done privately - should be about the price of a mid-range laptop right now, with whole genomes falling into this range within a couple of years. How useful it will actually be to you at this point is unclear, unless you happen to have a condition with a simple and well-defined genetic association. Note also that comparisons with anyone else's data will not be possible if DNA privacy laws become so strict that public databases can't be created in the first place...
Allow me to demonstrate, Mr Bond. When I push this button, 50,000 tons of compressive force will ensure that your body is as neatly pressed as your Savile Row suit.
The subtitle also has a stylistic difference from the article text--it has no comma or other punctuation. Every sentence of comparable length in the rest of the article (around 15 of them) has a comma, colon, dash, etc., with only one exception, supporting my "someone else wrote the title and subtitle" theory, perhaps someone more interested in page views than providing information.
This is why I love Slashdot - we'd rather spend ages analysing a secondary popular science article to death than talking about the interesting findings of the primary research! The author and/or editor deserve a break for trying to engage the attention of a general audience about a piece of significant work, and succeed in presenting the key points in relatively non-technical language. Both 'mistake' and 'error' are in any case used quite frequently by biologists when discussing mutations - a quick pubmed search will find many examples in the scientific literature (e.g. http://www.ncbi.nlm.nih.gov/pubmed/14616055 - this does not imply that the DNA polymerase is intelligent!).
Speaking of 'mistakes', this research discovered an interesting error in the human genome reference sequence. It turns out that the duplication event was previously obscured by 'mis-assembly' of the closely related copied sequences (the SRGAP2 gene was copied so recently in evolutionary terms that the copies hadn't diverged enough to be easily distinguishable). The researchers did some of their own sequencing using DNA from a 'hydatidiform mole' ( http://en.wikipedia.org/wiki/Hydatidiform_mole ), a non-viable pregnancy that only contains genetic material from the father - the lack of confounding allelic variation makes it easier to get clear cut results.
I couldn't possibly have listed all the languages and technologies I have done work with. But here's a sample.... BASIC, C, Pascal, Ada, COBOL, Perl, CGI, vbscript/asp, scripting (*ux shells mostly), VB, most recently PHP. I am only interested in general purpose work, utilities, hell I don't even know yet exactly where I will go with this.
I'm sure you'll enjoy checking out Python and Ruby etc., as suggested elsewhere in these comments, but with that background I'd also suggest taking a fresh look at Perl. Not the ugly stuff bodged together from fragments of 'Matt's scripts' linked with carelessly-constructed chunks of Perl 4-style code that was popular in the 90s, nor the permanently experimental Perl 6, but Perl 5 written in a modern, elegant style (no, really!) with decent coding standards and full use of current language features:
However, I don't see why I shouldn't be able to put the same content on another type of reader completely outside of the kindle system, but that would probably be considered another argument.
Well, this is one reason (maybe the main reason) why ebook DRM still exists - not to benefit the authors or publishers, but to lock buyers into the Kindle system (or equivalent). The locks are easy to pick, of course, and with even mainstream sites like Wired linking to DRM stripping guides, you have to wonder how long this will be sustainable:
This makes removal so easy and seamless, you almost (as with DVD DRM) forget it exists. Now that Amazon has such a strong market position, perhaps they'll decide this minimal 'protection' has served its purpose and get rid of it, just as Apple did with audio DRM when iTunes had blown away the competition.
Xfce is another good choice, though. If you start with a standard Ubuntu and just add the xfce4 package rather than installing Xubuntu, you end up with something quite similar to Ubuntu before Unity - most of the Gnome apps work well under xfce, and you get the standard default selection of software rather than 'lightweight' alternatives (LibreOffice instead of Abiword/Gnumeric, etc.).
Without MATE, Linux Mint 12 wouldn't even be an option for me (I'd stick with 11).
I might say the same for Ubuntu 12.04 (though to be fair, I could also live with Xfce). I just installed MATE 1.2 on the latest 12.04 beta and it works like a charm, as here:
For my money, Gnome 2/MATE is still the best available desktop for Linux. I've tried the other approaches to taming Gnome 3 (Cinnamon, the classic 'fallback mode' panel, even Unity) and all currently seem lacking in comparison, with more limited features, or lower performance on resource-limited systems, or (in the case of Unity) annoying design choices. The benefits to developers of building a desktop on the Gnome 3 foundation (ease of maintenance, etc.) are all very well, but as an end-user, I'm going to go for the more responsive, fully-featured alternative. The situation may be different in a year or two, but right now MATE remains my top choice.
MATE is independent of Mint and has its own team (Clem is a member, but Mint ddidn't start and doesn't run the project). The MATE team is small, but their goals are much more modest than Gnome's - they (thankfully!) have no ambitions to design a new 'desktop paradigm'.
Yea, okay, looks like a dead-end. I'm sticking with xfce.
A little more Googling might lead you to the official site, whiich has a support forum (in English), and actively updated repositories for various distributions:
Excellent! You are eminently qualified to invest in my company, which harnesses this technology to generate power from a workable perpetual motion machine!:
It's an active fork of Gnome 2, and is included in the current Mint distribution, though you can get a more recent version from the developers' repository (which also supports Debian and Ubuntu):
The Photosniper was my first thought. Though it's often thought of as a 'KGB' camera, they were made mostly for the civilian market, particularly (like the modern equivalent) for wildlife shots. They were exported to western Europe, and I remember seeing them in the catalogues of mainstream UK camera dealers in the 80s. Apparently they're surprisingly practical, despite the heavy lens and Zenit SLR:
Camera geeks might want to check out the very first version, which was designed in the 30s, came with a really nice wooden rifle stock, and used a FED I (Soviet copy of the Leica) as its camera:
Baen has been doing well with that model for over a decade now, the other publishers don't care. Even when Baen was literally the only company making any money on ebooks none of the other publishers would even give that model a second look. If it's not loaded down with DRM and badly overpriced, they just don't see the advantage.
Oddly enough, HarperCollins (one of the publishers warned by the DoJ) started Angry Robot, a rather Baen-like print and ebook imprint, as a sort of skunkworks project back in 2009. It probably makes your point that they dropped it the following year, but Angry Robot continues as an independent and is well worth checking out for interesting F&SF, sold as DRM-free epubs at reasonable prices:
The Inverted World is fantastic and the man can actually write...Also, Pavane or Kiteworld by Keith Roberts.
Priest is a good choice ('A Dream of Wessex' and 'The Glamour' were excellent), and I was also thinking of Keith Roberts. The alternate history 'Pavane' is great (up there with 'The Man in the High Castle') and almost well-known enough to be mainstream. 'Kiteworld' is just as good but more obscure, and currently published (along with much of his output) by a smaller press:
It's a pity that the other Kiteworld stories ('Tremarest', which I've never seen, and 'Drek Yarman', a short novel that was serialised in Spectrum SF) remain uncollected - someone should put together a definitive anthology. The subtly sketched background is an ingenious spin on the usual post-apocalyptic scenario. Manned observation kites ('Cody rigs', a reference to Samuel Cody) are used as a sort of cargo-cult early warning system to defend the Realm from 'demons', as nuclear weapons are now remembered. But, as with Le Guin, it's the quality of writing rather than the SF frame that really shines.
Slashdot Mirror
KDE4 caused me to switch to Gnome... and then unity came along and I'm not sure where to go next!
Here?: http://mate-desktop.org/
e.g.:
http://www.howtogeek.com/110052/how-to-install-the-mate-desktop-go-back-to-gnome-2-on-ubuntu/
http://www.webupd8.org/2012/04/mate-desktop-12-released-install-it-in.html
Will you be using the same selection criteria as this previous space-related 'media spectacle'?:
http://en.wikipedia.org/wiki/Space_Cadets_(TV_series)#Audition_process
'You seem to be forgetting that nobody has ever been able to "cure" a virus ever. EVER.'
Antiviral treatment of chronic Hep C infections has a 50-80% cure rate:
http://www.nhs.uk/Conditions/Hepatitis-C/Pages/Treatment.aspx
Yes, Larry David is very funny but I find it very easy to open a plastic package with a mini-box knife. X-Acto knives cost too much.
Jeff: Just get an X-Acto knife...
Susie: There you go.
Jeff: ...or a box-cutter, ok?
Larry: What? A box-cutter? Who am I, Mohamed Atta? I've got to, I've got to buy a box cutter? I mean it's crazy.
For a handy guide to opening clamshell packaging using standard kitchen implements, see this informative video by Larry David:
http://www.youtube.com/watch?v=HubZInAs0-A
If Oxford Nanopore lives up to their hype, we can expect the price of instruments to fall dramatically. Their technology is supposedly very scalable, with the cheapest gadget packaged as a self-contained disposable $900 (!) USB stick sequencer:
http://www.wired.com/wiredenterprise/2012/03/oxford-nanopore-sequencing-usb/
This isn't genome level, as it will 'only' do a few hundred megabases before it burns out, but the workhorse instruments will use many more replaceable nanopores in parallel, packaged in rackable server-like enclosures.
We may well reach a point where it becomes cheaper and easier to run off a whole genome than to do more than a handful of gene-specific assays.
For the human genome, where the reference sequence is already known, the shorts reads can simply be aligned to the genome with free software in a relatively short time on a decent PC, so the cost of the basic analysis is currently less than that of the sequencing (though on an average workstation class computer the time required for alignment, finishing and variant calling may well be longer than the sequencing run!). The linked article is talking about the more nebulous but obviously greater cost of doing a bunch of research on large genomic data sets to look for disease associations and drug targets.
Why should a coal miner, or perpetual student, subsidise the education of some city lawyers and bankers?
I'm descended from coal miners. They were people who cared about education; they built libraries in their working men's halls, organised festivals of music and culture, and wanted the best for their children. I think they would have been delighted to know that free university education was, for a few decades at least, available to any of their descendents who were able to take advantage of it. I think they would have been deeply disappointed that the idea of higher education as a public good, which allowed young people to develop their full potential without fear of debt, would soon be replaced by a system of career mortgages (to add to the huge housing mortgages that graduates will now also be paying).
We've played a pretty nasty trick on the current generation. Those of us who received free higher education did so in the expectation that our taxes would fund the next generation of students (and since we had degrees, we'd probably be earning higher salaries and paying more taxes). But it turns out we'll (supposedly) be able to get away with not paying for them after all, since they'll now have to cover their fees themselves. Hurrah for us!
This bit doesn't look quite so funny now:
'One change will immediately be instituted by Microsoft. "Currently students attend English universities yet they do not pay tuition. This is ridiculous. If students in the U.S. pay $50,000 to attend Harvard, Yale or Stanford, British students should do the same to attend Oxbridge." What about those students who cannot afford to pay such a high level of tuition? Gates responded, "Look, I am not totally heartless. Microsoft will be introducing its lifetime earnings program. They can attend any British university for free as long as they agree to pay us 20 percent of their annual earnings for the rest of their lives. I'm even willing to offer a one year moratorium after graduation."'
Their concern over the totally inflated number of $500K/year in administrative costs is sickening.
If anything, translating this to a $500k admin cost grossly underestimates the impact on research. Many types of work will become completely unworkable in California, if TFA is accurate:
"Under the newly proposed bill, a person's genetic information may only be accessed by individuals specifically named on a consent form, and only for purposes written on the form. Genetic information along with the original samples must be destroyed once their specified purposes are fulfilled."
We routinely run genetic tests, all the way up to whole exomes, on tumour and normal samples from a collection donated by thousands of different patients (anonymous to us). Most ot the people curently working in our lab (not to mention collaborators in other labs) had not even joined when the bulk of the samples were collected. It would be completely impractical to seek fresh consent from every relevant patient whenever a new researcher needed to run a test or access a piece of data. It would be a tragic waste to destroy data and precious samples prematurely (and usually against the wishes of the donors, who typically want us to do all we can with the material).
Far from being worried about 'lost profits', many researchers share your concern about gene patents (and very few profit from them directly!). But this is not the way to the address the problem - we need reform of the patent system, not unduly restrictive 'DNA privacy' laws.
It just kills me that I wont get a copy of my data.
Usually you'll be anonymous to the people with access to the raw exome data, and there's probably no mechanism for feeding it back to a named donor. This type of research will also be subject to a strict legal and ethical framework which will not permit the researchers to act as providers of genetic tests to named individuals. If you want an exome you'll probably have to get it done privately - should be about the price of a mid-range laptop right now, with whole genomes falling into this range within a couple of years. How useful it will actually be to you at this point is unclear, unless you happen to have a condition with a simple and well-defined genetic association. Note also that comparisons with anyone else's data will not be possible if DNA privacy laws become so strict that public databases can't be created in the first place...
Allow me to demonstrate, Mr Bond. When I push this button, 50,000 tons of compressive force will ensure that your body is as neatly pressed as your Savile Row suit.
Funny, all the watches I've seen have a strap that goes around your wrist to hold the watch on, which is not a bad idea if you think about it.
He's already thought of that. Guess what his next tattoo is going to be?
The subtitle also has a stylistic difference from the article text--it has no comma or other punctuation. Every sentence of comparable length in the rest of the article (around 15 of them) has a comma, colon, dash, etc., with only one exception, supporting my "someone else wrote the title and subtitle" theory, perhaps someone more interested in page views than providing information.
This is why I love Slashdot - we'd rather spend ages analysing a secondary popular science article to death than talking about the interesting findings of the primary research! The author and/or editor deserve a break for trying to engage the attention of a general audience about a piece of significant work, and succeed in presenting the key points in relatively non-technical language. Both 'mistake' and 'error' are in any case used quite frequently by biologists when discussing mutations - a quick pubmed search will find many examples in the scientific literature (e.g. http://www.ncbi.nlm.nih.gov/pubmed/14616055 - this does not imply that the DNA polymerase is intelligent!).
Speaking of 'mistakes', this research discovered an interesting error in the human genome reference sequence. It turns out that the duplication event was previously obscured by 'mis-assembly' of the closely related copied sequences (the SRGAP2 gene was copied so recently in evolutionary terms that the copies hadn't diverged enough to be easily distinguishable). The researchers did some of their own sequencing using DNA from a 'hydatidiform mole' ( http://en.wikipedia.org/wiki/Hydatidiform_mole ), a non-viable pregnancy that only contains genetic material from the father - the lack of confounding allelic variation makes it easier to get clear cut results.
I couldn't possibly have listed all the languages and technologies I have done work with. But here's a sample.... BASIC, C, Pascal, Ada, COBOL, Perl, CGI, vbscript/asp, scripting (*ux shells mostly), VB, most recently PHP. I am only interested in general purpose work, utilities, hell I don't even know yet exactly where I will go with this.
I'm sure you'll enjoy checking out Python and Ruby etc., as suggested elsewhere in these comments, but with that background I'd also suggest taking a fresh look at Perl. Not the ugly stuff bodged together from fragments of 'Matt's scripts' linked with carelessly-constructed chunks of Perl 4-style code that was popular in the 90s, nor the permanently experimental Perl 6, but Perl 5 written in a modern, elegant style (no, really!) with decent coding standards and full use of current language features:
http://onyxneon.com/books/modern_perl/
http://perl-tutorial.org/
However, I don't see why I shouldn't be able to put the same content on another type of reader completely outside of the kindle system, but that would probably be considered another argument.
Well, this is one reason (maybe the main reason) why ebook DRM still exists - not to benefit the authors or publishers, but to lock buyers into the Kindle system (or equivalent). The locks are easy to pick, of course, and with even mainstream sites like Wired linking to DRM stripping guides, you have to wonder how long this will be sustainable:
http://www.wired.com/gadgetlab/2011/01/how-to-strip-drm-from-kindle-e-books-and-others/
This makes removal so easy and seamless, you almost (as with DVD DRM) forget it exists. Now that Amazon has such a strong market position, perhaps they'll decide this minimal 'protection' has served its purpose and get rid of it, just as Apple did with audio DRM when iTunes had blown away the competition.
save yourself the time and just install xubuntu (XFCE)
MATE is very quick and easy to install on Ubuntu, including 12.04:
http://www.howtogeek.com/110052/how-to-install-the-mate-desktop-go-back-to-gnome-2-on-ubuntu/
Xfce is another good choice, though. If you start with a standard Ubuntu and just add the xfce4 package rather than installing Xubuntu, you end up with something quite similar to Ubuntu before Unity - most of the Gnome apps work well under xfce, and you get the standard default selection of software rather than 'lightweight' alternatives (LibreOffice instead of Abiword/Gnumeric, etc.).
Without MATE, Linux Mint 12 wouldn't even be an option for me (I'd stick with 11).
I might say the same for Ubuntu 12.04 (though to be fair, I could also live with Xfce). I just installed MATE 1.2 on the latest 12.04 beta and it works like a charm, as here:
http://www.howtogeek.com/110052/how-to-install-the-mate-desktop-go-back-to-gnome-2-on-ubuntu/
For my money, Gnome 2/MATE is still the best available desktop for Linux. I've tried the other approaches to taming Gnome 3 (Cinnamon, the classic 'fallback mode' panel, even Unity) and all currently seem lacking in comparison, with more limited features, or lower performance on resource-limited systems, or (in the case of Unity) annoying design choices. The benefits to developers of building a desktop on the Gnome 3 foundation (ease of maintenance, etc.) are all very well, but as an end-user, I'm going to go for the more responsive, fully-featured alternative. The situation may be different in a year or two, but right now MATE remains my top choice.
MATE is independent of Mint and has its own team (Clem is a member, but Mint ddidn't start and doesn't run the project). The MATE team is small, but their goals are much more modest than Gnome's - they (thankfully!) have no ambitions to design a new 'desktop paradigm'.
Yea, okay, looks like a dead-end. I'm sticking with xfce.
A little more Googling might lead you to the official site, whiich has a support forum (in English), and actively updated repositories for various distributions:
http://mate-desktop.org/
tour de france played the Danish nation anthem when Contador won in 2009
Well, they did play the Spanish anthem when Andy Schleck won in 2010...
Should have studied more in physics ...
Excellent! You are eminently qualified to invest in my company, which harnesses this technology to generate power from a workable perpetual motion machine!:
http://www.lhup.edu/~dsimanek/museum/unwork.htm#cheng
If you liked Gnome 2, then MATE is an obvious choice:
http://mate-desktop.org/
It's an active fork of Gnome 2, and is included in the current Mint distribution, though you can get a more recent version from the developers' repository (which also supports Debian and Ubuntu):
http://wiki.mate-desktop.org/download
Third party rpms for Fedora 16 are now available too.
The Photosniper was my first thought. Though it's often thought of as a 'KGB' camera, they were made mostly for the civilian market, particularly (like the modern equivalent) for wildlife shots. They were exported to western Europe, and I remember seeing them in the catalogues of mainstream UK camera dealers in the 80s. Apparently they're surprisingly practical, despite the heavy lens and Zenit SLR:
http://userpage.fu-berlin.de/tobiko/fotosniper.html
Camera geeks might want to check out the very first version, which was designed in the 30s, came with a really nice wooden rifle stock, and used a FED I (Soviet copy of the Leica) as its camera:
http://tomtiger.home.xs4all.nl/fs-2/fs-2.html
Apparently Khrushchev was a fan, which may have been one reason why the factory introduced a mass-market SLR version in the 60s.
Baen has been doing well with that model for over a decade now, the other publishers don't care. Even when Baen was literally the only company making any money on ebooks none of the other publishers would even give that model a second look. If it's not loaded down with DRM and badly overpriced, they just don't see the advantage.
Oddly enough, HarperCollins (one of the publishers warned by the DoJ) started Angry Robot, a rather Baen-like print and ebook imprint, as a sort of skunkworks project back in 2009. It probably makes your point that they dropped it the following year, but Angry Robot continues as an independent and is well worth checking out for interesting F&SF, sold as DRM-free epubs at reasonable prices:
http://angryrobotbooks.com/
The Inverted World is fantastic and the man can actually write...Also, Pavane or Kiteworld by Keith Roberts.
Priest is a good choice ('A Dream of Wessex' and 'The Glamour' were excellent), and I was also thinking of Keith Roberts. The alternate history 'Pavane' is great (up there with 'The Man in the High Castle') and almost well-known enough to be mainstream. 'Kiteworld' is just as good but more obscure, and currently published (along with much of his output) by a smaller press:
http://www.wildsidebooks.com/search.asp?keyword=keith+roberts
It's a pity that the other Kiteworld stories ('Tremarest', which I've never seen, and 'Drek Yarman', a short novel that was serialised in Spectrum SF) remain uncollected - someone should put together a definitive anthology. The subtly sketched background is an ingenious spin on the usual post-apocalyptic scenario. Manned observation kites ('Cody rigs', a reference to Samuel Cody) are used as a sort of cargo-cult early warning system to defend the Realm from 'demons', as nuclear weapons are now remembered. But, as with Le Guin, it's the quality of writing rather than the SF frame that really shines.