Most tools for doing anything useful with a genome sequence expect an ascii-encoded text file. The reference assembly is usually distributed as a conventionally zipped or gzipped ascii file, which is about 900Mb compressed, and >3Gb uncompressed. Unlike the existing reference assembly, the Watson genome is diploid (has both his maternally and paternally inherited DNA), which equates to >6Gb of ascii-encoded data. This is more than will fit on a single-layer DVD, even without the Director's commentary! You could certainly get the whole thing on a single DVD in a compressed or 2-bit encoded format (2-bit encoding is used for certain applications - see my reply above), but for most purposes this would be less useful (data couldn't be accessed directly by most sequence analysis software).
But remember that (for the first time, and unlike the current reference assembly) these are diploid genomes, so you have to double those numbers. They're presumably stored as uncompressed ascii for convenience (so around 6Gb of data - maybe they should have used a dual-layer DVD!). However, 2-bit encoding is in fact used where space is at a premium (e.g. to fit a database derived from an entire genome into available RAM for BLAT or BLAST analysis). Here's the scheme used by BLAT:
With this encoding, you can conformatably create an appropriate database from the ~3Gb reference assembly and BLAT against it on a desktop PC with 1.5Gb RAM.
Of course if you start with a lossy WMA you'll presumably get the usual additional loss of quality in transcoding to another lossy format This is a similar quality penalty to what you get when circumventing Apple's DRM via the 'burn to CD and re-encode route', but a bit more convenient, and possibly starting from a higher quality file if MS follows Apple in making its DRM-free stuff high bitrate.
Of course if MS is serious about selling music to anyone except Zune users, they might offer an mp3 option, and then perhaps we'll see a bit of competition on price (if the EMI deal allows enough of a profit margin). Presumably any other competing download stores that do a similar deal with EMI will be selling mp3s, and some will probably be happy to operate with pretty slim margins. We might even see 3rd party AAC downloads (expect AAC support in new hardware to be pretty much universal by the end of the year if the EMI iTunes 'experiment' is a success).
5) They release the tracks as unprotected (but iPod-incompatible) WMA and find they don't sell any better, then claim that consumers aren't really interested in DRM-free tracks.
How about a Zune virus that strips the DRM from the tracks on the infected machine and 'squirts' itself to all the other Zunes within wireless range? Think about it, if such a virus were released today the number of infections could soar into double figures by the end of the decade!
...and deeply ironic that the Trust's supposed role is to 'work on behalf of licence fee payers, ensuring the BBC provides high quality output and good value for all UK citizens'. In what way does tightening an already onerous DRM scheme provide 'good value'? Have they actually met a single 'license fee payer' who thinks this is a good idea?
"It is simply a technical matter to extend this compiler to deal with the whole of C. I could then cross-compile from Pop11, Lisp, or any other language for which there is a C source version. At that point I would be able to produce massive neural nets that implement operating systems, word processors, compilers and the like. It would be relatively straight forward to compile Linux into a neural net. This opens up the possibility of doing research on massively large neural networks. We could then move away from our toy implementations and start examining useful systems. "
Imagine a Beow...[Error in universe.pl line 15x10^9: Division by zero]
'It's another thing entirely to take huge liberties with the characters and create fictitious events in order to justify these "new" characters. Some of the greatest drama in Return of the King was reduced to petty bickering between the main characters - in order to leave more room for the "special effects".'
Tolkien said something rather similar about an earlier (unfilmed) treatment of the story (letter #210, June 1958):
"He has cut the parts of the story upon which its characteristic and peculiar tone principally depends, showing a preference for fights".
and:
"I do earnestly hope that in the assignment of actual speeches to the characters they will be represented as I have presented them: in style and sentiment. I should resent perversion of the characters (and do resent it, so far as it appears in this sketch) even more than the spoiling of the plot and scenery."
This seems rather appropriate, too:
"Part I in general respects the line of narrative in the book, and retains some of its original coherence. Part II exemplifies all the faults of Part I ; but it is far more unsatisfactory, & still more so Part III, in more serious respects."
And this really says it all:
"The canons of narrative an in any medium cannot be wholly different; and the failure of poor films is often precisely in exaggeration, and in the intrusion of unwarranted matter owing to not perceiving where the core of the original lies."
I don't think Jackson made 'poor films', but they're a very long way away from Tolkien. The BBC Radio version got much closer to 'the core of the original' in a different medium.
Perhaps University should be the place where any intelligent net user should learn how to circumvent this sort of thing (an increasingly important academic skill!). Actually, it's pretty simple. All you need to do is [Your organization's Internet use policy restricts access to the rest of this comment at this time. Reason: The Websense category "Proxy Avoidance" is filtered]
It's also worth noting that there are very few individual dSLR models currently in use (even counting those badged differently depending on region and minor upgrades like the D70s), but many barely distinguishable short-lived P&S cameras - i.e., the choice in this market is so large and rapidly evolving that any single P&S model may not rank very highly, even if most users shoot this type of camera. I wonder what proportion of flickr users actually shoot dSLRs in general?
"First, if both dogs and marsupials can have a contageous, directly-transmissable cancer, then so can any species, through ANY mechanism that involves a transfer of cells."
If you want a really scary Michael Crichton scenario, the authors reference work done in the 60s (this isn't a new idea) on another possible contagious tumour that "can even be transmitted via mosquitoes". Luckily that one was in hamsters.
'You can do that in the lab by injecting tumor cells from one mouse into another and letting a new tumor form, however I haven't seen examples of this occuring naturally and in those experiments the mice need to either be from the same genetic background or immunosuppressed SCID mice.'
I didn't know this either, but according to the article: "CTVT was frequently used by cancer researchers to study tumor transplantation" (presumably in dogs) "until the development of inbred strains of rats and mice afforded syngeneic models" while "CTVT can be transplanted into immunocompetent animals of other canine species, such as foxes, coyotes, and jackals...as well as into immunodeficient mice" (but presumably not immunocompetent mice). Interestingly, the typical course of the disease in dogs is "an initial stage of rapid and progressive growth, which is typically followed by spontaneous regression 3 to 9 months later", so the animal eventually mounts an effective immune response (passive immunity can also be transmitted by serum from a recovered dog).
The problem is that in at least some countries this only applies until you reach your lifetime 'sending limit' (read the small print). Once this limit is reached (I think this is $2000 in the US, but only £500 at most in the UK) you have to give PayPal direct access to a bank account, losing the 'insulation' provided by your credit card. This is the thing I hate most about PayPal, and they aren't exactly up-front about it either (the help information about account 'verification' just has some vague language about the supposed benefits to the buyer, and nothing about the very real advantages to PayPay of being able to suck cash straight out of your bank account).
'Well I've used it on dozens of different DVD drives, on lots of different DVDs and it has worked most splendidly for me. So in short, IME, Yes. Though these days i use xine. And I hear mplayer is getting menu support.'
VLC certainly gives region-free playback with many RPC2 drives (including mine), and of course has no problem with the old RPC1 drives. I think it's only fairly recently that some manufacturers have started to go beyond the original RPC2 spec and prevent even raw access to the DVD when there's a region mismatch. AFAIK, this additional measure currently blocks anything short of a firmware upgrade if you're unfortunate to have one of the afflicted drives and want to play a disk from a different region (so xine, mplayer or anything else that uses libdvdcss won't work either). I don't know what proportion of current RPC2 drives are crippled in this way - anyone?
Slashdot Mirror
Most tools for doing anything useful with a genome sequence expect an ascii-encoded text file. The reference assembly is usually distributed as a conventionally zipped or gzipped ascii file, which is about 900Mb compressed, and >3Gb uncompressed. Unlike the existing reference assembly, the Watson genome is diploid (has both his maternally and paternally inherited DNA), which equates to >6Gb of ascii-encoded data. This is more than will fit on a single-layer DVD, even without the Director's commentary! You could certainly get the whole thing on a single DVD in a compressed or 2-bit encoded format (2-bit encoding is used for certain applications - see my reply above), but for most purposes this would be less useful (data couldn't be accessed directly by most sequence analysis software).
Yes, and because they already hold the patent they'll be able to do it by 1-Click Ordering!
But remember that (for the first time, and unlike the current reference assembly) these are diploid genomes, so you have to double those numbers. They're presumably stored as uncompressed ascii for convenience (so around 6Gb of data - maybe they should have used a dual-layer DVD!). However, 2-bit encoding is in fact used where space is at a premium (e.g. to fit a database derived from an entire genome into available RAM for BLAT or BLAST analysis). Here's the scheme used by BLAT:
http://genome.ucsc.edu/FAQ/FAQformat#format7
With this encoding, you can conformatably create an appropriate database from the ~3Gb reference assembly and BLAT against it on a desktop PC with 1.5Gb RAM.
Yes, it will:
http://www.apple.com/itunes/hottips/
Of course if you start with a lossy WMA you'll presumably get the usual additional loss of quality in transcoding to another lossy format This is a similar quality penalty to what you get when circumventing Apple's DRM via the 'burn to CD and re-encode route', but a bit more convenient, and possibly starting from a higher quality file if MS follows Apple in making its DRM-free stuff high bitrate.
Of course if MS is serious about selling music to anyone except Zune users, they might offer an mp3 option, and then perhaps we'll see a bit of competition on price (if the EMI deal allows enough of a profit margin). Presumably any other competing download stores that do a similar deal with EMI will be selling mp3s, and some will probably be happy to operate with pretty slim margins. We might even see 3rd party AAC downloads (expect AAC support in new hardware to be pretty much universal by the end of the year if the EMI iTunes 'experiment' is a success).
5) They release the tracks as unprotected (but iPod-incompatible) WMA and find they don't sell any better, then claim that consumers aren't really interested in DRM-free tracks.
How about a Zune virus that strips the DRM from the tracks on the infected machine and 'squirts' itself to all the other Zunes within wireless range? Think about it, if such a virus were released today the number of infections could soar into double figures by the end of the decade!
You can have any of the 4 different base pairs at each position, though, so each base is equivalent to 2 binary digits, e.g.:
.2bit format:
T = 00
C = 01
A = 10
G = 11
(the paired base on the other DNA strand doesn't add any information, of course, since its identity is specified by its partner).
In fact, 2 bit binary formats are commonly used to represent large DNA sequences in a compact way, as in UCSC's
http://genome.ucsc.edu/FAQ/FAQformat#format7
This makes (e.g.) whole human genome BLAT alignment searches manageable on a 32-bit PC with 1.5 Gb RAM (less once the server is up and running).
...and deeply ironic that the Trust's supposed role is to 'work on behalf of licence fee payers, ensuring the BBC provides high quality output and good value for all UK citizens'. In what way does tightening an already onerous DRM scheme provide 'good value'? Have they actually met a single 'license fee payer' who thinks this is a good idea?
It's a story about the Green Party. OF COURSE it has to be re-cycled!
'The saddest thing about this, is that it's not legal in the UK to rip CDs to MP3.'
/ gowers_review_intellectual_property/gowersreview_i ndex.cfms tm
This at least may well change quite soon, if the government acts on the Gowers Review:
http://www.hm-treasury.gov.uk/independent_reviews
http://news.bbc.co.uk/2/hi/entertainment/6214108.
He doesn't stop there, either:
http://archives.nesc.ac.uk/gcproposal-5/0080.html
"It is simply a technical matter to extend this compiler to deal with the
whole of C. I could then cross-compile from Pop11, Lisp, or any other
language for which there is a C source version. At that point I would be
able to produce massive neural nets that implement operating systems, word
processors, compilers and the like. It would be relatively straight forward
to compile Linux into a neural net. This opens up the possibility of doing
research on massively large neural networks. We could then move away from
our toy implementations and start examining useful systems. "
Imagine a Beow...[Error in universe.pl line 15x10^9: Division by zero]
wotU sAyn gr&dad? txt S cheapR if u PAYG!
'It's another thing entirely to take huge liberties with the characters and create fictitious events in order to justify these "new" characters. Some of the greatest drama in Return of the King was reduced to petty bickering between the main characters - in order to leave more room for the "special effects".'
Tolkien said something rather similar about an earlier (unfilmed) treatment of the story (letter #210, June 1958):
"He has cut the parts of the story upon which its characteristic and peculiar tone principally depends, showing a preference for fights".
and:
"I do earnestly hope that in the assignment of actual speeches to the characters they will be represented as I have presented them: in style and sentiment. I should resent perversion of the characters (and do resent it, so far as it appears in this sketch) even more than the spoiling of the plot and scenery."
This seems rather appropriate, too:
"Part I in general respects the line of narrative in the book, and retains some of its original coherence. Part II exemplifies all the faults of Part I ; but it is far more unsatisfactory, & still more so Part III, in more serious respects."
And this really says it all:
"The canons of narrative an in any medium cannot be wholly different; and the failure of poor films is often precisely in exaggeration, and in the intrusion of unwarranted matter owing to not perceiving where the core of the original lies."
I don't think Jackson made 'poor films', but they're a very long way away from Tolkien. The BBC Radio version got much closer to 'the core of the original' in a different medium.
You mean like this?
Perhaps University should be the place where any intelligent net user should learn how to circumvent this sort of thing (an increasingly important academic skill!). Actually, it's pretty simple. All you need to do is [Your organization's Internet use policy restricts access to the rest of this comment at this time. Reason: The Websense category "Proxy Avoidance" is filtered]
We're already halfway there. How long can it be before someone makes the frikkin' obvious next development?
It's also worth noting that there are very few individual dSLR models currently in use (even counting those badged differently depending on region and minor upgrades like the D70s), but many barely distinguishable short-lived P&S cameras - i.e., the choice in this market is so large and rapidly evolving that any single P&S model may not rank very highly, even if most users shoot this type of camera. I wonder what proportion of flickr users actually shoot dSLRs in general?
"First, if both dogs and marsupials can have a contageous, directly-transmissable cancer, then so can any species, through ANY mechanism that involves a transfer of cells."
If you want a really scary Michael Crichton scenario, the authors reference work done in the 60s (this isn't a new idea) on another possible contagious tumour that "can even be transmitted via mosquitoes". Luckily that one was in hamsters.
'You can do that in the lab by injecting tumor cells from one mouse into another and letting a new tumor form, however I haven't seen examples of this occuring naturally and in those experiments the mice need to either be from the same genetic background or immunosuppressed SCID mice.'
I didn't know this either, but according to the article: "CTVT was frequently used by cancer researchers to study tumor transplantation" (presumably in dogs) "until the development of inbred strains of rats and mice afforded syngeneic models" while "CTVT can be transplanted into immunocompetent animals of other canine species, such as foxes, coyotes, and jackals...as well as into immunodeficient mice" (but presumably not immunocompetent mice). Interestingly, the typical course of the disease in dogs is "an initial stage of rapid and progressive growth, which is typically followed by spontaneous regression 3 to 9 months later", so the animal eventually mounts an effective immune response (passive immunity can also be transmitted by serum from a recovered dog).
The problem is that in at least some countries this only applies until you reach your lifetime 'sending limit' (read the small print). Once this limit is reached (I think this is $2000 in the US, but only £500 at most in the UK) you have to give PayPal direct access to a bank account, losing the 'insulation' provided by your credit card. This is the thing I hate most about PayPal, and they aren't exactly up-front about it either (the help information about account 'verification' just has some vague language about the supposed benefits to the buyer, and nothing about the very real advantages to PayPay of being able to suck cash straight out of your bank account).
"The acreage also has...a bat cave".
A secretive billionaire with advanced aerospace technology and a Batcave? Holy Amazon, Batman!
'Well I've used it on dozens of different DVD drives, on lots of different DVDs and it has worked most splendidly for me. So in short, IME, Yes. Though these days i use xine. And I hear mplayer is getting menu support.'
VLC certainly gives region-free playback with many RPC2 drives (including mine), and of course has no problem with the old RPC1 drives. I think it's only fairly recently that some manufacturers have started to go beyond the original RPC2 spec and prevent even raw access to the DVD when there's a region mismatch. AFAIK, this additional measure currently blocks anything short of a firmware upgrade if you're unfortunate to have one of the afflicted drives and want to play a disk from a different region (so xine, mplayer or anything else that uses libdvdcss won't work either). I don't know what proportion of current RPC2 drives are crippled in this way - anyone?
Oops! - I should have given the top page:
http://www1.wfubmc.edu/pathresearch/srmouse/
Thanks! I've dug out the direct link:
0 3v1
r tid=164507
. htm
http://www.pnas.org/cgi/content/abstract/06023821
Here's the first paper:
http://www.pubmedcentral.gov/articlerender.fcgi?a
and a nice website from the research group with lots of background:
http://www1.wfubmc.edu/pathresearch/srmouse/part1
'EVERY person is DIFFERENT and we do NOT come with a "Workshop Manual.'
No, you're right - it has to be ordered separately.