And what about the performance penalty incurred by needing to bitshift a nucleotide quartet around within a single byte register every single time you wanted to actually work with the data? Busses be damned; at some point you have to do individual base pair comparison, and that's by far the most common operation in sequence analysis.
Of course it willbut that's pretty inefficient when you need to decompress it regularly to work with it. At any rate, when you're working with data sets this big it really is more efficient to just buy more hard drives for most people, and the article is actually about not having the CPU and human power to do the analysis, anyway.
As an aside, BGI is not just any centre, it is the centre. Much like biochemists send their crystals to a synchrotron for X-ray crystallography, biologists send their sequences to BGI to get them sequenced. They own something like 180 high-throughput sequencing instruments, which is about 5-10% of the installed base, give or take.
Fortunately, most biologists are unimaginative, and the medical establishment's coffers are bottomless, so really only four genomes ever actually get much mileage: human, rat, mouse, and chimpanzee. Perhaps a parasite or virus here and there. I weep for plant biologists.
Transposons are interesting and complex, but they don't play much of a role in mammals. Intergenic DNA is still important in that it provides scaffolding (an active chromosome resembles a puff-ball with all of the important genes at the outside edges, where they're most accessible to incoming proteins) and flex room (sometime proteins will actually bend DNA and pinch it to make sure the important genes stick out) but so far we believe that the actual sequence of most of the human genome isn't very important. 95% of it appears to be under no evolutionary pressure (that is, even if it mutates, the organism is fine.)
Bioinformatics is indeed a very lucrative profession, but few programmers have the willingness to memorize the huge canon of data while they're in college that is required to be proficient in it. The curriculum is about 70% computer science and 30% life sciences, including organic chemistry at some universities.
ASCII storage of nucleotide and protein information is actually very standard. The most widespread format is called FASTA, named after the fast alignment program that introduced it. When you sequence a whole genome on a second-generation sequencing platform (like Illumina or SOLiD), there's a step in the process where you end up with a huge (10-100 GB) text file containing little puzzle pieces of DNA that must then be assembled by a specialized program. These files usually don't hang around very long, but the point of keeping them in this inefficient storage format is, simply, performance: CPUs are oriented toward byte-based computing at a minimum, and so frequent compression/decompression becomes prohibitively inefficient.
Big biotechnology purchases are typically hundreds of thousands of dollars though, so most labs are used to shelling out for this kind of price bracket.
Although that isn't quite what we're talking about here, reductionism in biology has been an ongoing problem for decades. Traditional biochemists often reduce the system they're examining to simple gene-pair interactions, or perhaps a few components at once, and focus only on the disorders that can be succinctly described by them. That's why very small-scale issues like haemophilia and sickle-cell anaemia were sorted out so early on. As diseases with larger and more complex origins become more important, research and money is being directed toward them. Cancer has been by far the most powerful driving force in the quest to understand biology from a broader viewpoint, primarily because it's integrally linked to a very important, complicated process (cell replication) that involves hundreds if not thousands of genes, miRNAs, and proteins.
Actually, short reads aren't that bad as they may seem from a distance—the lab for which I consult has spent about a year surveying second-gen sequencing platforms, and it turns out the the 5th-generation ABI SOLiD platform finally lives up to its name, even though it uses only ~20 nt reads instead of the Illumina's 100. The chemistry has improved to a point where read quality isn't the biggest issue any more.
Unfortunately the only flaw with such a system is that, unlike most forms of communication based on misunderstood quantum entanglement, your information gets leaked to the public before it arrives.
Besides the traditional pedantry of the proper use of "begging the question": it's pretty established at this point that Scientology isn't a bona fide religion. A number of countries have already banned it.
That being said, yeah. A single nematode lives for about 15 days and can have up to 400 offspring during that timeframe. They get lots of opportunity for cell division during the first week or so, but that younger tissue isn't necessarily representative of the whole organism. Another problem with using such a tiny worm is that the chance of a germline mutation (in the reproductive cells, therefore being carried on to all children) is much higher when the organism only has a few cells protecting it from space rather than all the flesh we have. Et cetera.
The genome size similarity is constant for most eukaryotes, with plants being an exception. Even yeast has around 20,000 genes, and it's not even an animal.
There's a reason C. elegans isn't used in basic cell cycle research as much as yeast. It doesn't continually replace its cells at maturity. Consequentially, DNA-damaging environmental conditions have a much lower chance of affecting them at maturity than humans.
To make life worse? 7 is actually Windows NT 6.1, Vista and 2008 are NT 6.0, 2003 and XP x64 are NT 5.2, XP x86 is NT 5.1, and 2000 is 5.0.
It's not the seventh release either! (1.01, 2/286, 2/386, 3.0, 3.1, 3.11 For Workgroups, NT 3.51, NT 4, 95, 98, Me, 2000, XP, and Vista all preceded it—it's more like Windows 15.)
Slashdot Mirror
Pretty much. I was asked to flip through some Illumina sequence data from BGI in August—more than half of the reads were garbage.
spending is about 160% of revenue
Doubtful, but introducing an optimization into a novel domain can always be valuable incremental progress.
Right, but then you're faced with the 'blistering' speed of Python. I was thinking of C—still, good to think about for the future.
I'll remember that! You might win me a paper some day. :)
And what about the performance penalty incurred by needing to bitshift a nucleotide quartet around within a single byte register every single time you wanted to actually work with the data? Busses be damned; at some point you have to do individual base pair comparison, and that's by far the most common operation in sequence analysis.
I don't think too many Latinists would support that construction, but it's certainly semantically correct.
Of course it willbut that's pretty inefficient when you need to decompress it regularly to work with it. At any rate, when you're working with data sets this big it really is more efficient to just buy more hard drives for most people, and the article is actually about not having the CPU and human power to do the analysis, anyway.
I think the point is more like "in 20 years, there won't be any men left in the STEM fields."
As an aside, BGI is not just any centre, it is the centre. Much like biochemists send their crystals to a synchrotron for X-ray crystallography, biologists send their sequences to BGI to get them sequenced. They own something like 180 high-throughput sequencing instruments, which is about 5-10% of the installed base, give or take.
Done: NCBI, DDBJ, and Ensembl all perform that role. The problem is what to do with all of it.
Can't analyse a compressed sequence. Gotta decompress it first. Disks are cheaper than time.
Fortunately, most biologists are unimaginative, and the medical establishment's coffers are bottomless, so really only four genomes ever actually get much mileage: human, rat, mouse, and chimpanzee. Perhaps a parasite or virus here and there. I weep for plant biologists.
Transposons are interesting and complex, but they don't play much of a role in mammals. Intergenic DNA is still important in that it provides scaffolding (an active chromosome resembles a puff-ball with all of the important genes at the outside edges, where they're most accessible to incoming proteins) and flex room (sometime proteins will actually bend DNA and pinch it to make sure the important genes stick out) but so far we believe that the actual sequence of most of the human genome isn't very important. 95% of it appears to be under no evolutionary pressure (that is, even if it mutates, the organism is fine.)
Bioinformatics is indeed a very lucrative profession, but few programmers have the willingness to memorize the huge canon of data while they're in college that is required to be proficient in it. The curriculum is about 70% computer science and 30% life sciences, including organic chemistry at some universities.
ASCII storage of nucleotide and protein information is actually very standard. The most widespread format is called FASTA, named after the fast alignment program that introduced it. When you sequence a whole genome on a second-generation sequencing platform (like Illumina or SOLiD), there's a step in the process where you end up with a huge (10-100 GB) text file containing little puzzle pieces of DNA that must then be assembled by a specialized program. These files usually don't hang around very long, but the point of keeping them in this inefficient storage format is, simply, performance: CPUs are oriented toward byte-based computing at a minimum, and so frequent compression/decompression becomes prohibitively inefficient.
Big biotechnology purchases are typically hundreds of thousands of dollars though, so most labs are used to shelling out for this kind of price bracket.
Although that isn't quite what we're talking about here, reductionism in biology has been an ongoing problem for decades. Traditional biochemists often reduce the system they're examining to simple gene-pair interactions, or perhaps a few components at once, and focus only on the disorders that can be succinctly described by them. That's why very small-scale issues like haemophilia and sickle-cell anaemia were sorted out so early on. As diseases with larger and more complex origins become more important, research and money is being directed toward them. Cancer has been by far the most powerful driving force in the quest to understand biology from a broader viewpoint, primarily because it's integrally linked to a very important, complicated process (cell replication) that involves hundreds if not thousands of genes, miRNAs, and proteins.
Actually, short reads aren't that bad as they may seem from a distance—the lab for which I consult has spent about a year surveying second-gen sequencing platforms, and it turns out the the 5th-generation ABI SOLiD platform finally lives up to its name, even though it uses only ~20 nt reads instead of the Illumina's 100. The chemistry has improved to a point where read quality isn't the biggest issue any more.
Unfortunately the only flaw with such a system is that, unlike most forms of communication based on misunderstood quantum entanglement, your information gets leaked to the public before it arrives.
The link is actually an ugly frame-wrapping news aggregator. The actual story is from Entertainment Weekly. For shame, submitter. For shame.
Besides the traditional pedantry of the proper use of "begging the question": it's pretty established at this point that Scientology isn't a bona fide religion. A number of countries have already banned it.
That being said, yeah. A single nematode lives for about 15 days and can have up to 400 offspring during that timeframe. They get lots of opportunity for cell division during the first week or so, but that younger tissue isn't necessarily representative of the whole organism. Another problem with using such a tiny worm is that the chance of a germline mutation (in the reproductive cells, therefore being carried on to all children) is much higher when the organism only has a few cells protecting it from space rather than all the flesh we have. Et cetera.
The genome size similarity is constant for most eukaryotes, with plants being an exception. Even yeast has around 20,000 genes, and it's not even an animal.
There's a reason C. elegans isn't used in basic cell cycle research as much as yeast. It doesn't continually replace its cells at maturity. Consequentially, DNA-damaging environmental conditions have a much lower chance of affecting them at maturity than humans.
To make life worse? 7 is actually Windows NT 6.1, Vista and 2008 are NT 6.0, 2003 and XP x64 are NT 5.2, XP x86 is NT 5.1, and 2000 is 5.0.
It's not the seventh release either! (1.01, 2/286, 2/386, 3.0, 3.1, 3.11 For Workgroups, NT 3.51, NT 4, 95, 98, Me, 2000, XP, and Vista all preceded it—it's more like Windows 15.)