The benefit of creating scaffolds first from long reads is that it's a lot easier to capture regions where there is a Very-long Complex Tandem Repeat (VeCTR). These regions are collapsed in scaffolds assembled from short reads.
Some errors are random, some are systematic. The systematic errors tend to be either small shifts in long stretches of the same base, or interesting features of the DNA (e.g. methylation), and there are a few people trying to work out what those interesting features are.
A key obstacle to getting people interested in nanopore sequencing (or other types of observational sequencing) is that we have been locked in for so long to the idea of DNA as a sequence of letters that we forget there are other things attached to it that also have functional roles. Nanopore is more accurate when matching sequences at the signal/electrical level, but almost no one is doing that yet.
The technology has improved substantially since then. Feel free to ask me any more questions about the sequencing. Although I'm not an author on this paper, I'm fairly familiar with the sequencing project that was done, and am happy to answer any general questions you might have on this technology.
You can find out yourself for the low, low price of $1000 USD.... or wait a few months for SmidION to come out, which will be a bit cheaper, and plug into your iPhone or Android device.
https://slashdot.org/comments....... although my guess is that these people are still trying to teach computers how our brain works, rather than the other way round.
* Probably the closest slashdot comment I've written to TFA.
As far as I know, the number of current manufacturers of these treatments are limited, with Colgate Pro-Argin for arginine-containing toothpaste, and GC Tooth Mousse for CPP-ACP.
this has been obvious for decades. Centuries, even. Keep a stiff upper lip and soldier on instead of emoting.
This research suggests the opposite. Instead of trying to ignore (or cancel out) the emotions, recovery to a better state is quicker if individuals accept their emotional state.
They could if they wanted to. A MinION DNA sequencer only costs $1000 USD, and a single run would provide plenty of coverage for a whole-genome assembly of any yeasts in the beer.
Except when you need to account for arguments appearing out of order. Or multiple arguments. Or the same argument that can override or revert itself. Or a mixture of short and long arguments, where all long arguments have a short alias, but not necessarily the other way round. Or if you want parsing to stop (or pass-through) at the first unexpected argument. Or if you want environment variables to influence the method of argument parsing. Or if you want to allow long arguments to start with a single '-' rather than the usual '--'.
I though the whole idea of science was reproducible and open research.
Yes, one of the ideas of science is reproducible and open research. The realities involve things like "publish or perish", boys clubs of peer review, and a funding preference for things that no one else has done before, but already have substantial research done to back them up.
the free software idealism has lost and will never win
It's becoming more popular in the biology / medical research community, as people start to understand the importance of reproducible and open research. Every thing that can be opened up and inspected is another thing that doesn't need months (or years) of work to repeat.
Most Linux users don't have a strong opinion on systemd either way,
Maybe not on slashdot, but you will probably find that people over at soylentnews have a different opinion. The systemd issue was a contributing factor to the creation of soylentnews.
My first home computer was a 286 XT. I have fond memories of playing Alley Cat, Railroad Tycoon, Leisure Suit Larry, Jack Nicholson's Golf, Grand Prix, and Digger (to name a few). We were one of the late comers in my group of friends to get a computer, but that meant that we had VGA, a hard drive, and a 300dpi printer before most other people.
This won't prevent all allergic responses. We've carried out research that indicates there are at least two types of allergic responses, one TSLP-dependent and another Interferon alpha-dependent:
The TSLP response seems to be most associated with chemical-related irritants (e.g. cinnamon oil, SLS), while the IFN-a response seems to be most associated with small organism irritants (e.g. house dust mites, parasites).
Slashdot Mirror
Or just Cassava-killing viruses:
How a TED Fellow is working to save African cassava from whiteflies
The benefit of creating scaffolds first from long reads is that it's a lot easier to capture regions where there is a Very-long Complex Tandem Repeat (VeCTR). These regions are collapsed in scaffolds assembled from short reads.
minimap2 works better for long reads, and can be used in the Canu assembler as the overlapper component for doing read correction.
It's already done:
https://en.wikipedia.org/wiki/...
Some errors are random, some are systematic. The systematic errors tend to be either small shifts in long stretches of the same base, or interesting features of the DNA (e.g. methylation), and there are a few people trying to work out what those interesting features are.
A key obstacle to getting people interested in nanopore sequencing (or other types of observational sequencing) is that we have been locked in for so long to the idea of DNA as a sequence of letters that we forget there are other things attached to it that also have functional roles. Nanopore is more accurate when matching sequences at the signal/electrical level, but almost no one is doing that yet.
I did a Q&A on this sequencer on SoylentNews a couple of years ago:
https://soylentnews.org/articl...
The technology has improved substantially since then. Feel free to ask me any more questions about the sequencing. Although I'm not an author on this paper, I'm fairly familiar with the sequencing project that was done, and am happy to answer any general questions you might have on this technology.
Direct RNA sequencing can be done with the MinION as well, no hardware change needed:
https://store.nanoporetech.com...
Depending on how important it is to sequence all RNA, polyadenylation prior to sequencing might also be needed.
You can find out yourself for the low, low price of $1000 USD. ... or wait a few months for SmidION to come out, which will be a bit cheaper, and plug into your iPhone or Android device.
Someone needs to read their own summary: this looks like the Atlantic Ocean, not the Pacific Ocean.
Finally, someone [else] has realised that the brain is not necessary for a computer interface:
https://slashdot.org/comments....
https://slashdot.org/comments.... *
https://slashdot.org/comments.... ... although my guess is that these people are still trying to teach computers how our brain works, rather than the other way round.
* Probably the closest slashdot comment I've written to TFA.
The following tooth treatments discourage cavity-causing bacteria and encourage remineralisation of teeth:
* Arginine-containing toothpaste -- https://www.ncbi.nlm.nih.gov/p...
* CPP-ACP-containing treatment -- https://www.ncbi.nlm.nih.gov/p...
As far as I know, the number of current manufacturers of these treatments are limited, with Colgate Pro-Argin for arginine-containing toothpaste, and GC Tooth Mousse for CPP-ACP.
this has been obvious for decades. Centuries, even. Keep a stiff upper lip and soldier on instead of emoting.
This research suggests the opposite. Instead of trying to ignore (or cancel out) the emotions, recovery to a better state is quicker if individuals accept their emotional state.
Furthermore, it's a deliberately introduced bug
Or a couple of weeks with a 3D printer, arduino, and a few other accessories.
They could if they wanted to. A MinION DNA sequencer only costs $1000 USD, and a single run would provide plenty of coverage for a whole-genome assembly of any yeasts in the beer.
I thought parliament had dissolved on 3rd May. Why are they still around when the new government hasn't been assigned yet?
https://en.wikipedia.org/wiki/...
All the cells in the body will become cancerous after so many generations of subdivision.
Naked Mole Rats suggest otherwise:
https://en.wikipedia.org/wiki/...
Twitter is like a cut-down version of a global IRC with fancy filtering. If twitter disappears, I expect that something else will quickly replace it.
Except when you need to account for arguments appearing out of order. Or multiple arguments. Or the same argument that can override or revert itself. Or a mixture of short and long arguments, where all long arguments have a short alias, but not necessarily the other way round. Or if you want parsing to stop (or pass-through) at the first unexpected argument. Or if you want environment variables to influence the method of argument parsing. Or if you want to allow long arguments to start with a single '-' rather than the usual '--'.
I though the whole idea of science was reproducible and open research.
Yes, one of the ideas of science is reproducible and open research. The realities involve things like "publish or perish", boys clubs of peer review, and a funding preference for things that no one else has done before, but already have substantial research done to back them up.
the free software idealism has lost and will never win
It's becoming more popular in the biology / medical research community, as people start to understand the importance of reproducible and open research. Every thing that can be opened up and inspected is another thing that doesn't need months (or years) of work to repeat.
Most Linux users don't have a strong opinion on systemd either way,
Maybe not on slashdot, but you will probably find that people over at soylentnews have a different opinion. The systemd issue was a contributing factor to the creation of soylentnews.
My first home computer was a 286 XT. I have fond memories of playing Alley Cat, Railroad Tycoon, Leisure Suit Larry, Jack Nicholson's Golf, Grand Prix, and Digger (to name a few). We were one of the late comers in my group of friends to get a computer, but that meant that we had VGA, a hard drive, and a 300dpi printer before most other people.
This won't prevent all allergic responses. We've carried out research that indicates there are at least two types of allergic responses, one TSLP-dependent and another Interferon alpha-dependent:
https://growkudos.com/publicat...
The TSLP response seems to be most associated with chemical-related irritants (e.g. cinnamon oil, SLS), while the IFN-a response seems to be most associated with small organism irritants (e.g. house dust mites, parasites).
So, it looks like the open Web has a new enemy, and its name is EnEME.