6 ms·

Until you also realize you need a Qubit and the library preps and oh now you need NEB next gen enzymes and wow turns out pipette technique really matters. That

by koeng 6y ago

Until you also realize you need a Qubit and the library preps and oh now you need NEB next gen enzymes and wow turns out pipette technique really matters. That said, I love Nanopores, I use them in my business, and those error rates you can hack around if you know what’s going on under the hood.

samchorlton 6y ago
Exactly. Better analytics can enable this technology to produce better results than competing technologies in less time. Once automated/easy/rapid sample prep comes, there will be mass adoption in the space. Disclaimer: Co-Founder of BugSeq[0] 0: https://bugseq.com https://bugseq.com
- matthew_stone 6y ago
  > Once automated/easy/rapid sample prep comes, there will be mass adoption in the space. Sounds like Elon calling biology a “software problem”. Not saying that you’re wrong, just saying that the computational folk tend to discount the challenges and skills required in the wet lab.
  - samchorlton 6y ago
    Agreed - Definitely a different class of problem than "software". There are large barriers, eg. lab contamination, biocontainment, low input protocols, etc; however, technological innovation will help with these. That being said, we see a future where someone without advanced molecular training can put a sample (whether that's a nasal swab, concerning white powder received in the mail or lab-grown meat) in a black box and get out a meaningful report.
  - phkahler 6y ago
    >> Not saying that you’re wrong, just saying that the computational folk tend to discount the challenges and skills required in the wet lab. It's time to bring in the industrial automation folks. They probably won't invent a fancy new algorithm to reduce the time to splice the pieces together, but they'll fine tune and automate your reader to the 9's.
    - exikyut 6y ago
      Question: a majority of software environments will take on individuals without traditional qualifications, throw a dozen books' exam sections at them, and keep those who can hack it. I just realized industrial automation sounds really interesting. What would my chances be for someone who never got the chance to study math? (Basically in 1998 it was illegal to change schools in Australia regardless of how much of an eyebrow-raising situation you might've been in. Had to homeschool, without any resources. Only realized ~20 years on just how much opportunity I'll never get back.) (Heh, I'm pretty much expecting the only obvious possible answer at this point, I was just curious if the answer is "yeah no" or "it depends".)
- koeng 6y ago
  Yea automated sample preps are key for me. The main thing that is overlooked in synthetic biology about nanopore is it has the capability to dramatically lower cost of indexing, which turns out to be one of the main prohibiting costs for dropping the cost of plasmid production.
dekhn 6y ago
"wow turns out pipette technique really matters" <- one of the most underrated comments of all time.
- andi999 6y ago
  Pipette skills improve rapidly if you practice with a microscale.
  - dekhn 6y ago
    that's how we calibrated ours. turns out: most pipettes in the lab were miscalibrated, with 50+% error. Then it turned out our scale wasnt properly calibrated, so we had to replace that too.
  - dekhn 6y ago
    I spent some more time thinking about this and wrote the following. Modern scientists move small amounts of biological materials using a tool called the pipette. Pipettes can work with very small amounts of liquid- down the microliter. When you're running a delicate experiment being able to deliver the precise amount of liquid is critical. Pipettes need to be calibrated. How do you calibrate a device that works with volumes of liquid? Volumes of liquid are hard to measure. Fortunately, water at STP (standard temp and pressure) has a known mass, so you attempt to draw 1 mL, and weigh it. 1 mL of water weighs 1 gram at STP (this is not a coincidence- it's by definition). OK so you're weighing 1 gram of water and adjusting the pipette's calibrator knob so that 1mL on the pipette weighs 1 gram. I guess that means your weighing scale needs to be calibrated, too. Huh. These sorts of scales aren't just "weigh some flour for baking", either. They have to be accurate to the hundredth of a gram, and have walls to avoid fluctuations due to air currents(!!!!) and minor temp changes. The scales are calibrated using calibrated test weights. Oh dear. Calibrated test weights? If you follow the turtles all the way down, you find that there is actually a tracebility chain from your calibrated scale back to one of the defined weights held by NIST, the NIST equivalents in France and Japan (they all share their weights). So you can actually calculate- using those weird rules of error propagation you forget in high school- the error of your scale as a product of the errors in that chain (often, knowing your error bars is more important than knowing the accurate answer). But that's not all. Those defined weights? They're obsolete. Le Grand K (the origin of the kilogram, still kept under lock and key) changed weight over time due to subtle metallurigcal details. The new definition of the standard is created by an obscure machine at NIST, just like the time standards. https://en.wikipedia.org/wiki/Kibble_balance https://en.wikipedia.org/wiki/Kibble_balance is the tool used to do it, and it depends on the NIST time reference. So, turtles all the way down until you get the rubidium fountain.
tdido 6y ago
I don't think you need the Qubit with the rapid prep.
- koeng 6y ago
  it works but your efficiency drops by quite a bit
Florin_Andrei 6y ago
> those error rates Do a thousand readings, fix the parts that don't match across the board?
- et2o 6y ago
  Then you have to do 1000x the sequencing, which can get expensive on long read technologies :) That said, that’s basically how a lot of NGS works in things like cancer sequencing on Illumina platforms.
  - Florin_Andrei 6y ago
    > Then you have to do 1000x the sequencing Seems to me, that stuff is getting cheaper all the time.
husamia 6y ago
RE: library prep. Voltrax from ONT automates the library prep process.

by koeng 6y ago

samchorlton 6y ago

Exactly. Better analytics can enable this technology to produce better results than competing technologies in less time. Once automated/easy/rapid sample prep comes, there will be mass adoption in the space. Disclaimer: Co-Founder of BugSeq[0] 0: https://bugseq.com https://bugseq.com

matthew_stone 6y ago
> Once automated/easy/rapid sample prep comes, there will be mass adoption in the space. Sounds like Elon calling biology a “software problem”. Not saying that you’re wrong, just saying that the computational folk tend to discount the challenges and skills required in the wet lab.
- samchorlton 6y ago
  Agreed - Definitely a different class of problem than "software". There are large barriers, eg. lab contamination, biocontainment, low input protocols, etc; however, technological innovation will help with these. That being said, we see a future where someone without advanced molecular training can put a sample (whether that's a nasal swab, concerning white powder received in the mail or lab-grown meat) in a black box and get out a meaningful report.
- phkahler 6y ago
  >> Not saying that you’re wrong, just saying that the computational folk tend to discount the challenges and skills required in the wet lab. It's time to bring in the industrial automation folks. They probably won't invent a fancy new algorithm to reduce the time to splice the pieces together, but they'll fine tune and automate your reader to the 9's.
  - exikyut 6y ago
    Question: a majority of software environments will take on individuals without traditional qualifications, throw a dozen books' exam sections at them, and keep those who can hack it. I just realized industrial automation sounds really interesting. What would my chances be for someone who never got the chance to study math? (Basically in 1998 it was illegal to change schools in Australia regardless of how much of an eyebrow-raising situation you might've been in. Had to homeschool, without any resources. Only realized ~20 years on just how much opportunity I'll never get back.) (Heh, I'm pretty much expecting the only obvious possible answer at this point, I was just curious if the answer is "yeah no" or "it depends".)
koeng 6y ago
Yea automated sample preps are key for me. The main thing that is overlooked in synthetic biology about nanopore is it has the capability to dramatically lower cost of indexing, which turns out to be one of the main prohibiting costs for dropping the cost of plasmid production.

dekhn 6y ago

"wow turns out pipette technique really matters" <- one of the most underrated comments of all time.

andi999 6y ago
Pipette skills improve rapidly if you practice with a microscale.
- dekhn 6y ago
  that's how we calibrated ours. turns out: most pipettes in the lab were miscalibrated, with 50+% error. Then it turned out our scale wasnt properly calibrated, so we had to replace that too.
- dekhn 6y ago
  I spent some more time thinking about this and wrote the following. Modern scientists move small amounts of biological materials using a tool called the pipette. Pipettes can work with very small amounts of liquid- down the microliter. When you're running a delicate experiment being able to deliver the precise amount of liquid is critical. Pipettes need to be calibrated. How do you calibrate a device that works with volumes of liquid? Volumes of liquid are hard to measure. Fortunately, water at STP (standard temp and pressure) has a known mass, so you attempt to draw 1 mL, and weigh it. 1 mL of water weighs 1 gram at STP (this is not a coincidence- it's by definition). OK so you're weighing 1 gram of water and adjusting the pipette's calibrator knob so that 1mL on the pipette weighs 1 gram. I guess that means your weighing scale needs to be calibrated, too. Huh. These sorts of scales aren't just "weigh some flour for baking", either. They have to be accurate to the hundredth of a gram, and have walls to avoid fluctuations due to air currents(!!!!) and minor temp changes. The scales are calibrated using calibrated test weights. Oh dear. Calibrated test weights? If you follow the turtles all the way down, you find that there is actually a tracebility chain from your calibrated scale back to one of the defined weights held by NIST, the NIST equivalents in France and Japan (they all share their weights). So you can actually calculate- using those weird rules of error propagation you forget in high school- the error of your scale as a product of the errors in that chain (often, knowing your error bars is more important than knowing the accurate answer). But that's not all. Those defined weights? They're obsolete. Le Grand K (the origin of the kilogram, still kept under lock and key) changed weight over time due to subtle metallurigcal details. The new definition of the standard is created by an obscure machine at NIST, just like the time standards. https://en.wikipedia.org/wiki/Kibble_balance https://en.wikipedia.org/wiki/Kibble_balance is the tool used to do it, and it depends on the NIST time reference. So, turtles all the way down until you get the rubidium fountain.

tdido 6y ago

I don't think you need the Qubit with the rapid prep.

koeng 6y ago
it works but your efficiency drops by quite a bit

Florin_Andrei 6y ago

> those error rates Do a thousand readings, fix the parts that don't match across the board?

et2o 6y ago
Then you have to do 1000x the sequencing, which can get expensive on long read technologies :) That said, that’s basically how a lot of NGS works in things like cancer sequencing on Illumina platforms.
- Florin_Andrei 6y ago
  > Then you have to do 1000x the sequencing Seems to me, that stuff is getting cheaper all the time.

husamia 6y ago

RE: library prep. Voltrax from ONT automates the library prep process.