3 ms·

Considering this is HN, there is enough engineering brainpower to build open source clones of this. Biology is not the same as electronics, it is closer to soft

Considering this is HN, there is enough engineering brainpower to build open source clones of this. Biology is not the same as electronics, it is closer to software in the sense that a lot of things can be easily (for some definition of easy) cloned once you figure out how it works. The only difference is that biology is slow and expensive and takes a lot of equipment. Caveats: getting to Roche level of throughput and scale would be tricky with just Arduinos and off the shelf stuff and there are some magic numbers that you will have to figure out through experimentation. Building a usable machine just for a small number of people is not that tricky if you have e.g. 5 bio and 5 CS/EE people working on getting a design shipped.

deng 7y ago
I think you greatly underestimate how complicated these machines are. For instance, I just cannot imagine how these machines keep themselves so clean. My guess is "lots of disposables" but still, that must take years to get right. Just read "Bad Blood" to see how Theranos struggled with the machines not simply becoming a bloody mess, and they had some great engineers on the team.
- yourapostasy 7y ago
  Look at the FDA testing protocol [1] for their Covid-19 test kit. They use molecular water (double-distilled, deionized, likely de-salted water), and DNA and RNA degradation solutions, some PPE, autoclaves, bleach, and lots of workflow procedures to carefully mitigate cross-contamination. I'm curious why the life sciences folks aren't standardized upon something like semiconductor SMIF to isolate the samples and point of contact of equipment into a modular sterile environment, and limit cleaning to interface ports optimized for sterile operations and maintenance. My first swag at such interface ports might look into some design that can be clamped and autoclaved, and submerged in some degradation solution, for example. Generally, the current open standard is terrifically manual labor intensive and prone to mistakes. All the automated solutions I've been able to read up on so far (BD MAX, Seegene All-In-One Platform, Roche Cobas 6600/8800, BioFire FilmArray Torch and FilmArray 2.0) seem to lock in customers to proprietary panels. I'm curious whether that is more of a commercial decision or a scientific decision. Of these, only BD MAX allows user-designed protocols at all. So far, I've yet to see a persuasive argument that an automated molecular diagnostics system must use a proprietary platform for scientific reasons. A generic automated platform that can use anyone's glassware, molecular water, primers, master mixes, etc., will need many more sensors for quality monitoring, and those need constant calibration, so there is a significant engineering tradeoff. But I'd be surprised if any of the proprietary solutions are much more cost-effective; it seems all of these kinds of solutions are following the John Deere lock-in servicing model to generate profits. [1] https://www.fda.gov/media/134922/download https://www.fda.gov/media/134922/download
  - nkrumm 7y ago
    The Hologic Panther Fusion is another automated open platform. The decision to lock people is for FDA approval. FDA approval means more labs can run your test and reimbursement is more of a sure thing.
  - milksteak42 7y ago
    It's mostly a commercial decision. Reagents have very high margins and recurring revenue is more attractive than large one-time purchases. Illumina does this with genetic sequencing as well. edit: There are some informal standards like 96- and 384- well plates that make it possible to have third-party consumables with some machines, but there is no incentive for a for-profit company to design open platform.
  - CptFribble 7y ago
    The lion's share of the test volume is done by commercial labs like LabCorp and Quest, who don't care that much about designing their own tests, they just want to maximize patient volume. One of the companies I used to work for had a large chemistry system that could be run "open" but only a few customers used it that way, a couple research laboratories and I think a winery. Thousands of other instruments were used for plain ol' medical testing. Even if you designed a sufficiently open system that could run Roche or Siemens reagents or whatever, any problem with the reagents and the company will just shrug and say "it's not our instrument, no guarantees."
yourapostasy 7y ago
These folks [1] are working on an open Covid-19 test. There is a pretty significant logistical train that I haven't seen systematically addressed yet in the project, though lots of those pieces have open projects that can be picked up, adapted and integrated. Even failing will be valuable: that identifies gaps to address. [1] https://app.jogl.io/project/118#about https://app.jogl.io/project/118#about

deng 7y ago

I think you greatly underestimate how complicated these machines are. For instance, I just cannot imagine how these machines keep themselves so clean. My guess is "lots of disposables" but still, that must take years to get right. Just read "Bad Blood" to see how Theranos struggled with the machines not simply becoming a bloody mess, and they had some great engineers on the team.

yourapostasy 7y ago
Look at the FDA testing protocol [1] for their Covid-19 test kit. They use molecular water (double-distilled, deionized, likely de-salted water), and DNA and RNA degradation solutions, some PPE, autoclaves, bleach, and lots of workflow procedures to carefully mitigate cross-contamination. I'm curious why the life sciences folks aren't standardized upon something like semiconductor SMIF to isolate the samples and point of contact of equipment into a modular sterile environment, and limit cleaning to interface ports optimized for sterile operations and maintenance. My first swag at such interface ports might look into some design that can be clamped and autoclaved, and submerged in some degradation solution, for example. Generally, the current open standard is terrifically manual labor intensive and prone to mistakes. All the automated solutions I've been able to read up on so far (BD MAX, Seegene All-In-One Platform, Roche Cobas 6600/8800, BioFire FilmArray Torch and FilmArray 2.0) seem to lock in customers to proprietary panels. I'm curious whether that is more of a commercial decision or a scientific decision. Of these, only BD MAX allows user-designed protocols at all. So far, I've yet to see a persuasive argument that an automated molecular diagnostics system must use a proprietary platform for scientific reasons. A generic automated platform that can use anyone's glassware, molecular water, primers, master mixes, etc., will need many more sensors for quality monitoring, and those need constant calibration, so there is a significant engineering tradeoff. But I'd be surprised if any of the proprietary solutions are much more cost-effective; it seems all of these kinds of solutions are following the John Deere lock-in servicing model to generate profits. [1] https://www.fda.gov/media/134922/download https://www.fda.gov/media/134922/download
- nkrumm 7y ago
  The Hologic Panther Fusion is another automated open platform. The decision to lock people is for FDA approval. FDA approval means more labs can run your test and reimbursement is more of a sure thing.
- milksteak42 7y ago
  It's mostly a commercial decision. Reagents have very high margins and recurring revenue is more attractive than large one-time purchases. Illumina does this with genetic sequencing as well. edit: There are some informal standards like 96- and 384- well plates that make it possible to have third-party consumables with some machines, but there is no incentive for a for-profit company to design open platform.
- CptFribble 7y ago
  The lion's share of the test volume is done by commercial labs like LabCorp and Quest, who don't care that much about designing their own tests, they just want to maximize patient volume. One of the companies I used to work for had a large chemistry system that could be run "open" but only a few customers used it that way, a couple research laboratories and I think a winery. Thousands of other instruments were used for plain ol' medical testing. Even if you designed a sufficiently open system that could run Roche or Siemens reagents or whatever, any problem with the reagents and the company will just shrug and say "it's not our instrument, no guarantees."

yourapostasy 7y ago

These folks [1] are working on an open Covid-19 test. There is a pretty significant logistical train that I haven't seen systematically addressed yet in the project, though lots of those pieces have open projects that can be picked up, adapted and integrated. Even failing will be valuable: that identifies gaps to address. [1] https://app.jogl.io/project/118#about https://app.jogl.io/project/118#about