6 ms·

Open-sourcing bioinstruments

77 points by homarp 8y ago

kemitchell 8y ago
The BioBricks Foundation, an organization bringing the spirit of open source to genetic programming, engaged me to develop Public Domain Chronicle, a fast, easy, and free way to secure scientific methods and findings for the public domain. https://publicdomainchronicle.org/ https://publicdomainchronicle.org/ Public Domain Chronicle combines elements of defensive publication, open-access scholarship, and commons licensing to make public domain advocates the fastest runners in the race to publish, preventing others from patenting their findings. PDC's disclosure form for findings in biology is shorter and easier than any standard corporate or academic invention-disclosure process, and produces an immediate, public, republishable prior art record. https://pdc.biobricks.org/publish https://pdc.biobricks.org/publish It's early days for the project, and we're seeking out as many potential researcher-contributors as possible. We're particularly keen to hear from academic scientists and folks in corporate tech transfer offices who may prefer PDC to expensive defensive publication services.
amelius 8y ago
Some critical questions: who is the target audience for these instruments? Aren't academic budgets sufficient to provide for a lab with proper basic instruments? Are these kind of instruments a financial bottleneck when setting up a lab? And do we want biology PhD students and postdocs to spend time on instrument-making (and publish papers on that) rather than on biology?
- lwindyb 8y ago
  No, yes, and yes
- jcelerier 8y ago
  > Aren't academic budgets sufficient to provide for a lab with proper basic instruments? sobs
- sinab 8y ago
  Hey amelius! Great questions. The target audience for these instruments are scientists and hobbyists who don't want to spend a ton of money on similar commercial systems, and want the flexibility to modify their operation (e.g., poseidon can run custom flow profiles per experiment whereas off-the-shelf commercial systems typically only run one flow rate per experiment). The purpose of poseidon is to show that open source biological instruments can be developed and used by a community, similarly to how open source software tools in biology are developed and used. Academic budgets vary from institution to institution and are sometimes determined by exogenous forces beyond the lab's control. A complete commercial system to do single-cell RNA sequencing costs tens of thousands of dollars! Using alternatives such as the Harvard Apparatus syringe pumps and DropSeq [0] to run the same experiment will still cost you into the thousands of dollars. With the poseidon system, we greatly reduce these costs. Users can build the instruments to run these experiments for less than $400 and are not restricted to additional costs and tedious firmware upgrades to expand the system. In response to your point on time management and instrument-making, I think that if there exists a need to develop these systems such that they will advance biological experiments then it's totally cool to have academics work on these sorts of projects! Biologists and bioengineers have always developed tools alongside discovery and this is no different from developing bioinformatics tools. [0] https://www.cell.com/abstract/S0092-8674(15)00549-8 https://www.cell.com/abstract/S0092-8674(15)00549-8
  - amelius 8y ago
    Thanks for these great answers. The only point where I would disagree is your comparison with bioinformatics software. The difference there is that installing a bioinformatics package and learning to use it takes far less time than crafting an instrument, especially considering tasks like finding the right suppliers of components, and calibrating and testing the device (for which you might need other instruments). But on the other hand, perhaps building these self-made instruments can become a task for specialized, facilitating instrument-makers that are already part of many institutions.
    - munfred 8y ago
      Note: I also helped develop poseidon The poseidon system was explicitly designed with ease of assembly in mind. If you look at the build videos [1] you'll see that assembly of the entire system (3 pumps + microscope station) takes less than an hour and requires just pliers and screwdrivers. The importance of ease of assembly was a lesson that we took from assembling the miniDrops microfluidics station [2] developed specifically for one kind of experiment (dropSeq) [3]. The miniDrops is very good at what it does but assembly was somewhat cumbersome: it required ordering a custom PCB, specialized parts only available from one vendor (whom I had to nag over the phone to send me a quote!) and assembly of the device itself took 10-20h. Not every kind of equipment can be made as easy to source and assemble as we did with poseidon, but we really think that keeping this at the front of your mind can make or break the adoption of a piece of open source hardware. This is especially true in the context of biology laboratories, where many people are not what you could call "hackers" or "makers" and will be immediately put off by a daunting assembly process. [1] https://pachterlab.github.io/poseidon/hardware https://pachterlab.github.io/poseidon/hardware [2] https://metafluidics.org/devices/minidrops/ https://metafluidics.org/devices/minidrops/ [3] https://www.nature.com/articles/s41467-017-0265 https://www.nature.com/articles/s41467-017-0265
- bsder 8y ago
  > And do we want biology PhD students and postdocs to spend time on instrument-making (and publish papers on that) rather than on biology? This is an age old question. And the answer is: yes, we actually do. Even if a lab can afford all its instruments, sometimes you are researching something that requires a different approach. Most commercially available lab machines are NOT hackable, and you will have a difficult time bending them into a different configuration.
  - neltnerb 8y ago
    Yeah, for my grad thesis I had to figure out how to incorporate a fuel injector into a chemical reactor to meter fluid flow. Novel research equipment is by definition not off-the-shelf, so the skills to roll your own is often necessary to push the envelope. And a lot of the time that equipment isn't funded by a current project and you need to prove the idea is sound before you can justify asking for the money to do it. Of course if that proof of concept is good enough to keep being used all the better.
- jryb 8y ago
  We couldn't find a programmable temperature controller for a microscope that met our requirements so I ended up building it from scratch. It took me a month and I didn't know electronics when I started, but now we can do our experiments, and I have a skill that will benefit me and my employers for the rest of my career. I'd argue that that's a great use of a PhD, as long as it's not the only thing I'm doing. Additionally, in my lab and many others, there simply wasn't any tool we could use to answer all the questions we have, so we had to invent them. That said, these are much more bespoke systems, but as we push the envelope of what we need to observe, instrument making and method development are only going to be more critical. The inflation in the scientific equipment market is also ludicrous. Since I've been in grad school some of the things I have to buy have doubled in price. And it really is pathetic when it's something like a syringe pump - I mean you're rotating a screw with an electric motor to push a piece of plastic. I get that it's a small market and the vendor has to make a living, but this isn't the best way for a civilization to direct its resources.
sinab 8y ago
My name is Sina Booeshaghi a second year PhD student at Caltech and I built and designed the poseidon system (with the help of Eduardo Beltrame, Jase Gehring, Dylan Bannon, and Lior Pachter) in the Pachter Lab. If you have any questions I'm happy to answer them!
- kasbah 8y ago
  Nice work. You (and others interested in open science hardware) should come join our community at http://openhardware.science http://openhardware.science.
  - sinab 8y ago
    Thanks for the link! I'll check it out and send it to the other authors.
- sbr464 8y ago
  I was needing a fully digital (controlled) microscope stage and stand recently. I was suprised to find a lack of motorized stages compared to other items. It would be nice to have a modular stage so it could be used with different stands. Rotation and height adjustment would be nice as well. Have you came across anything similar? It seems like it would be trivial to build similar to your other designs.
  - sinab 8y ago
    Ooo this could be a great extension of the current microscope system! The only thing I've found is this https://www.thingiverse.com/thing:2525155 https://www.thingiverse.com/thing:2525155 which while not motorized, allows for height adjustments. Consider making an issue (tagged improvement) on the GitHub page! https://github.com/pachterlab/poseidon https://github.com/pachterlab/poseidon
  - munfred 8y ago
    I have been thinking about this problem for a while. I would like a cheap, open source, commercially available kit for xyz gantry systems. That's essentially what desktop CNC machines and 3D printers are and people hack them for all kinds of purposes. Unfortunately my current conclusion is that there is no solution that satisfies all 3 at the moment. Your best bet for building such a system is looking at cheap 3D printers and CNC machines, but it'll always be a little bit of a hack and extra work because you'll have to remove parts (hot end, drill bit..) and adapt something that was not designed with the intent of being entirely re-purposed. If anyone here knows of a xyz gantry system kit that satisfies all 3 (cheap, open source, commercially available) please let me know.
neltnerb 8y ago
Oh, this is awesome. I build a lot of random equipment, how do I help? This kind of thing could kickstart a lot of novel systems that'd take forever to design or cost a ton otherwise.
- sinab 8y ago
  I love your enthusiasm! Why don't you shoot me an email and we can chat some point next week.. It would be really cool to get a great community around the project, extending capabilities and adapting the core technology to random equipment. My email should be in my profile.
GautamGoel 8y ago
I work with Lior at Caltech. He's an amazing guy, probably the only person I know who is capable of doing first-rate work in both biology and mathematics.
AndrewGYork 8y ago
A different target audience, but in the same spirit, here's an open source microscopy project from our lab: https://andrewgyork.github.io/remote_refocus/ https://andrewgyork.github.io/remote_refocus/ My friend André Maia Chagas is doing some inspiring work in open hardware too: https://mobile.twitter.com/chagas_am https://mobile.twitter.com/chagas_am

77 points by homarp 8y ago

The BioBricks Foundation, an organization bringing the spirit of open source to genetic programming, engaged me to develop Public Domain Chronicle, a fast, easy, and free way to secure scientific methods and findings for the public domain. https://publicdomainchronicle.org/ https://publicdomainchronicle.org/ Public Domain Chronicle combines elements of defensive publication, open-access scholarship, and commons licensing to make public domain advocates the fastest runners in the race to publish, preventing others from patenting their findings. PDC's disclosure form for findings in biology is shorter and easier than any standard corporate or academic invention-disclosure process, and produces an immediate, public, republishable prior art record. https://pdc.biobricks.org/publish https://pdc.biobricks.org/publish It's early days for the project, and we're seeking out as many potential researcher-contributors as possible. We're particularly keen to hear from academic scientists and folks in corporate tech transfer offices who may prefer PDC to expensive defensive publication services.

amelius 8y ago

Some critical questions: who is the target audience for these instruments? Aren't academic budgets sufficient to provide for a lab with proper basic instruments? Are these kind of instruments a financial bottleneck when setting up a lab? And do we want biology PhD students and postdocs to spend time on instrument-making (and publish papers on that) rather than on biology?

lwindyb 8y ago
No, yes, and yes
jcelerier 8y ago
> Aren't academic budgets sufficient to provide for a lab with proper basic instruments? sobs
sinab 8y ago
Hey amelius! Great questions. The target audience for these instruments are scientists and hobbyists who don't want to spend a ton of money on similar commercial systems, and want the flexibility to modify their operation (e.g., poseidon can run custom flow profiles per experiment whereas off-the-shelf commercial systems typically only run one flow rate per experiment). The purpose of poseidon is to show that open source biological instruments can be developed and used by a community, similarly to how open source software tools in biology are developed and used. Academic budgets vary from institution to institution and are sometimes determined by exogenous forces beyond the lab's control. A complete commercial system to do single-cell RNA sequencing costs tens of thousands of dollars! Using alternatives such as the Harvard Apparatus syringe pumps and DropSeq [0] to run the same experiment will still cost you into the thousands of dollars. With the poseidon system, we greatly reduce these costs. Users can build the instruments to run these experiments for less than $400 and are not restricted to additional costs and tedious firmware upgrades to expand the system. In response to your point on time management and instrument-making, I think that if there exists a need to develop these systems such that they will advance biological experiments then it's totally cool to have academics work on these sorts of projects! Biologists and bioengineers have always developed tools alongside discovery and this is no different from developing bioinformatics tools. [0] https://www.cell.com/abstract/S0092-8674(15)00549-8 https://www.cell.com/abstract/S0092-8674(15)00549-8
- amelius 8y ago
  Thanks for these great answers. The only point where I would disagree is your comparison with bioinformatics software. The difference there is that installing a bioinformatics package and learning to use it takes far less time than crafting an instrument, especially considering tasks like finding the right suppliers of components, and calibrating and testing the device (for which you might need other instruments). But on the other hand, perhaps building these self-made instruments can become a task for specialized, facilitating instrument-makers that are already part of many institutions.
  - munfred 8y ago
    Note: I also helped develop poseidon The poseidon system was explicitly designed with ease of assembly in mind. If you look at the build videos [1] you'll see that assembly of the entire system (3 pumps + microscope station) takes less than an hour and requires just pliers and screwdrivers. The importance of ease of assembly was a lesson that we took from assembling the miniDrops microfluidics station [2] developed specifically for one kind of experiment (dropSeq) [3]. The miniDrops is very good at what it does but assembly was somewhat cumbersome: it required ordering a custom PCB, specialized parts only available from one vendor (whom I had to nag over the phone to send me a quote!) and assembly of the device itself took 10-20h. Not every kind of equipment can be made as easy to source and assemble as we did with poseidon, but we really think that keeping this at the front of your mind can make or break the adoption of a piece of open source hardware. This is especially true in the context of biology laboratories, where many people are not what you could call "hackers" or "makers" and will be immediately put off by a daunting assembly process. [1] https://pachterlab.github.io/poseidon/hardware https://pachterlab.github.io/poseidon/hardware [2] https://metafluidics.org/devices/minidrops/ https://metafluidics.org/devices/minidrops/ [3] https://www.nature.com/articles/s41467-017-0265 https://www.nature.com/articles/s41467-017-0265
bsder 8y ago
> And do we want biology PhD students and postdocs to spend time on instrument-making (and publish papers on that) rather than on biology? This is an age old question. And the answer is: yes, we actually do. Even if a lab can afford all its instruments, sometimes you are researching something that requires a different approach. Most commercially available lab machines are NOT hackable, and you will have a difficult time bending them into a different configuration.
- neltnerb 8y ago
  Yeah, for my grad thesis I had to figure out how to incorporate a fuel injector into a chemical reactor to meter fluid flow. Novel research equipment is by definition not off-the-shelf, so the skills to roll your own is often necessary to push the envelope. And a lot of the time that equipment isn't funded by a current project and you need to prove the idea is sound before you can justify asking for the money to do it. Of course if that proof of concept is good enough to keep being used all the better.
jryb 8y ago
We couldn't find a programmable temperature controller for a microscope that met our requirements so I ended up building it from scratch. It took me a month and I didn't know electronics when I started, but now we can do our experiments, and I have a skill that will benefit me and my employers for the rest of my career. I'd argue that that's a great use of a PhD, as long as it's not the only thing I'm doing. Additionally, in my lab and many others, there simply wasn't any tool we could use to answer all the questions we have, so we had to invent them. That said, these are much more bespoke systems, but as we push the envelope of what we need to observe, instrument making and method development are only going to be more critical. The inflation in the scientific equipment market is also ludicrous. Since I've been in grad school some of the things I have to buy have doubled in price. And it really is pathetic when it's something like a syringe pump - I mean you're rotating a screw with an electric motor to push a piece of plastic. I get that it's a small market and the vendor has to make a living, but this isn't the best way for a civilization to direct its resources.

sinab 8y ago

My name is Sina Booeshaghi a second year PhD student at Caltech and I built and designed the poseidon system (with the help of Eduardo Beltrame, Jase Gehring, Dylan Bannon, and Lior Pachter) in the Pachter Lab. If you have any questions I'm happy to answer them!

kasbah 8y ago
Nice work. You (and others interested in open science hardware) should come join our community at http://openhardware.science http://openhardware.science.
- sinab 8y ago
  Thanks for the link! I'll check it out and send it to the other authors.
sbr464 8y ago
I was needing a fully digital (controlled) microscope stage and stand recently. I was suprised to find a lack of motorized stages compared to other items. It would be nice to have a modular stage so it could be used with different stands. Rotation and height adjustment would be nice as well. Have you came across anything similar? It seems like it would be trivial to build similar to your other designs.
- sinab 8y ago
  Ooo this could be a great extension of the current microscope system! The only thing I've found is this https://www.thingiverse.com/thing:2525155 https://www.thingiverse.com/thing:2525155 which while not motorized, allows for height adjustments. Consider making an issue (tagged improvement) on the GitHub page! https://github.com/pachterlab/poseidon https://github.com/pachterlab/poseidon
- munfred 8y ago
  I have been thinking about this problem for a while. I would like a cheap, open source, commercially available kit for xyz gantry systems. That's essentially what desktop CNC machines and 3D printers are and people hack them for all kinds of purposes. Unfortunately my current conclusion is that there is no solution that satisfies all 3 at the moment. Your best bet for building such a system is looking at cheap 3D printers and CNC machines, but it'll always be a little bit of a hack and extra work because you'll have to remove parts (hot end, drill bit..) and adapt something that was not designed with the intent of being entirely re-purposed. If anyone here knows of a xyz gantry system kit that satisfies all 3 (cheap, open source, commercially available) please let me know.

neltnerb 8y ago

Oh, this is awesome. I build a lot of random equipment, how do I help? This kind of thing could kickstart a lot of novel systems that'd take forever to design or cost a ton otherwise.

sinab 8y ago
I love your enthusiasm! Why don't you shoot me an email and we can chat some point next week.. It would be really cool to get a great community around the project, extending capabilities and adapting the core technology to random equipment. My email should be in my profile.

GautamGoel 8y ago

I work with Lior at Caltech. He's an amazing guy, probably the only person I know who is capable of doing first-rate work in both biology and mathematics.

AndrewGYork 8y ago

A different target audience, but in the same spirit, here's an open source microscopy project from our lab: https://andrewgyork.github.io/remote_refocus/ https://andrewgyork.github.io/remote_refocus/ My friend André Maia Chagas is doing some inspiring work in open hardware too: https://mobile.twitter.com/chagas_am https://mobile.twitter.com/chagas_am