4 ms·

Sure. Right now, Opentrons rules with their open source robots, so liquid handling robots are pretty well handled. Xarm makes good arms for interfacing with Op

by koeng 6y ago

Sure. Right now, Opentrons rules with their open source robots, so liquid handling robots are pretty well handled. Xarm makes good arms for interfacing with Opentrons, so then it comes to everything else necessary to get to full automation. 1. Automated plate hotels I need plate hotels to storage samples that interfaces with my robot arm and robot systems. This I'm basically using Theo Sanderson's designs for this https://www.thingiverse.com/thing:2668120 https://www.thingiverse.com/thing:2668120 since buying them commercially is so darn expensive. I really need this for my system, so I am building em. 2. Plate sealer / unsealers My entire full automation pipeline is built around NOT needing a plate sealer or un sealer (something you can't do with the vast majority of screening systems). Automated versions of just the sealer itself cost more than 2 liquid handling robots and a robotic arm combined (and all it does is seal plates!) I think there is an opportunity for building simple but effective automated plate sealers and unsealers. 3. A train system I think Concentric (Ginkgo's COVID company) uses something similar, but basically a system that can use small trains to bring plates and reagents around a lab to different robotic stations. I'll probably just do that with lines of robotic arms, but I definitely spent quite a bit of time thinking of how to do this. (in my factorio megabase I really learned how to route trains, and I think it's exactly the same problem I face with my robotic work stations). I'm not sure how to scale the selling of that though.

dekhn 6y ago
Are you really doing this at home, in a room converted to a lab, with actual live biology? I did that in my garage but after having to clean up a big contamination and debug experiments due to temperature fluctations, I realized there was a reason people use real labs.
- koeng 6y ago
  Yes I am really doing this at home with actual living biology. Garages are terrible for biotech because of contamination problems. I have a bedroom that I've sealed quite well with 2 box fans constantly running filtering the air (tape a 20x20 filter to a box fan and it works great). When I work with media or anything I also use a flame. I still have some problems with contamination, but it is manageable. There are also biological ways to get around contamination problems. So long as your media is clean, if you use a strain like Vibrio natriegens, it just outgrows literally everything, so it's not that big of a worry. I have a few ruuvitags + a raspberry pi to monitor the temperature, and I live in Coastal California, so we don't have that much fluctuation. It hasn't mattered for my experiments, anyway, which are mainly just DNA cloning.
daemonk 6y ago
I completely agree with your point about being good at software/hardware/biology is the key to running a successful production biotech lab because you can try to supplement various weak points with the other domains. I've been 3d-printing devices that helps with DNA extraction in my lab. I am interested in automating the lab I am running now. We have an opentrons that we bought couple years ago that I never got around to using. But now that we are regularly getting a decent amount of samples in a week, I really want to get it going. Are you starting a lab automation service? I agree with your point about plate sealer/unsealer. It is a huge pain point in automation. However, I am not sure if you can convince regulatory bodies to approve it. Are you doing some kind of mineral oil top layer to prevent evaporation? We've actually tried that before and it kinda worked, but the problem is that the mineral layer messes with the SPRI bead purification step. I am sure it can be solved with more testing, but it just wasn't worth the inconsistency at the time.
- koeng 6y ago
  I'm starting what could be thought of as a DNA cloning company. So sort of automation service, but for one specific application. > Are you doing some kind of mineral oil top layer to prevent evaporation The opposite: the process is pretty much based off of dessication (plus a little bit of tube opening by the bots for important chemicals). For thermocycling stuff, I'm planning on just using Opentrons module with the reusable seals. I really wanted to find a way to use reusable seals everywhere, but I just couldn't think of a way to do it well robotically. Thankfully, I don't need to convince the regulatory bodies of anything, since I'm just doing DNA cloning. > We have an opentrons that we bought couple years ago If you need to do multichannel stuff, do yourself a favor and go buy Gen2 multichannels and toss your old Gen1. The Gen1 multichannels are hilariously unreliable, but the Gen2 are pretty solid. Love those bots overall though - I got two of em so I can work in parallel!
  - daemonk 6y ago
    Desiccation is an interesting approach. I don't see it as being used for every step of a reaction though? It would take too long to wait for desiccation between every step? And depending on the buffers you are using, you might be increasing the salt concentrations after you re-constitute? I guess you can take that into account when you add the reconstitution buffer. Are you open to discussing some kind of consulting arrangement between you and my company? If so, how do I reach out?

by koeng 6y ago

dekhn 6y ago

Are you really doing this at home, in a room converted to a lab, with actual live biology? I did that in my garage but after having to clean up a big contamination and debug experiments due to temperature fluctations, I realized there was a reason people use real labs.

koeng 6y ago
Yes I am really doing this at home with actual living biology. Garages are terrible for biotech because of contamination problems. I have a bedroom that I've sealed quite well with 2 box fans constantly running filtering the air (tape a 20x20 filter to a box fan and it works great). When I work with media or anything I also use a flame. I still have some problems with contamination, but it is manageable. There are also biological ways to get around contamination problems. So long as your media is clean, if you use a strain like Vibrio natriegens, it just outgrows literally everything, so it's not that big of a worry. I have a few ruuvitags + a raspberry pi to monitor the temperature, and I live in Coastal California, so we don't have that much fluctuation. It hasn't mattered for my experiments, anyway, which are mainly just DNA cloning.

daemonk 6y ago

I completely agree with your point about being good at software/hardware/biology is the key to running a successful production biotech lab because you can try to supplement various weak points with the other domains. I've been 3d-printing devices that helps with DNA extraction in my lab. I am interested in automating the lab I am running now. We have an opentrons that we bought couple years ago that I never got around to using. But now that we are regularly getting a decent amount of samples in a week, I really want to get it going. Are you starting a lab automation service? I agree with your point about plate sealer/unsealer. It is a huge pain point in automation. However, I am not sure if you can convince regulatory bodies to approve it. Are you doing some kind of mineral oil top layer to prevent evaporation? We've actually tried that before and it kinda worked, but the problem is that the mineral layer messes with the SPRI bead purification step. I am sure it can be solved with more testing, but it just wasn't worth the inconsistency at the time.

koeng 6y ago
I'm starting what could be thought of as a DNA cloning company. So sort of automation service, but for one specific application. > Are you doing some kind of mineral oil top layer to prevent evaporation The opposite: the process is pretty much based off of dessication (plus a little bit of tube opening by the bots for important chemicals). For thermocycling stuff, I'm planning on just using Opentrons module with the reusable seals. I really wanted to find a way to use reusable seals everywhere, but I just couldn't think of a way to do it well robotically. Thankfully, I don't need to convince the regulatory bodies of anything, since I'm just doing DNA cloning. > We have an opentrons that we bought couple years ago If you need to do multichannel stuff, do yourself a favor and go buy Gen2 multichannels and toss your old Gen1. The Gen1 multichannels are hilariously unreliable, but the Gen2 are pretty solid. Love those bots overall though - I got two of em so I can work in parallel!
- daemonk 6y ago
  Desiccation is an interesting approach. I don't see it as being used for every step of a reaction though? It would take too long to wait for desiccation between every step? And depending on the buffers you are using, you might be increasing the salt concentrations after you re-constitute? I guess you can take that into account when you add the reconstitution buffer. Are you open to discussing some kind of consulting arrangement between you and my company? If so, how do I reach out?