Interested in Automated Cell Culturing?

[Nathaniel Chen]

I have always wondered if a desktop cell culturing machine would be feasible or useful for DIY biologists. I think it would be interesting to simplify some aspects of a wet lab into a black box sort of device. 

Has anyone else considered this / would anyone have a use for such a device?

[Enrico]

do you have an example of this machine?

[Mega]

You mean bacterial cells? There are bacterial/fungal fermentors in our university. I think they even sell a home-beer brewing device, but don't know how sterile/automated that is. probably not so much.


As for the eukaryotic cells: the ''tips'' for eukaryotic cells aren't autoclavable I assume. They were said to cost 1€ each...


However the idea is great.

[Jonathan Cline]

See the Dunham Lab Chemostat manual for the ultimate bio machine.
   http://www.google.com/search?q=dunham+lab+chemostat

I've suggested building a continuous flow culturing system for the local biohacker lab though have mostly received "what for?" so far since the experiments planned are one-offs not continuous or evolution.   Also search back in the archives for the controller board I proposed which I called "the sensomatic".    These aren't exactly "desktop culturing machine" though they are the start.

BTW there are a couple low cost desktop culturing machines already sold mass market for $50-$200 range, maybe we can list them all?
 
 - bread maker.. = yeast

 - yogurt maker..  = yeast

 - diy beer kit = yeast  ; though I haven't seen a "machine" just a manual kit which requires a lot of human labor so far. Does a "beer machine" exist?

 - aquarium automated dosing setups = algae ; though again not a complete machine as needed here, could add specific sensors and pumps.

Also I think it'd be fun/interesting to take a cheap/discarded bread maker and replace the control panel to add more bio culturing functionality.  At a minimum they would make great tabletop incubators for single-flask operations - replace the mixer bar with a magnetic stir bar.

The ultimate in automated culturing would be a tiny wireless sensor module which could be dropped into a flask, which is also autoclavable, and reports OD, pH, temperature, and CO2 or other gas.  It's a big engineering challenge on multiple fronts.


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[Enrico]

answer is Arduino

[Cathal Garvey (Phone)]

Cue lots of grumbling from grumpy EE-heads.. :P

Enrico <enr.t...@gmail.com> wrote:

answer is Arduino

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[Cathal Garvey (Phone)]

Cue lots of grumbling from grumpy EE-heads.. :P

Enrico <enr.t...@gmail.com> wrote:
>answer is Arduino
>
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[Nathaniel Chen]

My line of thinking is that making the whole cell line upkeep / implement protocol / assay process more hands-off could open up DIY Bio to people who want to understand and build from a higher level without getting messy with pipettes and haemocytometers and just doing it all by hand. Like some of you said, autoclavable parts would be huge. I think plug-in style assay instruments would help too.

This is an example of what I am picturing, but I want something smaller scale, more modular, and hackable.

(PDF)

http://logosbio.com/down/celf/celf_brochure.pdf

[jarlemag]

Great link! Regarding "Beer machine", there is this: http://linux.slashdot.org/story/13/05/16/1727256/linux-is-an-obvious-choice-for-automating-the-beer-brewing-process-video

- JP

[Cathal Garvey (Phone)]

Along same lines I've often wondered about a microwave-powered stirbar. As in, magnetic strip/plate under flask, magic bar in flask absorbs microwaves and self-propels. Would be great for keeping temperature even in drinks, let alone flasks of broth..

[jarlemag]

Could you explain the physics of that in a bit more detail?

- JP

[John Griessen]

On 07/06/2013 06:00 PM, jarlemag wrote:
> Could you explain the physics of that in a bit more detail?
>
> - JP
>
> kl. 23:57:10 UTC+2 lørdag 6. juli 2013 skrev Cathal Garvey (Phone) følgende:
>
> Along same lines I've often wondered about a microwave-powered stirbar. As in, magnetic strip/plate under flask, magic bar in
> flask absorbs microwaves and self-propels. Would be great for keeping temperature even in drinks, let alone flasks of broth..

Magic might be required, but you can kinda sort of imagine a tortuous path
to getting microwave energy, running a computer programmed gizmo, balancing
heating vs stirring power somehow would be tough...

It's all so much easier to imagine a time slicing do this, do that, do this,
do that kind of machine without much magic required. You'd use a no-permanent
magnet stir bar -- just paramagnetic iron with a plastic wrap. Move that for a while with
magnetic fields, stop that, blast with microwave energy field, stir again, repeat while necessary.

And sure, Arduino IDE can be used to develop it.

[Simon Quellen Field]

We used to build microwave leak detectors by putting an LED across the leads of a 1N914 diode. The diode's leads were just the right length to make a resonant dipole antenna for the microwaves. If there was enough energy in the rectenna to light the LED, the seals on the microwave were deemed inadequate. If you placed it inside the microwave, the LED got too much current and became a Dark Emitting Diode (DED).

If instead of the LED, you put a small DC motor, it would spin. If it spins too fast you can add a resistor. Put a magnet on the motor's axle, and you have a magnetic stirrer. Put all of that in a housing and you're good to go. No integrated circuits required.

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[Nathan McCorkle]

Would you need a diode? Would you need to decouple the motor from the
antenna, how would you tune it's resonant frequency? If you can't
change the motor circuit's resonant frequency, where can you get a
high-enough power tunable microwave emitter?

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[Simon Quellen Field]

The emitter is inside the microwave oven. Mine has 1400 watts, which seems to be plenty of power to boil water.

You need the diode. It converts the gigahertz frequencies into DC that the motor can use.

A dipole antenna is simply two conductors whose length determines the frequency at which the antenna is resonant. For collecting power, you don't actually need to be resonant. You'd collect less power, but there is 1400 watts to play with, and the motor only needs 50 milliwatts or so.

The microwave oven frequency is 2.45 GHz. A wavelength is thus 12.24 centimeters. A half-wave dipole would thus be 6.12 centimeters across, with each leg being a bit over 3 centimeters long. Cut each lead of the diode down to 1.2 inches and you have your rectifying antenna for 2.45 GHz.

Other antenna structures can be used, such as the quad discussed here. Better diodes might also be useful, as the ones we used are not that good at 2.45 GHz, and if you want to actually draw more power than you need to light an LED, a better diode might be a good idea. I think I said 1N914, but on further recollection we probably used a 1N34A (it was a long time ago). A 1N60 diode is about 60 cents.

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[Nathan McCorkle]

On Sat, Jul 6, 2013 at 6:46 PM, Simon Quellen Field <sfi...@scitoys.com> wrote:
> The emitter is inside the microwave oven. Mine has 1400 watts, which seems
> to be plenty of power to boil water.
>
> You need the diode. It converts the gigahertz frequencies into DC that the
> motor can use.
>
> A dipole antenna is simply two conductors whose length determines the
> frequency at which the antenna is resonant. For collecting power, you don't
> actually need to be resonant. You'd collect less power, but there is 1400
> watts to play with, and the motor only needs 50 milliwatts or so.
>
> The microwave oven frequency is 2.45 GHz. A wavelength is thus 12.24
> centimeters. A half-wave dipole would thus be 6.12 centimeters across, with
> each leg being a bit over 3 centimeters long. Cut each lead of the diode
> down to 1.2 inches and you have your rectifying antenna for 2.45 GHz.
>

Aren't you discounting the length of the coils in the motor? We don't
really know how long they are, and they're probably a different gauge,
if the thickness matters (but it sounds like you say the length only
matters).

[Jonathan Cline]

Arduino is a toy meant for teaching junior high school students simple
electronics. Similar to the basic stamp 15 years ago.
As long as you're okay with that... plus the extra $$$.. then....

## Jonathan Cline
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On 7/6/13 12:28 PM, Enrico wrote:
> answer is Arduino
>

[Jonathan Cline]

To place a smart device in a flask (which doesn't rely on a battery) would likely use wireless power which has recently come into production silicon:

 http://www.google.com/search?q=ti+wireless+power

The designs use RF beam forming to transmit energy and data thru the air (without wires) or thru short distances of water.  RF energy behaves differently in water however so it is more difficult.  The neat thing is that the RF does include both a power phase and a data phase so the target device can be remotely powered.    Motors use a significant amount of current so not sure it would be possible to self propel using this. (Not sure why it would be necessary since magnetic stir bars work fine.)   A well designed circuit though could run sensors on the wireless power (i.e. not arduino, hah).

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[Nathan McCorkle]

On Sat, Jul 6, 2013 at 5:40 PM, Simon Quellen Field <sfi...@scitoys.com> wrote:
> We used to build microwave leak detectors by putting an LED across the leads
> of a 1N914 diode.

I tired simply microwaving an LED, it flashed briefly in the first few
seconds, then nothing, and a battery won't light it anymore.

[Simon Quellen Field]

The motor and its coils are getting the rectified DC from the rectenna.

They are not part of the resonant system.

The main problem is that the motor needs a lot more current than the LED did.

Rather than power the thing with microwaves, the simple approach of using batteries is probably so easy and cheap that implementing Cathal's dream machine would never be as practical or cheap. I was just trying to rise to the challenge. :-)

Has anyone on the list built their own magnetic stirrer yet?

A motor, a bar magnet glued to the axle, a couple batteries, and a non-ferrous metal enclosure to prevent the microwaves from cooking the batteries, and you are all done. Add a rheostat to control the speed. You could drill a hole in the metal box for the axle and glue the magnet on the outside of the metal box, then put a glass plate above it to hold the beaker to be stirred.

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[Simon Quellen Field]

Now you have what we call a Dark Emitting Diode.

It's DED Jim.

You don't put the leakage detector inside the microwave. :-)

We were measuring milliwatts, not the kilowatts you were feeding your LED.

If you replace the LED with a motor, the motor would be fine, but the microwave diode would probably fry because they aren't designed for kilowatts. Cutting the leads shorter (so they are no longer resonant) would reduce the current in the diode to something it could handle. Whether that is enough to drive the motor is the question. Using batteries seems so much simpler. :-)

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[Cathal Garvey]

Ah, I assumed including a battery would be effectively a no-no, good to
know you could potentially create a conventional-but-shielded device.

Also, in your other email you suggest that absorbing "too much" power
into a rectenna-powered device would fry the microwave: is this an
EM-coupling thing? I assumed a Microwave was like a "bath", and that
absorbing all the EM in there would just deplete the available wattage
for cooking with, rather than causing the diode to emit even more EM?

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[John Griessen]

On 07/07/2013 01:30 PM, Simon Quellen Field wrote:
> Has anyone on the list built their own magnetic stirrer yet?

no, but...

> A motor, a bar magnet glued to the axle, a couple batteries, and a non-ferrous metal enclosure to prevent the microwaves from
> cooking the batteries, and you are all done. Add a rheostat to control the speed.

What would the interaction of the bar magnet field and the microwaves be like? What I can find on resonances suggests
iron can move and have resonances much higher than the 2.4GHz of microwave oven, so they would interact, but what are the relative
strengths of fields? Does the 2.4GHz E & M field peak out higher than the bar magnet, or the other way around?
How much would the bar magnet field bend and rearrange the microwaves?

You could drill a hole in the metal box for the
> axle and glue the magnet on the outside of the metal box, then put a glass plate above it to hold the beaker to be stirred.

What would that get you vs. the bar magnet inside a brass can?

Supposing you have a strong magnet rotating under a beaker of water in a
microwave oven that's on for 30 seconds, will you get:

a. better diffuse heating by magnetically deflected microwaves.
b. A hot bar magnet.
c. all of the above.
d. none of the above.
e. a bar magnet with decreased permanent magnetism.

[Simon Quellen Field]

Good questions, but they have easy answers.

1. Microwaves don't penetrate conductors. The magnet will not heat up, and it will not be affected by the microwaves. Only the conduction electrons on the surface will participate in an microwave activity, and they will basically just reflect the microwaves. Most microwave ovens have a little fan hidden between the inside top surface of the oven and the microwave emitter, so 'stir' the microwaves, to avoid hot spots caused by resonance. The magnet would just look like an extra (and much smaller) stirrer.

2. Having the magnet above the metal box means that there are no eddy currents between the magnet on the motor and the magnet in the glassware. I doubt that this would be much of an issue, but I have not done the experiment, so I gave both methods. Certainly having the magnet sealed in the can would make cleaning and sterilizing easier. But you would still have to open the can to turn the device on and off, and to replace the batteries.

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[John Griessen]

On 07/09/2013 06:53 PM, Simon Quellen Field wrote:
> Having the magnet above the metal box means that there are no eddy currents between the magnet on the motor and the magnet in the
> glassware.

I'm thinking a stirrer bar that is just paramagnetic with an inert plastic coat might do. Kind of like an induction motor does.

[John Griessen]

It's on my to do list. let's talk.

[Nathaniel Chen]

> It's on my to do list.  let's talk. 

Sounds good! I can't seem to find your email address, mine is nathanielchen1(at)gmail.com

[Nathaniel Chen]

My posts weren't going through before. Here is something very similar to what I have in mind: (PDF)

http://logosbio.com/down/celf/celf_brochure.pdf

I would love to have one of these on my desk. I would prefer something open source, low cost, and hackable, of course :)

[Nathan McCorkle]

On Wed, Jul 10, 2013 at 4:53 PM, Nathaniel Chen
<nathani...@gmail.com> wrote:
> My posts weren't going through before. Here is something very similar to
> what I have in mind: (PDF)
> http://logosbio.com/down/celf/celf_brochure.pdf

That's pretty cool! I like it! The 10 inch touchscreen is telling of
it's size though, you'd need a big desk to keep it on!

[John Griessen]

On 07/10/2013 06:53 PM, Nathaniel Chen wrote:
> http://logosbio.com/down/celf/celf_brochure.pdf
> I would love to have one of these on my desk.

It mentions CO2 -- is that for mammal cell culture, or more general?

I think approaching bacterial and plant tissue culture first is a
better business path for me, (and the OSHW lab gear community).

The embedded winXP is not on my list of 'to do's.

[Nathaniel Chen]

> It mentions CO2 -- is that for mammal cell culture, or more general? 

Yeah, it is almost certainly for mammalian cells.

> I think approaching bacterial and plant tissue culture first is a 

> better business path for me, (and the OSHW lab gear community). 

I think it would be cool to have something like automated transformation. 

Design a plasmid, insert into machine, get transformed bacteria and products.

> The embedded winXP is not on my list of 'to do's. 

I guess they weren't terribly concerned about price. I've heard good things 

about Yocto for embedded systems https://www.yoctoproject.org/

[Nathan McCorkle]

On Wed, Jul 10, 2013 at 5:39 PM, Nathaniel Chen
<nathani...@gmail.com> wrote:
>> It mentions CO2 -- is that for mammal cell culture, or more general?
>
> Yeah, it is almost certainly for mammalian cells.

Yes, that's also why there is a trypsin reservoir and it uses the word
'passage' (meaning to decant and rinse an adhesion culture with serum-free
buffer, adding trypsin to 'trypsinize' or get the cells off the wall
of the chamber, agitating,
then sucking/pouring off a bit into a fresh growth chamber with fresh media).

--
-Nathan

[Cathal Garvey]

> The embedded winXP is not on my list of 'to do's.

If you include a UVC lamp and cycle biocidal gas through the growth
chamber, you can prevent proliferation of proprietary software in a
lab-scale incubator. In a DIYbio environment, it's best simply not to
culture bad software in the first place. :)

[Nathaniel Chen]

I am thinking that any sort of automated culturing system would have reusable tubes in lieu

of disposable pipette tips for removing old media / picking up cells / adding new media.

Does anyone know of a practical way to sterilize such a thing short of autoclaving?

From what I have gathered, an ethanol bath is not enough, and OpenWetWare hasn't

yielded any answers. 

[Nathaniel Chen]

Actually ended up finding a great source for pipette cleaning here:

https://groups.google.com/forum/#!searchin/diybio/clean/diybio/_deN5xNc6Wk/ze3zV9yb2TMJ

A compact DIY autoclave would be interesting.

[Eugen Leitl]

On Wed, Jul 17, 2013 at 08:52:24PM -0700, Nathaniel Chen wrote:

> A compact DIY autoclave would be interesting.

Hmm, heat, pressure, steam. What could possibly go wrong?

[Nathan McCorkle]

What is wrong with a hotplate and a small pressure cooker controlled by an arduino?

Or, just buy a digital pressure cooker, which are becoming more available in brick and mortar stores here, but also easily findable on amazon.com

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[CG]

Found 1n34a cheap at http://www.bgmicro.com/1n34a-germanium-diode.aspx