[harrison]

Hello,
What version of the reactor do you have? It should say on the outside of it V1.1, V1.2, etc…
Some of the older versions sometimes had stalls with stirring, which we fixed in subsequent generations.
Regardless, the best approach to avoid this would be to use a smaller stir bar, or one that is “easier” to turn (e.g. has few sharp edges), and run at a higher speed.

[harrison]

No, just fresh media with no cells (i.e. LB just out of the autoclave…)

[harrison]

We have used 70% ethanol, as have several other labs I know, and we have not had such issues. Potentially might it be due to media/cells or residue thereof in the tube?

[harrison]

They were done by calibrating against a spectrophotometer in our old lab. If you wish to see how it is done, check the supplementary material of the Chi.Bio paper in PLoS biology which shows this raw data + the fitting used. In that case various standard solutions were used in the calibration, but you could also use whatever cell type you are using in your research to make sure it matches up perfectly across your different instruments.

[harrison]

They were done by calibrating against a spectrophotometer in our old lab. If you wish to see how it is done, check the supplementary material of the Chi.Bio paper in PLoS biology which shows this raw data + the fitting used. In that case various standard solutions were used in the calibration, but you could also use whatever cell type you are using in your research to make sure it matches up perfectly across your different instruments.

[harrison]

Yes, the laser is generally set to a constant power output – there is an optical feedback loop regulating this (there is a photodiode inside the laser diode which is used to ensure the same optical output power e.g. regardless of temperature fluctuations).
There isn’t really an optimal level to set it at – generally you want it fairly bright so you use the dynamic range of the sensor, but in fact the sensor can have its gain increased (usually it is only set to 1x for the laser but can go up to 512x) if you wish to runt he laser at lower power.

[harrison]

That does look like a potentially faulty pump board, or fault in the communication lines somewhere between the reactor and pump.
Is it a new system you have recently started working with? If so it might be a manufacturing defect there.
If it is an old system that worked well previously, I’d recommend swabbing/cleaning the pump circuit and USB connectors with ethanol and letting them dry, then having another go.

[harrison]

Hello,
Are you referring to the current through the LED itself?
If yes – the answer is it depends on what power setting you have it set to. The power setting of “1” is ~700mA (i.e. quite a lot of power!). Lower power settings should be in a linear relationship to this (e.g. 0.1 setting means 70mA). That said, it is worth noting that the same current through different LEDs will give different luminous fluxes. The LED is a “LZ7” from LedEngin. If you want more detail the datasheet they provide is the best source.

[harrison]

You need to set the OD to 0.5, and thet set the value of the “zig” parameter to 0.1, Then it would go from 0.5-0.1=0.4 up to 0.5+0.1=0.6. This can be done in the sysData structure. Or you could re-code it (i.e. re-write) the zigzag function itself if you prefer.

[harrison]

Hello,

Yes, one tube does need to be higher than another, but the absolute difference doesn’t have to be ~meters. It is OK if only 20cm. How is it set up at the moment?

As to your second point – I think if the pump is still turning then it should be OK. From my experience yes, adding tape can slow it down, but unless it is REALLY struggling (i.e. going like 10% of the default speed without tape) then it should not be a major issue.

Likely the reason you may have these difficulties is that the particular pumps came from a batch manufacturered with slightly different tolerances etc. The Chi.Bio suppliers Labmaker source these pumps in bulk so there is pump-to-pump variation, I guess this is what we expect when going for a cheap pump model!

[harrison]

Hello,
If it is visibly turning slower / seeming to struggle it seems to imply that there is plenty of resistance in there (you want the resistance since this is arising from compression of the pipe – which leads to sealing).
So – how do you know they are not making a good seal? It is unclear to me what you mean by “air moving through the tubing”. If air is going in the direction you want liquid to travel, this doesn’t necessarily mean anything. The problem would be if air is going the opposite way (perhaps this is what you meant).

If air is going the opposite way other fixes might be to make sure neither end of the tubing is MUCH lower than the other. Or, make sure when you put the pipe into the pump head you push it down into the head – e.g. so that it touches the bottom of the cream coloured plastic below the rotor, and is not bulging up and out of the rotor (e.g. touching the clear lid) as it rotates. Let me know if this explanation doesn’t make sense…

[harrison]

Hello,
Thanks for the additional information. If it is measuring OD then that means the Laser is working – but not necessarily the LED.
This might make sense if the fault is in the PWM chip in the main reactor, which incidentally also controls the hot plate.
One possibility is that there is a bad solder joint on some of the pins of that chip, and consequently the software is not able to communicate with it. Hence it somehow gets stuck in a state where the LEDs don’t respond and the hot plate is on.

It is however quite strange that this would just “break”, in the sense that it was previously working fine, and then stopped working all of a sudden. Can you think of anything that might have happened after those runs where it was working fine that may have caused a problem? (e.g. it being dropped, cleaned, etc).

It does sound like the fault is in hardware so indeed Labmaker would be the best to talk to about a replacement.

[harrison]

Hi Brandon,

It needs a 12V supply, ideally greater than 2A (so 24W total). The connector itself is a very standard power jack with 2.1 or 2.5mm interior diameter, with positive voltage on the inside (which is the standard).
You can get many such models from e.g. searching “12V power supply” on amazon.
Harrison

[harrison]

Hello,
Thanks for the helpful diagnosis.
The one thing not quite mentioned is – when you start without the reactor, then connect reactor, then scan devices – if you THEN try to do control something other than the pumps (for example, turn on a LED) does it work? I assume based on what you said the answer is yes but it was not explicit.
Is this only a problem on one reactor? Do yo have others working fine?

It sounds to me as if there is a hardware fault in your pump board, or at the very least, somewhere downstream of the digital connection that goes out to the pump board. Could you take a look at the soldering under the pump board and check if anything looks suspect? Also, look at the microUSB connectors on both ends of that connection, are these all OK, not broken?
In parallel it might be worthwhile contacting Labmaker to tell them it seems the pump board is defective, and request a new one.

[harrison]

Hello,
Since there is quite a bit of variability between the pumps we do not have an approximate calibration. The easiest thing to do if you wish to work this out is to set the pump to some low speed e.g. 0.01 then time how long it takes to pump 5ml or such into a measuring cylinder.

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