[harrison]

Hello
So are you saying that if you have only one reactor connected, to a port that it is NOT M0, that it still fails in this way? Further, that this behaviour is replicated for each of the different reactors? If yes it would imply potentially some mess/short/broken part on the control computer.

Is there any combination of connectionrs/reactors (except from nothing connected) that gets this to happen?

Some things to note – you shouldn’t have any reactors connected and not have them powered, as this leads to crashes. Another – try swapping out the USB cables for a given reactor in case it is borked. Also, _maybe_ you have some unhappy reactor you don’t know about, so I would try each of them individually connected to e.g. M1 and see if ANYTHING works – because if one combination works it implies it is not the control computer…!

[harrison]

Thanks, this is really cool!!

[harrison]

Hello,
If you are putting in a clean test tube and it is still jumping around a lot, it might be that the reactor is faulty, i.e. the light source isnt on properly.
WHat is the raw OD0 readings you typically see? If these are <500, likely reactor has a defect. You could ask Labmaker about possibility of fixing this.

Harrison

[harrison]

Hello! Yes, you could just multiply the reading (e.g. FP1_Emit) by the baseband reading, and that gives you the absolute value of the reading (without normalising for excitation light/density)

[harrison]

Hello,
Yes, indeed it will return flat curves. But, the LEVEL of that flat curve should reflect the constant production rate. I.e. if you have twice the production rate you should get twice the measured fluorescene signal.
You can get the raw info from the .csv file by multiplying the FP reading by the baseband signal which gives you absolute amount of light/fluorecence that has been delivered.
However, there may be greater inter-reactor variability due to any change in LED intensity now not being normalised away…

[harrison]

Hey Griffin,

Yes, there is a maximum pumping rate of 0.02. It is set on line 2020 of the current app.py on github, here:
if(Pump1>0.02):
Pump1=0.02

You could increase that.
In practice the reason for it failing shouldnt be air pressure but rather that if your peristaltic pump is not making a good seal with the tubing through it, the liquid will slowly retract backward through the tube as the seal in the pump head isn’t fully blocking this. This CAN be an annoying problem as it may lead to fresh media bottle getting contaminated. I’d strongly recommend fixing that rather than the code – which can be done by adding some tape to the pump head as described in the troubleshooting guide.

[harrison]

This is not an issue I have come across, is it possible the beaglebone control board got wet or otherwise damaged at some point? If this is the issue you could try replacing the beaglebone alone, or the entire control computer form labmaker. FIrst I would take it apart and look closely at the control board to see if anything is obviously damaged. If not, you could try connecting it to various other computers and maybe it will come alive, however, if not likely it is some hardware fault there that is not going to be easy to rectify yourself…

[harrison]

Hello Sofia,

GOod question – you would need to ask Labmaker. They would have a stock of those blue PCBs that they may be able to sell you one in isolation (i.e. without the computer).

This being said, if you already have one (and a not-working beaglebone) you CAN take it off and connect to the new beaglebone. It is a bit stuff, likely you need to use a flat head screwdriver to slowly prise apart the black headers, and do so iteratively moving around the device so you don’t bend the pins too bad

[harrison]

Hello,

I am not sure about the CSV_WRiter error. It implies you have changed something w.r.t the data structures being written to CSV.
If IN GENERAL your goal is to have the 3rd pump on at some rate during an experiment, what I would do is add it to the main runExperiment function. It will need to turn the pump on again every loop (i.e. put this around the line “LightActuation(M,1)”, so that the pumping happens after measurement. Otherwise, the problem may be that you are indeed turning the pump on manually with the GUI but given the automated experiment is running it will turn it OFF again every loop since it wants all pumping to be disabled to do measurements… Hope this makes sense!

[harrison]

Hello

I am afraid no, not really. THe pumps need the power and I2C communications from the reactor, as well as the multiplexer on the main board. It might just about be possible to de-solder some of the connectors from the pumps, add your own 6V supply to the power rails, and then connect pumps directly to the control computer, but this would potentially lead to other issues and be quite difficult to do. If you just need miscellaneous pumping you may be better served getting some off-the-shelf programmable pumps?

[harrison]

OK – suggest you go back to make a fresh micro SD card with the flasher, flash it once only and give it plenty of time at each step (e.g. very important not to de-power it half way through or unplug it), and then try to flash it and connect to DIFFERENT PC’s. If it absolutely doesnt work and somehow the beaglebone has been corrupted beyond repair you may need to get another one…

[harrison]

Basically if you can’t get the beaglebone to talk to your PC (i.e. you cant Putty SSH into it) then the problem is in the beaglebone driver, NOT in the CHi.BIo operating system itself. The CHi.BIo operating system says nothing about how your PC and the beaglebone should interact. I’d recommend taking your control computer and trying it on some different computers to see if it works on ANY of them, and if it does it tells you the beaglebone is working fine and the PC needs tweaking

[harrison]

Great, thanks for sharing. It does sound like a weird system on behalf of Fisher to not sell certain items in certain geographies (those tubes are used very widely in the UK for all kinds of laboratory work/samples…)

[harrison]

Have a look here at recent BioRxiv paper where this is done: https://www.biorxiv.org/content/10.1101/2024.03.03.582641v1.abstract

[harrison]

Hello all,
In practice the primary requirement is the diameter that must be 24.5mm or less to fit in the device. You could therefore find similar tubes from other manufacturers with claimed 24mm diameter and see if they work?

[Author]

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