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harrison
KeymasterThe stirring system can be quite sensitive if it is a large stirrer with strong magnet, FOr this reason I would strongly suggest the recommended stirrer and running it at higher speed if you need better stirring.
Pump – It could be a hardware issue, have you tried a different pump board on the same reactor? If that works, but the othe rpump doesnt, likely that pump is broken.
For the OD function, the Pump=0.02 is the maximum rate. So, this is what you might expect it to deliver if you are way above the target OD. If you are delivering this amount of pumping but you are still unable to reduce the OD of growing cells, it could be the pump is not making a good seal on the tubing or for other reasons it isn’t ACTUALLY pumping. Look at the troubleshooting guide in the manual as there are various ways to improve this, e.g. putting some tape in the pump head, or putting a one way check valve between the pumps and the reactor so liquid cant flow backward at any time.Harrison
KeymasterHello,
THe answer is there ARE differences between reactors and how important they are depends on the biological system + media + fluorescence signal + choice of excitation/emission bands. FOr example, each of the LEDs and each of the spectrometers have slight differences in manufacturing, and the “zero” level of the signal can depend very sensitively on these, so it is important to calibrate it out.GENERALLY in our lab what we do is measure a “zero” signal for each reactor. For example putting the same non-fluorescent sample in each (i.e. just cells +media) , do the measurement, record the value as the “zero” value. Then, we subtract that zero from the experimental data to bring them to a common baseline. Doing this we find we can get very reproducible results, though admittedly it is much easier if you have a strongly expressed fluorescent protein and limited background (e.g. a non-fluorescent media)
Best wishes
HarrisonKeymasterYep, we have done this following that manual thing. If you do “cd //” can you see the etc directory? Or keep doing “cd ..” until you reach top directory then go down from there to find it 🙂
KeymasterIt is unfortunate, I can try to email them as well and cc you. Are you happy for me to do that with your @rug.nl email?
KeymasterHello! Try support@labmaker.org if you haven’t already.
Something you could do is take off the blue PCB (one with microusb connectors) from the beaglebone, and look at it closely to see if anything seems off. If there is any dried residue etc try to clean it with a cotton bud and ethanol.KeymasterHello
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…!
KeymasterThanks, this is really cool!!
KeymasterHello,
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
KeymasterHello! 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)
KeymasterHello,
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…KeymasterHey 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=0.02You 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.KeymasterThis 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…
May 28, 2024 at 9:13 am in reply to: Parallelisation: Control up to eight Chi.Bio reactors simultaneously #1819KeymasterHello 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
KeymasterHello,
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!KeymasterHello
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?
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