[harrison]

Hello
There is already an optogenetics mode which is basically doing this. It is not set up to run 10s every 5 minutes, but rather at variable intensities during each 1 minute cycle. Do you explicitly need the 5 minute cycle or are other ways OK?

In general if you want to implement from scratch, then yes, custom program is fine. I would look at the optogenetics one to use as a template for how to switch LEDs as and when needed.

[harrison]

Hello Sven
I don’t KNOW of anyone that has done this but It shouldn’t be too difficult. Main challenge will just be to write some python code that gets data into and out of the chi.bio back end. You could do this with http requests (i.e. the same mechanism currently used to update the GUI on the host computer). That should be fairly easy if you take a look at how the existing python (e.g. app.py) is structured.

[harrison]

ALas I dont believe it has been done. You would probably be best to just take a slow-motion video on a phone and then count rotations/time to get a rough estimate of RPM

[harrison]

The 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

[harrison]

Hello,
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
Harrison

[harrison]

Yep, 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 🙂

[harrison]

It 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?

[harrison]

Hello! 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.

[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…

[Author]

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