[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?

[harrison]

Hello,
You need to go through the software instructions step by step. For example the SD card is just used for flashing the memory of the device, and so indeed it shouldn’t work right after you plug in the SD card (since it will be doing the flashing). The driver for the BEAGLEBONE is computer-dependent and is not something we designed – it is just standard Beaglebone. For this you’d need to look online at what is compatible with your PC (which I have no knowledge of)

[harrison]

Hello, you should be able to go in and directly add commands to turn it on when the stirring starts in each cycle and off when the stirring stops. Find those commands in the main loop and add it at that point.

[harrison]

Yes, all perfectly possible. There might be challenges if you want very unusual frequencis for the LED, it would be fairly easy to go down to a fraction of a second (say, >0.1s) pulses. If you wanted to do much faster you might need to implement it in a differnt way e.g. using the PWM chips on the device to pulse it on and off in hardware rather than software.

Assuming your frequencies are on the timescale of seconds it will be easy to do both of your requests with a a little programming in Python.

THe minimum culture volume is ~15ml, and is set by how far the extraction tube from the lid goes down into the tube. But, you cant put it below the optical sensors or they wouldn’t have anything to measure!

[harrison]

It is defined in the measureOD functions. You can define it in there, or if you wished do some external post-experiment recalibration to the OD – but of course this would mean your in-experiment set point OD would be different.

[harrison]

Hello Karl,

That is correct. The LED has I believe had a few changeovers at Labmaker depending on availability. Often these parts seem to go obsolete. The one you have identified (Wurth 15335327CA452) looks like a perfect replacement, in terms of wavelength and current/voltage profile. One difference between emitters is some have a focusing lens and others not. However, given its proximity to the test-tube this may not be supremely important as a large fraction of light will reach the cells regardless.

[harrison]

Hmm, so the system is still running and responding but it isn’t writing to csv? I have not seen this before and it is difficult to speculate on why that could be. I suppose the Beaglebone might be out of memory, but unlikely if a reboot fixes it, or one of the data arrays has managed to pick up an entry which the csv write function can’t handle. But again seems odd, not sure what that would be. Is there anything suspicious in the data that WAS stored?

[harrison]

Hello Karl,

The PCB design is available at the bottom of the page here: https://chi.bio/forums/topic/pcb-source-files-and-changelog/
It doesn’t have a changelog explicitly, I think the major change for V1.3 was removing a “I2C extender” chip that was between reactor->pumps because it seemed to be achieving the opposite (less reliable signalling).

[harrison]

Hello Paupasme,

I haven’t tested this but I would expect almost certainly they would not work. The peristaltic pumps are designed around a very specific dimension of tubing and if you depart from this by about more than 0.1mm they can either jam and not turn (if tubing too thick) or not make a sufficient seal and hence not pump (if tubing too thin). I would therefore strongly recommend getting the 2.5×4.5mm dimensions specified.

Harrison

[harrison]

I am not sure. I THINK I have heard of people succeeding in the past, perhaps a search through the forums? IMO it is generally much more reliable to have it attached on USB as therea re various other weird issues that seem to crop up sometimes with Ethernet (e.g. the Beaglebone dropping the connection for unknown reasons)

[Author]

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