[harrison]

JJJ wrote:

Hi all,

Does anyone know where I can get the chibio tubings that go through the peristaltic pump?

The powdery ones I mean. The ones I see on the chibio website seems to be for connecting to the pumps/reactors/media bottles.

Hi JJJ – the ones linked on the website you CAN put through the pumps on the chi.bio. Or you can connect it to the powdery tube with barb fittings if you wish. BUt you don’t NEED that powdery tube to go through the pump head. Look at the setup guide – it shows how to put tube into the pumps.

[harrison]

BenjA wrote:

Hi,

I am using the magnetic stirred recommended in the manual, but it doesn’t stir properly. It seems to start shaking without rotating for 10 to 20 seconds in each cycle, before it settles and stir properly. I try different stirrers (from the same model) and the problem is consistent. It set at 0.4, if I try higher rates, the problem persist. Any way I can fix it?

Bests!

Hi BenjA – if it is stirring properly for some of the period that is probably a good sign, and note that the device turns OFF stirring for 10-20 seconds each minute to take measurements.
You might have a bad batch of stirrers. Or, you could try running with a larger model of stirrer (e.g. something with a stronger magnet) that is less likely to bounce.
The other thing you could try is reducing the rate at which the chibio ramps up stirring in the code – currently when you activate stirring it goes to an intermediate speed for a while, but you could make this longer/slower so it is more settled.

[harrison]

Abdurrahman Adam wrote:

Hi,I would like to ask if anyone has successfully removed the cable from the Chi/Bio extension housing? it is locked and difficult to release even with pinset. There is no lock release from what I understand? Thank you.

Hello Abdurraham.
Which cable exactly do you mean? The one on the BACK of the main side PCB that is by default having nothing connected? Or the internal one that connects the side PCB onto the board with the laser/spectrometer/IR temp sensor? Either way there is no lock – you should just have to pull (hard, but carefully!) to get it out.

[harrison]

For external CO2 sensors I believe simple devices lik this were used: https://thepihut.com/products/gravity-uart-infrared-co2-sensor-0-50000ppm?
It was connected to an external arduino/microcontroller to record data alongside the experiment.
To calibrate you could buy a cheap desktop CO2 moniutor and calibrate it against the room air 🙂

[harrison]

I believe the question here was:

Hi All,

Been using the chibio for a while now and recently noticed that our .csv exports no longer have a header line (they used to – currently I have to copy paste that header line into every file every time). The data looks ok and no other weirdness I’ve noticed in the UI or the files. Any ideas? Could you point me to the lines of code which govern the .csv build so I can check it?

Thanks,

Kate

In response – I am not sure. If you search for the text that WAS in the csv header in the .py file you will be able to find the default config. I can’t see how this can have stopped unless you have made a change to the code – e.g. something has to have changed for it to be unhappy! It might alternatatively be something to do with space available on the beaglebone so you could clear off some old files, though this seems a very unlikely reason…

[harrison]

In response – have you edited the code at all? That exception on threading is unusual, and I suppose must lead to the rest of the issues given it is so close in time. I am not sure what the linux reasons can be for it not being able to start a new thread, hence my concern that a bug may have been introduced…

[harrison]

I think the forum is showing a weird bug with first posts missing, but this is bwhat I believe was the first post:

I’m currently experiencing an issue with my experiment. The Chibio system stopped running automatically after about a week, and I’m not sure why. I’ve attached the Chibio notebook/log for your reference.
I would really appreciate it if anyone could take a look and help me identify the cause.

Thanks so much in advance!

Hien

[2021-04-11 19:56:19 +0000] [1915] [INFO] Spectrometer measurement was saturated on device M1
[2021-04-11 19:56:20 +0000] [1915] [INFO] Spectrometer measurement was saturated on device M1
[2021-04-11 19:56:23 +0000] [1915] [INFO] Spectrometer measurement was saturated on device M2
[2021-04-11 19:56:24 +0000] [1915] [INFO] Spectrometer measurement was saturated on device M2
Exception in thread Thread-2716517:
Traceback (most recent call last):
File “/usr/lib/python3.7/threading.py”, line 917, in _bootstrap_inner
self.run()
File “/usr/lib/python3.7/threading.py”, line 865, in run
self._target(*self._args, **self._kwargs)
File “/root/chibio/app.py”, line 199, in runWatchdog
sysItems[‘Watchdog’][‘thread’].start();
File “/usr/lib/python3.7/threading.py”, line 847, in start
_start_new_thread(self._bootstrap, ())
RuntimeError: can’t start new thread

[2021-04-11 19:56:29 +0000] [1915] [WARNING] Failed Multiplexer Comms 1 times
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Error is 1
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Failed Multiplexer Comms 2 times
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Error is 2
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Failed Multiplexer Comms 3 times
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Error is 3
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Failed to recover multiplexer on device M2
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Failed Multiplexer Comms 4 times
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Error is 4
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Failed to recover multiplexer on device M2
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Failed Multiplexer Comms 5 times
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Error is 5
[2021-04-11 19:56:29 +0000] [1915] [WARNING] Failed to recover multiplexer on device M2
[2021-04-11 19:56:30 +0000] [1915] [WARNING] Did multiplexer hard-reset on M2
[2021-04-11 19:56:31 +0000] [1915] [WARNING] Failed Multiplexer Comms 1 times
[2021-04-11 19:56:31 +0000] [1915] [WARNING] Error is 1
[2021-04-11 19:56:31 +0000] [1915] [WARNING] Failed Multiplexer Comms 2 times
[2021-04-11 19:56:31 +0000] [1915] [WARNING] Error is 2
[2021-04-11 19:56:31 +0000] [1915] [WARNING] Failed Multiplexer Comms 3 times
[2021-04-11 19:56:31 +0000] [1915] [WARNING] Error is 3
[2021-04-11 19:56:31 +0000] [1915] [WARNING] Failed to recover multiplexer on device M2
[2021-04-11 19:56:32 +0000] [1915] [WARNING] Failed Multiplexer Comms 4 times
[2021-04-11 19:56:32 +0000] [1915] [WARNING] Error is 4
[2021-04-11 19:56:32 +0000] [1915] [WARNING] Failed to recover multiplexer on device M2
[2021-04-11 19:56:32 +0000] [1915] [WARNING] Failed Multiplexer Comms 5 times
[2021-04-11 19:56:32 +0000] [1915] [WARNING] Error is 5
[2021-04-11 19:56:32 +0000] [1915] [WARNING] Failed to recover multiplexer on device M2
[2021-04-11 19:56:32 +0000] [1915] [WARNING] Did multiplexer hard-reset on M2
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Failed Multiplexer Comms 1 times
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Error is 1
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Failed Multiplexer Comms 2 times
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Error is 2
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Failed Multiplexer Comms 3 times
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Error is 3
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Failed Multiplexer Comms 4 times
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Error is 4
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Failed Multiplexer Comms 5 times
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Error is 5
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:56:55 +0000] [1915] [WARNING] Did multiplexer hard-reset on M0
[2021-04-11 19:56:58 +0000] [1915] [WARNING] Failed Multiplexer Comms 1 times
[2021-04-11 19:56:58 +0000] [1915] [WARNING] Error is 1
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Failed Multiplexer Comms 2 times
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Error is 2
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Failed Multiplexer Comms 3 times
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Error is 3
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Failed to recover multiplexer on device M2
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Failed Multiplexer Comms 4 times
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Error is 4
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Failed to recover multiplexer on device M2
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Failed Multiplexer Comms 5 times
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Error is 5
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Failed to recover multiplexer on device M2
[2021-04-11 19:56:59 +0000] [1915] [WARNING] Did multiplexer hard-reset on M2
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Failed Multiplexer Comms 1 times
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Error is 1
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Failed Multiplexer Comms 2 times
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Error is 2
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Failed Multiplexer Comms 3 times
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Error is 3
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Failed Multiplexer Comms 4 times
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Error is 4
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Failed Multiplexer Comms 5 times
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Error is 5
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:57:05 +0000] [1915] [WARNING] Did multiplexer hard-reset on M0
[2021-04-11 19:57:07 +0000] [1915] [WARNING] Failed Multiplexer Comms 1 times
[2021-04-11 19:57:07 +0000] [1915] [WARNING] Error is 1
[2021-04-11 19:57:07 +0000] [1915] [WARNING] Failed Multiplexer Comms 2 times
[2021-04-11 19:57:07 +0000] [1915] [WARNING] Error is 2
[2021-04-11 19:57:07 +0000] [1915] [WARNING] Failed Multiplexer Comms 3 times
[2021-04-11 19:57:07 +0000] [1915] [WARNING] Error is 3
[2021-04-11 19:57:07 +0000] [1915] [WARNING] Failed to recover multiplexer on device M1
[2021-04-11 19:57:07 +0000] [1915] [WARNING] Failed Multiplexer Comms 4 times
[2021-04-11 19:57:07 +0000] [1915] [WARNING] Error is 4
[2021-04-11 19:57:08 +0000] [1915] [WARNING] Failed to recover multiplexer on device M1
[2021-04-11 19:57:08 +0000] [1915] [WARNING] Failed Multiplexer Comms 5 times
[2021-04-11 19:57:08 +0000] [1915] [WARNING] Error is 5
[2021-04-11 19:57:08 +0000] [1915] [WARNING] Failed to recover multiplexer on device M1
[2021-04-11 19:57:08 +0000] [1915] [WARNING] Did multiplexer hard-reset on M1
[2021-04-11 19:57:10 +0000] [1915] [WARNING] Failed Multiplexer Comms 1 times
[2021-04-11 19:57:10 +0000] [1915] [WARNING] Error is 1
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Failed Multiplexer Comms 2 times
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Error is 2
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Failed Multiplexer Comms 3 times
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Error is 3
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Failed Multiplexer Comms 4 times
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Error is 4
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Failed Multiplexer Comms 5 times
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Error is 5
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:57:11 +0000] [1915] [WARNING] Did multiplexer hard-reset on M0
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed AS7341 comms 1 times on device M0
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed AS7341 in I2CCom while trying to send 3 and 0
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed to disconnect multiplexer on device M0
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed Multiplexer Comms 1 times
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Error is 1
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed Multiplexer Comms 2 times
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Error is 2
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed Multiplexer Comms 3 times
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Error is 3
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed Multiplexer Comms 4 times
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Error is 4
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed Multiplexer Comms 5 times
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Error is 5
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Failed to recover multiplexer on device M0
[2021-04-11 19:57:13 +0000] [1915] [WARNING] Did multiplexer hard-reset on M0
[2021-04-11 19:57:14 +0000] [1915] [WARNING] OD Measurement exception on LASER650
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 1 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 2 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 3 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 4 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 5 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 6 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 7 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 8 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 9 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 10 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [WARNING] Failed PWM comms 11 times on device M3
[2021-04-11 19:57:15 +0000] [1915] [CRITICAL] Failed to communicate to a device 10 times. Disabling hardware and software!
[2021-04-11 19:57:15 +0000] [1912] [INFO] Shutting down: Master
[2021-04-11 19:57:15 +0000] [1912] [INFO] Reason: App failed to load.
root@beaglebone:/root/chibio#

[harrison]

No that should be fine, i suppose just test it! IMO you might want to make sure it isn’t CONSTANTLY turning off and on each cycle and instead do some period in each one e.g. to give the turbidostat some time to react

[harrison]

For some reason I can’t see the message here but I believe it says:

Hi there,

we would like to implement an hybrid experiment, in which the culture is diluted at fixed intervals (i.e. a chemostat), but with a ceiling for the OD (i.e. a turbidostat). Both functionalities exist already in the software, but currently is not possible to set both so that they work from the same pump (i.e. pump1). Would it work if I moved the RegulateOD function call into one of the custom programs? Or would the two modalities interact in unpredictable ways?

Thanks a lot,
Marco

————————-

In answer to this – yes, it sounds like a sensible solution. Turn on the pumps to do chemostat and have a logic check in a custom function which activatres RegulateOD depending on whatever conditions you require (and then turns it off when these conditions are not being violated)

[harrison]

Excellent, sorry that I have been slow on the responses sometimes!

• This reply was modified 1 month, 3 weeks ago by harrison.

[harrison]

Hello!

Yes, indeed, this was run in turbidostat mode, and using the “zigzag” function in the software.
You could set it up to do things differently. For example you could calculate approximate/rough growth rates from the pump rate data – i.e. doing a time average of this (and assuming OD is approxiamtely constant over time i.e. population is not net increasing/decreasing) you can get a rate of population growth.
Or you could even do a series of standard growth curves (without dilution) and fit exponential growth rates to these using any method of your choice (e.g. entirely separate to the Chi.BIo software, such as with R)

[harrison]

hmm. that may not work since the main loop of the experiment turns the pumps on and off each time it iterates (60 seconds). What you could instead do is put some logic check around the part in pumpmodulation which turns them on, and (for example) check if experiment cycle modulo 10 is 1 (or whatever) and if so turn it on, if not leave it off. This way you would let pumpmodulation run on the same timer but 9 out of 10 times it would do nothing.

[harrison]

Hello,
You could try that with the pump, but I am not sure it is the best idea. Why do you need to slow things down?
It sounds as if it would work though, you can easily test it in a dry run etc before actually tryhing in an experiment

[harrison]

– TO fix the flow rate thing, have a look at the user guide about this troubleshooting challenge – probably best method is to add a one way check valve to inflow media line.
– 5 times higher probably ideal. Or you could set it to do something like keep same rate as inflow then every ~10 minutes do a bigger pump out… But this would require some programming in python

[harrison]

Apologies for not being clear. What I suggest is start experiment. then DON’T click switch to activate OD control – since that is not a chemostat, but rather a turbidostat. Instead, once the experiment is started, go to the pump control section and enter a rate for each one and manually switch on the pumps. Then the system will run with constant inflow/pump rate (i.e. a chemostat).

Does this make sense?

[Author]

Posts