Increasing media pumping rate/duration during dither

[gchure]

Hi all,

Thanks for all of your excellent work making the Chi.Bio reactors and making everything open source. It’s been fun using these things and getting some (very, very nice) preliminary data.

I’m running into an issue getting the pumping to work reliably during dithered growth. As context, I’m trying to run a repeated bottleneck dilution set up while growing E. coli where the optical density is kept between a wide range (OD 0.2 – 0.6). To achieve this, I’ve adjusted the Zig parameter in the source code to be 0.2 (0.04 is default) and I set the target OD to be 0.4.

However, I’ve run this several times where the fresh media simply isn’t making through the tubing. I will see Pump 1 initiate at a low rate (0.02) and very short duration (< 1s). This means that the pumped media can’t overcome the air pressure at the tip of the tube at lid port. If I manually set the pump rate to 1 and switch it on, I can reliably pump media in, so it seems more like a duration thing than a rate issue. I have followed the set up instructions closely with the reactor being above the media and waste. I have maybe 1 – 1.5 m of tubing total from the bottom of the media bottle to the top of the bioreactor.

I’ve looked through the source code, but am not quite sure where the default pump duration is being set. Could you help me troubleshoot this, or point me in the right direction?

Thanks!

Griffin

[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.

[Author]

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