Thus far I managed to get to the point where I was able to connect to the eVOLVER using command line stuff. I’m playing around with water just to get a grip of Python language (I’m a complete noob) and I’m trying to get the eVOLVER to simply just pump 20 ml of water into vial 0 and nothing more. I understand that you need to adapt the referral to your ‘custom_script’ in the eVOLVER.py file, but how do I change the custom_script template such that it could only test pumps for example?
Are there any video tutorials made by any of you on how to change code for various eVOLVER applications so that I can understand in real-time. Any quick cheat sheets for anything Python related that is applicable to eVOLVER? I’m looking for (a) shortcut(s) into being proficient in changing code for eVOLVER without having to learn Python from the ground up? ChatGPT has been helpful so far, but still, any other resource that you know of, please share.
Unfortunately, we don’t have solid resources for changing the eVOLVER custom_script.py code for your purposes yet. @ezirayw is working with software developers to make a whole new eVOLVER code base, so that the code will be easily modifiable and well documented, but it’s not out yet.
ChatGPT is somewhat helpful, but has issues understanding the whole eVOLVER code base so may make bad recommendations.
My recommendation right now is for you to post a detailed description of what it is you want to do and we can advise on how to accomplish that.
Great to hear that the software is being further developed (Can’t wait!). Would be extremely helpful to have a built-in GUI-friendly ‘mode selection‘ option or something, including a ‘standard’ ePACE like-feature.
So our specific (test) setup is mentioned here: How and where do I reconfigure pump assignments?
If I understand correctly, instead of trying to reassign pump positions or so in the eVOLVER.py or server.py code, I can just adapt the custom_script.py file and only insert numbers in the fluid command message in the pumps I would use, right? However, I am now just trying to ‘actuate’ stuff in order to teach myself how coding works to control ‘something’ (again - and I keep mentioning this - I have 0 coding experience). Can I just run a pump test with water if I set OD threshold values to ‘not used’ in the turbidostat mode? Do I need to have a calibration first so that the custom_script.py pulls this file in? Can I simply run a calibration with having fast pumps 0-3 (to vial 0-3) and 4-7 (to vial 8-11) as influx, while pumps 8-15 are for efflux (same pump array). The slow pumps are then to transfer from T-stat to lagoon and do efflux at same rate. Can I give commands at the beginning of an experiment to pull media from the carboy into the T-stat (30 ml) from which next 10 ml will be pulled into the lagoon? That way you don’t have to fill each T-stat or lagoon vial manually (more contamination risk…?). These things I wanted to test first with water, but I’m not sure if this will work if the OD treshold things aren’t reading anything in the t-stat mode.
I understand that you can write your own ‘mode’ in the custom_script and I went through the ePACE adapted one, but still am not sure where to begin to make something for like a ‘fluidics test’ or so.
Maybe this sounds trivial and is not very relevant, but we are awaiting complete installation of our eVOLVER (splash box ordered, biosafety cabinet pending), and I am simply trying to train/prepare myself to be ‘ready’ once our machine is ready-to-go.
Is there a scientific reason you need to use the high flow rate pumps for the reservoir/turbidostat media influx? Because if you just use the low flow rate for all influx (plug them in to ports 1 and 2 on the back) and fast pumps for all efflux (plugged into ports 3 and 4) you can use the ePACE code unmodified. This seems best because you are new to coding.
I’ll still respond to your other questions:
Correct
Sure! However, if you turn off the upper/lower thresholds in a turbidostat (by setting them to 999) then you won’t get any pumping though. But any time I drastically change the code I always run a water experiment to avoid screwing things up.
The eVOLVER will have a default calibration it is currently set to in the GUI under ‘Setup’. To calibrate OD you will need a calibration file, but it’s fine to test your experiment using the default.
Do you mean a pump calibration? Assuming so, you will need to designate which pump racks are fast vs slow in the GUI pump calibration.
We usually do a 4+ extra seconds of efflux to make sure that you don’t get overflows
Yes, but we recommend doing this manually and double checking that everything is correct before running the experiment. Check out the wiki Starting an Experiment pages for a detailed explanation of the process.
From what I understand, you should probably just use the ePACE code I linked to with modified pump indexing. You can then test that the pumps are actuating correctly without fluid in them, then do a water test, then do a full experiment.
At this point I think we will indeed go for the path of least resistance and comply with the standard setup as much as possible. So here’s what I’m thinking: Hook up vial 0-7 (turbidostats) to a fast pump for media influx (Port 1: IN1, Top rack), then hook up all vials (turbido’s and lagoons) to the second fast pump array (Port 3 and 4: Efflux (all vials), Bottom rack), and then have the slow pumps pump from turbido’s (e.g. vial 0) to lagoons (e.g. vial 8) (Port 5: IN2).
Do you see any problem with (or any tips for…) the lagoons having a slow pump for influx and a fast pump for efflux?