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Hi Sina,
I must say the description confused me; would it be possible for you to write down precise steps you want to achieve point-by-point?There is some ambiguity in what is meant by “volume reduction” in my mind. In particular, as the Chi.Bio is set up by default the “outlet” tube is only some way down into the reactor. It is set at a fixed height so that you can never reduce the volume in the reactor below the normal amount (20ml or so). That said, you can dilute it by adding fresh media and taking out a mixture of media + cells, but during that process the total volume remains (approximately) constant.
If you really want to reduce the volume this is possible (but would require changing the height of the tube and would not be very effective), but it is somewhat unclear to me what you would gain based on your description.
In my subsequent messages you referenced I suggested another approach which is to use the OD Regulation function already in the system. You could on a X hour loop do something like:
1. Measure current OD (say, it is equal to 1.0)
2. Turn on OD regulation with a target of 0.5 (i.e. half the measured value).
3. Wait until OD has reached 0.5 (probably will take 5 minutes, though pumps are only on a fraction of the time). At this point half the cells + media have been removed (and replaced with fresh media).
4. Turn off OD regulation and wait 12 hours before beginning step 1 again.Does that make sense?
I am afraid I may have misinterpreted your specific goal, if so please do let me know what was meant 🙂
The difference between that proposal and what I am suggesting is that my suggestion is pumping out/in at the same time, while keeping the volume constant.
I don’t necessarily have to pump out first, then back in. But I would have to pump out (& in at the same time) a fixed volume, not to reach a fixed OD. Can I do that using RegulateOD()? Maybe by calculating the OD I would reach if I replaced the volume I want to remove with medium? (Which then supposedly should result in what I want when setting the right target OD?)
This is roughly what I have right now (in a custom program):
timept=int(sysData[M][‘Custom’][‘Status’]) #This is the timestep as we follow in minutes
sysData[M][‘Custom’][‘Status’]=timept+1 #Increment time as we have entered the loop another time!#We have 2 custom parameters. Max volume and “reduced volume” (goal volume)
sysData[M][‘Custom’][‘param1’] =float(Params[0]) #max volume, probably 20.0
sysData[M][‘Custom’][‘param2’] = float(Params[1]) #goal volume
#For now I am just trying to do something every hour
timelength = 60 # time interval in minutes
if (timept % timelength == 2): # So this happens every hour!GoalVolume = sysData[M][‘Custom’][‘param2’]
sysData[M][‘Volume’][‘target’] = GoalVolume
ODNow = sysData[M][‘OD’][‘current’]
ODTarget = 0 #We probably also need to set that, based on ODNow and GoalVolume
sysData[M][‘OD’][‘target’] = ODTarget#Now we can have it regulate the OD based on OD and/or Volume target
RegulateOD(M)Volume = sysData[M][‘Volume’][‘target’]
The question is do I need to calculate the ODTarget, or can I just co with a GoalVolume? If I need to calculate it, how?
OK – but I think the two goals (volume change vs OD change) can be made to go hand in hand.
That is, if you have a calibrated OD then in theory OD is linearly proportional to cells per unit volume.
Thus if I halve my OD (from 1.0 to 0.5 say) then that is the same as taking 20ml of cells, reducing volume to 10ml, then adding in fresh media back to 20ml – right?I think confusion might have come from the use of the sysData[M][‘Volume’][‘target’] in the system. This parameter does not “control” anything. The volume in the software is only there to help the OD regulation algorithm’s accuracy. So setting a Goal Volume there would not solve it.
What I think you need to do is as in my above post with the steps laid out. You have the right time check in there (i.e. the timept % timelength==2) to start the process, but what you should instead do is inside that if statement set OD target = 0.5*ODNow (for example), then turn on Regulate OD.
Then, OUTSIDE that If statement, have another check which does something like (if ODNow
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