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the biochamber-makers will only pick up an egg if i have below a certain treshold of biochambers in storage.
like this there is never an egg "stuck" in limbo where it could hatch at all and the egg-breeder chambers themselves always get first dibs on the eggs, so they never run out.
The main application for a cold boot would be when your factory breaks, nutrient supply runs dry, everything stops, and your pentapod eggs get used up (or hatch).
There would be a secondary application with a planned shutdown of pentapod operations. (and opt not to use a 'keepalive' factory that keep an egg circulating indefinitely)
For all intents and purposes though, that circulating egg is more of a cold start than a warm start. Because the egg mitosis recipe ignores ingredient freshness and always produces a 100% fresh result, you can just leave an egg in a chest for ~12min (it spoils at 15) and then take it through one recipe cycle in the biochamber; and discard the 2nd egg resulting from that cycle in a heating tower while putting the 1st back into the chest. For another 12 minutes.
It consumes so ridiculously little nutrients that you would have to really actively try to screw it up and have it be starved.
I actually set up an analog timer; a series of splitters that loop back to the start to make for a long belt path. I do plan to eventually replace it with a digital timer, but that probably won't happen until a distant future where I need to move it somewhere else.
I actually forego the nutrient feed entirely, to minimize the dependence on the rest of the world. It owns one of my spoilage chests, and I have it wake up from spoilage every time the egg comes back around.
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And to circle around to the situation prompting the OP, this kind of solution doesn't survive a disaster that stops bioflux intake. Be it the rest of the factory just died entirely, or defenses fail and a stomper comes through, or whatnot.
Set them to produce a random pick of the inputs every N seconds.
And then provide them only one input. They'll pulse the same input for one tick every N seconds. Which will be enough to flip an RS-latch into the set position, until the bio-chamber finishes its recipe cycle, which can trip a latch reset.
The whole thing is super compact.
This is what I do as well, actually.
The whole thing consumes so little nutrients you could literally just make them from spoilage just-in-time and leave like 1k spoilage in a chest and be good for hundreds of hours.
Of course, we don't do that, and we make it a requester chest for spoilage. Which basically guarantees it will stay sorted out forever -- unless the entirety of Gleba goes to sleep for more than a few hundred hours on end and never produces any spoilage byproduct over that time.
But I've done timers by counting ticks before (adding a firing delay so a rocket turret using explosive rockets so it doesn't overkill groups of asteroids). So what I'd probably do is have it forget the count for a tick when recipe finishes, and then you can read the elapsed time in the conditions for reenabling things.
Would somebody really want to throw away almost 100% of gleba production while researching something without bio-science?
Yes, you can keep everything running but no real engineer would consider this approach graceful.
You can throttle production as to keep a singular biochamber running, much like a hibernating animal's metabolism slows down to a crawl but never actually stops.
You can also store the steam needed to restart the factory from a complete blackout by having a power switch that isolates a set of backup generators.