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For starters, quickly processing the whole line after harvesting the items allows you to get science packs as close to maximum durability as possible, which means a longer spoil timer as well.
Since items inherit the percentage of spoilage from the ingredients, you can design a factory that takes advantage of this to maybe craft less but with a higher spoil time, then increase the scale.
Alternatively, you could also opt to mass-produce the science packs even if it means a lower time left on them by the time they reach the lab.
Three times as many but at 1/3 durability left is better than the original amount at 80% after all, assuming that you have enough labs to not waste them of course.
Quality increase the durability of items like science packs, increasing the maximum time to spoil.
This means that if you go for quality you could get at least a decent portion of a higher quality, giving you more research per item.
Another valid method is to produce a small amount of the basic sciences locally and have a research station near your for the rocket, since consuming small amounts of a good and reinforcing it with new goods will prevent spoilage since the fresh items piling in helps replenish freshness.
So, active offloading with proactive refilling will actively boost freshness in cases where your ability to ship science to nauvis is the bottleneck.
You generally want to do research on nauvis eventually, so this has its flaws in that.
a. This anti-spoilage system only runs optimally when you use agriculture science. (It offloading the most spoiled science from the launch pad does slightly improve freshness still. So a passive lab row technically can still work as an active offloader if its long enough. Still, its likely better to set it up to actually run.)
b. Can't be biolabs so there is a little waste when it runs, but its also eating what is effectively waste.
c. Usually won't be integrated with your fulgora and vulcanis research network, blocking it from running sometimes.
Still, it gives slightly more research speed and acts as an active offloading system for agriculture research.
What I did was that I only did the science packs.... and I did build a big wall around everything so that the spores wouldn't spread. I had a rocket that went back and forth, but the spoillage really isn't too much of a problem. The techs just tick on nicely. Some packs spoil, but the are also free so it's not that bad.
I brought a tank and materials for ammo (shells and armour piercing). The big stompers were one-shot by the tank shells and the machine gun took the small ones. I put a few Tesla towers in the pack production to not have the base overrun by the little critters when eggs spoilt (maybe you can set it up better).
Remember that you can landfill to get more out of the trees. You need the special land fill for the two types of trees. Afterwards you get even better land fill, but that requires biter eggs and a bit more work.
I did not even bother with the bacteria. My Nauvis base is so robust that I just sent science packs in one direction, and materials for the rocket parts in the other. Worked out fine, but it's not an end-game solution.
I have now finished all non-infinite research from Gleba and I'm working on the Aquillo rocket. Then I'm going to have to figure out how to sew this entire interplanetary enterprise together.
The other thing is probably to make a exclusive platform where it ships it to the planet
where your research is at the moment because sitting at the launch pad doesn't help spoilage either. If you are overproducing, don't use logistic network to insert into the silo but have actual inserters loading it with spoil priority (fresh) on and it would launch automatically anyway.
The third thing is probably your other science outputs. If agriculture is overproducing any other science, it's going to spoil regardless so strengthen the other sciences before even making agriculture science. Or at least have a decent stockpile.
Quality packs need to use the custom minimum payload feature set to the lowest amount of science you can make inbetween a platform's round trip.
That's when narrow, fast ships that are able to keep ammo and fuel supplies for constant trips between Gelba and Nauvis become very valuable, and all the above tips help.
Every harvested and processed fruit/bioflux moves by the science and it takes what it needs. The leftover goes into the rest of my factory. This makes sure, that the science is made with the freshest bioflux.
Pentapod eggs always start at 100% freshness it seems. Move them into a chest, if you produce more than you need. After X eggs, a inserter grabs the "most spoiled" eggs and throws them into a heater. Now you always got X fresh eggs.
Similar to the pentapod design, just keep X gleba science in storage and don't stop producing. Just let the old science spoil. This makes you, that you won't accidentally ship science with 5min freshness left.
The longest travel time is usually the space platform. Here you can build a fast one.
Last but not least, overproduce gleba science compared to the others. You won't get a 1:1 ratio with other science but Gleba science is technically easier than blue science, once Gleba logistic is figured out.
With all that, you can easely get 75%+ freshness science on Nauvis.
1. Have as fast full-rocket set (1000 bottles) as possible, so those bottles stay idle on Gleba as little time as possible. For that, the faster you produce bottles, the fresher they all will be when getting to Nauvis.
2. Fast ship, I do not know about others, mine is slow and get to Nauvis for ~4 minutes. I believe it's not that difficult to make it less than 2.
3. Landing pad should be as close to research cluster as possible.
4. Manage your researches - some tech does not require agriscience, so if there is a delay in your supply, use it to research something else. A little inconvenient as you have to check research queue from time to time, but you need other science either way so why not.