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Conversely, Mash/Jelly spoil rather quickly. Do not put them on long transport lines: plan to use them quickly after creation. Similarly for Nutrients: make them locally.
Rocket Fuel is an efficient fuel source (if all the steps are made in biochambers) and is an agricultural product that doesn't spoil. So it's a good choice for production target, and you can use it to power your furnaces, boilers, and heating towers. And you need them to launch rockets anyways.
The Mash/Jelly recipes for using Yumako Fruit and Jellynut are seed-neutral. You need net-positive seed production, and thus a productivity bonus, for a sustainable factory. The main method is to use Biochambers to do the processing.
Be ready for spoilage everywhere. Every building can output spoilage; use filters to give it special outputs, or dump it with the rest of the building's output. The ends of your belts need something removing spoilage. You used a splitter to filter out the spoilage to another belt? Whoops, stuff spoiled after it passed the splitter, you need to remove it.
However you design your logistics, you'll need to make sure things can keep flowing and inserting new fresh materials into the system and removing spoilage. There are a variety of approaches to this.
The initial hard part is getting the 2 farms simultaneously started so you can actually start producing bioflux. Starting base location is very important because you can initially only farm on specific natural tiles and the distance between each other matters a lot.
After you have a jellynut farm, you can probably just feed jellynut directly into the heater with enough left over to produce whatever from a single farm.
One more thing, multiply your bacteria to get ore. You probably don’t need a machine doing the bacteria extraction from the processed fruits
If you don't have recyclers you can also use a chest area to compost the excess and let it spoil.
I really recommend limiting how much you take out of the Harvesting towers.
For example my gleba science is doing around 300 spm with only a yellow inserter worth of the brain fruit and a blue inserter of the red fruit.
If you just dump the tower on a belt there is too much waste if you're not really scaled up.
https://youtu.be/PNmTJBQ6hN0?si=P6scggFSOea9f3Rw
Things are going to spoil regardless unless you get perfect balance of items being taken off both sides of the belt.
Quite a few things require you to pick up product that was just made to refill the machine like nutrients, pentapod eggs and both iron and copper bacteria.
Aslong as everything is able to get rid of spoilage, it should work fine, for example you aren't going to have a rocket fuel line that is constantly being used 100%, unless you have a ton of rockets, so things are going to spoil, don't be afraid of it.
I also recommend his videos. He explains things well. He also has blueprints for the things he made, available for you, if you choose to go that route.
Note: his blueprint for the factory with carbon fiber DOES have a few minor missing pieces. (Specifically, the spoilage line leaving the science pack storage near the rocket is incomplete)
He also has no spoilage removal for the raw fruit lines, which can cause a shutdown if the raw fruit backs up and spoils before it ever gets into the base.
Both of these are easily added on to his build
First, you have to build a sufficient amount of biochambers to start something decent. I'd say 25-30 will be enough. Without those ready to use when you run your factory, you will just mess everything up.
Second, nutrients. "Fuel" of Gleba. The best way to obtain those is bioflux recipe. So you unlock bioflux, get the recipe, bring yumako and nuts into chamber, get good amount of good nutrients and you are ready to go.
Before you do the previous, you have to reckon Gleba tech tree and see what you need for 3 things: bio-rocket-fuel, agritech bottles and rocket components. Arrange everything the way you feel like it will work and then run the process. It's faster end easier to start with drones, but the more you demand from you base, the less efficient drones become, so you start solely with drones and then substitute production lines with belts+inserters.
The fastest way (and we are in a hurry) to proceed with production lines is to connect chambers directly, so they can unload items straight in the next biocamera/assembly in the production line. Saves a lot of headache with spoilage.
Always, from any chamber, do not forget to organize an additional lane for possible spoilage. I recommend to gather it all in one place - spoilage->nutrients chamber. People find it bad, but I do not see why is that so.
Run jellynut processing first, since you need that and bioflux for energy. Create bio-rocket-fuel, feed it to heat towers and enjoy free almost-nuclear electricity. )
Do not be obsessed with big bases. I have mine barely 8 chunks big and it literally produces everything I need, with auxiliary materials like fibre and rocket turrets.
Same goes to base resources. 2 farming machines for each base resource is more than plenty, though be sure to make yumako field a little bigger since you will need it slightly more that jelly.
Biofluids (local analog of pollution) attract local fauna, so be sure to really defend your farming field first, since they will attract pentapods the most. Then goes you chamber cluster, the goes you whole base. For that, be sure to mine a lot of stone and create land coverage from it in big quantities, or you defense line will be worse than drunkard after the 3rd bottle of rum. ))
Before Gleba, I advice you to visit Fulgora first and brings some teslas from there, they cost a lot of energy, but without them you will be overwhelmed by pentas pretty fast, that will be a nightmare, I'm telling you. )
As for stromalites as bacteria of the most short latency - they are the most difficult to not mess up with, you have to organize fast loop (chests, green inserters) to scale their production, get a steady supply of bioflux and nutrients first, then run their multiplying. They become ore in 1 minute, so sort out the most fresh in chamber loop, the less fresh in outer chest and then on belt for usual Nauvis routine. Be sure your factory consume of ores is higher than their production, since, if any belt is full it will result in chests overflow and process termination. You'll have to start it manually anew then again.
You may be having troubles with explosives for rockets - I've organized orbit supply of carbon from platforms, no need to be shy to use those for small things.
The last thing - do not be afraid of this mechanic, it's a great challenge which potentially can give you infinite amount of resources to operate with in the way and proportion you'd like to have. )
Embrace dirt nature man! ^__^
(unless that yellow inserter is doing double duty picking up bioflux; then you might have a mistake where bacteria slips by while it's moving bioflux)
A trick that I was doing is that I had several biochambers in a row running bacteria cultivation; it was set up so that the overflow from each biochamber could be picked up by the next one in line.
Then what I did was that I monitored the size of my iron ore buffer. As soon as it passed a sufficient threshold, I disabled the nutrient intake to all of the biochambers except the first one in line.
This way, my iron production slows way down so I'm not likely to fill my iron buffer... and when iron consumption picks back up and the nutrient feeds turn back on, all of the other cultivation loops can restart automatically on the overflow from the first one.
(and similarly for copper production)