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However, as a general rule of thumb I would say mine and loot the crap out of the first biome, keep everything you can get your hands on for free, deconstruct items from wrecks such as headsets, keep any items such as welding tools that you need, fill your cabinets but that's all - do not have loose items on the floor. Use storage containers when steel allows to increase your cabinet storage capacity.
To give you some idea, my fabricator cabinet is full of storage containers (it's taken me three biomes to accrue the steel and necessity to make so many, don't do it straight off the bat), most of these are nearing or at capacity of 96 materials in each, I sell any excess over this amount at stations. Same applies to the medical cabinet, I hoard every medicine I find.
I usually make sure I have at minimum some bandages, saline or blood, abx, and morphine or opium, these can easily be found in wrecks or made from plants etc. On rare occasions I might buy a few of the cheaper ingredients such as stabilozine from a station.
In the first biome I made only a handful of uranium fuel rods, maybe as many as ten, after that I seemed to find them in wrecks, abandoned stations, and beacon stations so the supply of free uranium fuel rods became quite constant. As my engineer bot's skill increased and materials allowed I made higher quality thorium and then fulgurium rods but honestly I've hardly used any of them, I have a storage case with about 8 masterwork quality fulgurium rods just sitting there in case of emergency, I'll probably needs these for the last biome but my reactor has been upgraded to the max so even a normal quality uranium fuel rod lasts a long time (I use these as I want the depleted fuel for fabricating ammo etc).
Repeat a reckless sortie until you die from another cause.
This is more fun than calculating everything you need to have in exact quantities.
Ultimately, are we here to haul everything that is badly lying and unscrew the last bolts from sunken boats? XD
It's very simple - drag everything that lies badly and save it as if you were Smaug on a mountain of gold. Check your stock after a while. Are all the cupboards full and nowhere to store resources? Do you have 10 stacks of copper? So many bandages lying around on the deck? Time to sell!
You will quickly realize that some resource is more important when people start dying or when you have nothing to shoot. In all other cases, the resources just lie in a big pile. Sell if this pile gets too big.
There is nothing that does not make sense to accumulate. Any resource would be helpful. If it is not needed in its pure form, it can be disassembled (for example, specific medicines or extra headsets). If there are a lot of some clean resources, it makes sense to just make something useful out of them and use them more often, without worrying about saving.
I would note a few things that are always better to stock up, because even an excess of them can be used later:
1) Fuel rods (if they are of ordinary quality, remake them in a better quality)
2) Lead - (cartridges and ammunition)
3) Basic medicines - bandages, morphine (opium), physiotherapy, antibiotics, stabilocin and caliscanide (a little antirad)
4) Steel (needed for everything)
5) Any rare alien resources.
You should also always have plenty of fuel tanks and oxygen tanks to keep in stock in the cabinets.
Of course cartridges and ammunition. Instead of a firearm, it is better to use a harpoon, its cartridges are more affordable. Ammunition for cannons is voracious in terms of resources.
You may also run out of titanium-aluminum, or rubber for your upgraded suits or equipment.
It usually accumulates a lot of copper, plastic, and other resources that are used in things that you usually already have.
Turn excess iron into steel.
Ethanol is a fuel bottle, sell the excess.
Bandages - in elastic bandages.
In general, just see what you have too much and is it possible to craft something out of it? If nothing comes to mind, sell.
But to be honest, in the middle of the game, there is nowhere to spend money, resources will accumulate in warehouses and you will stop collecting some of them.
Always having bandages at hand is the only minimum requirement. Burns and bleeding are commonplace afflictions inside and outside the submarine. Other damage types are considered internal damage and can be treated by various opiates, but only bandages, plastiseal and antibiotic glue can treat superficial/external skin damage effectively. If you need to save someone's life, it doesn't really make huge difference if you run out of morphine if you still have fentanyl, so long as you're aware of the risk of overdosage and the skill level of the person administering the drugs. But plain old morphine is the second most important medical commodity after bandages. It may be prudent to equip your medic bot with a single stack of Naloxone in case of misadministration of opiates.
Speaking of misadministration, don't let bots waste blood bags. Hoard them for yourself. They are better used in combat situations since they restore such a great deal of blood loss that it's unlikely to ever truly need it over plain old saline injection. Manufacturing blood bags is also a waste of resources; though saline and alien blood should be plentiful. Stabilozine has many other, more important uses.
If you have a good (custom) sub and competent captain who can avoid monster intrusions, and a crew that can shoot and patch up the sub effectively, it's unlikely that you will need large quantities of medicine. However, opiates like morphine can be further refined into powerful stimulants and outright panacea (Deusizine) so hoarding all the opiates is by no means wrong.
You probably won't run into many monster packs that get to breach inside your sub in the first couple biomes anyway, but it's not a bad idea to have your security officer equipped with harpoon gun and a close combat weapon. Medics and the captain are to be geared up next, followed by mechanics, engineers and finally clowns and clown kids (aka assistants). Generally speaking, only human players should possess guns while inside the sub, but as you pick up on more and more loot and materials, that is up to the captain's discretion. You can later on upgrade into excellent quality harpoon guns and physicorium harpoons for bots to better ward off monsters that intrude the sub.
You also shouldn't allow bots to access plastiseal or antibiotic glue, they'll almost always just waste it or even damage the patient if their skill is insufficient. Even the player should rarely need those. Save your antibiotics (ABX) for when you need go outside the submarine, from the Aphotic Plateau onwards. Beacons, wrecks and ruins may contain Husks. Extra ABX should be used to create AB glue for Deusizine only and not use the glue on its own. Plastiseal is only really useful when dealing with ballasta flora and steam cannon guardians in the ruins so there's no need to "upgrade" your bandages to plastiseal. Just buy some when it's on sale or loot them.
You can set bots to ignore installations, containers and loose objects by pressing shift+MMB and selecting the "Ignore this" order.
Other users mentioned Stabilozine, that's another essential but plentiful medical material. It will counteract any poison in the game (even radiation poisoning). Husk infection is not poison however, it's an infection against which you need ABX and Calyxanide. So all those three should be kept at hand, especially from the third biome onwards.
Deeper in the ocean you will also be inspected by Watchers. Early on the psychosis afflictions they inflict are not a big deal, but later on the swarms of enemies they attract can be a problem. Haloperidol will immediately remove Psychosis completely, and since it doesn't contain any valuable materials (no Stabilozine), there's little harm in having a stack of it around. Cigars can also be used and tobacco is easy to grow, but Cigars unfortunately cannot be stacked so they take more space. But it's also kind of fun to have a suitcase full of Cigars. :)
Sooner or later you will also run into Thalamus, typically in the Great Sea or the biome before that. Anaparalyzant is an essential preventative medicine then, both inside and outside the sub (or only inside if you manage to avoid having the sub injected with Terminal Cells). Antirad is also not a bad thing have, as others stated, but the only scenario where it could come useful is if you have Volatile Fulgurium Rods on board, and they were not avoided for some reason, or if there's a meltdown. Both of those scenarios can be easily avoided.
I have dedicated storage containers inside the medicine cabinet for Stabilozine and ABX. All other medicine should ideally fit into the medicine cabinet. Even with a large crew, it's unlikely that you will need to treat more than one or two people with opiates in a single hostile encounter, but some intrusions like Thalamus or its precursor ballast flora, as well as letting a Husk inside the sub, will obviously warrant greater spending of available medicine.
TL;DR
On my medicine cabinet for crew of 8, I have one row of bandages, one row of morphine, one row of saline bags, half row of Anaparalyzant, half row of Stabilozine, half row of ABX, half row of Calyxanide, and then some other stuff. It never runs out.
This is all assuming that you have enough marks and other resources to maintain such inventory however. It's useless to hoard medicine if you can't kill enemies, and that's a more complicated matter and depends a lot on your sub, crew, game mode and so on. :P
Going through the second last biome and hunting Abyss monsters, I've only really found one material to be in chronic short supply: Titanium.
Magnesium, Lead, Phosphorus and some other elements have valuable use as well, but you can usually make do even if you run out of them. Laser turrets use Alien Blood and Lithium or Fulgurium, Physicorium or C-4 charges can be used to replace or supplement Lead used in Coilguns, Chaingun eats Titanium.
If you have a mechanics with talents (solo campaign play or multiplayer with human mechanic), you probably won't run out of minerals easily. Engineers make more effective fuel and can convert spent fuel into munitions. As soon as you have access to their talents, the material economy should become rather trivial aspect.
Keeping just one full or 3/4 (6 pcs) stack of each mineral is generally fine, so long as you're already fully stocked on munitions and medicines. Later on you will likely switch to armaments like physicorium railgun shells with explosives, so you'll have more iron to spare. Some materials like alien resources or Titanium should be hoarded liberally because they are more rarely available by other means like deconstructible loot (although a xenologist medic will basically poop out alien materials). You may also stash unrefined mineral chunks into basic crates to save space, and only refine them as they are needed.
Some materials like aluminium will eventually pile up, which is a good thing because you can replace your entire sub's oxygen tanks with Excellent/Masterwork quality tanks, and do the same for Welding Fuel over time as the regular tanks run out. You may also end up with large quantities if Lithium and Zinc if you replace your batteries with fulgurium variants, but those too can be spent on laser munitions as well as Tonic Liquid so having a bit of surplus is not a bad thing.
Dementonite is one of the least useful materials if you don't have a mechanic with talents. If you play campaign solo, it's going to come handy, but in multiplayer with bot mechanics, it's useless on its own... so feel free to sell it (should get best price at habitation outposts). Silicon also has very limited uses unless you want to pump up your electronical engineering skill or pimp out your sub with wiring contraptions like remotely triggered stun grenades and monster detectors. Fiber Plants are also not very valuable, though they do hold greater amount of Organic Fiber than a stack of Organic Fiber does, so they could be stored away as a sort of emergency resource supply if you run out of bandages. That just might happen if your sub becomes trapped by Thalamus, but I've not yet had the pleasure of having my bot crew deal with that so I'm not sure how well they can do.
I play campaign in multiplayer, so I'm not sure how solo players look out for minerals to mine while steering the sub... It may be handy to compile a list of most needed mineral chunks and their raw elements.
Deeper biomes will have abundant quantities of Thorium to mine and spend on fuel rods. I find it very unlikely that a sub should run out of fuel after early campaign. You may also increase the sub's fuel efficiency, but other upgrades may be more desirable. However, a solo player may have more difficulty in locating those thorium deposits, so it doesn't hurt to be prepared. All stations should sell fuel rods. You probably should stock up on them if they are on sale. Fuel rods are sometimes needed to refuel beacon stations so it's nice to have a separate, if not full, stack of plain uranium rods at hand somewhere near your diving equipment. They don't even need to be full to be used successfully for beacons, but full rods are easier to stack.
Having a variety of different fuel rods is probably more relevant issue than simply running out of fuel completely. If you are exploring alien ruins, abandoned outposts and wrecks by your lonesome, you probably shouldn't leave that Fulgurium rod in the tank. 8) I think bots prefer rods stashed in a cabinet's own inventory slots instead of in storage containers inside the cabinet, and you may use the previously mentioned ignore orders to designate a fuel rod storage container as off-limits for the bots.
You will have to pay attention to your sub's capabilities while making most use of its equipment, especially the engine and weapons. Cruising through passageways should be doable with plain uranium rods, but since that material is also used for nuclear weapons, you probably don't want to spend all of it as fuel just because it's "cheap" in comparison to thorium. For intense combat situations against Abyss monsters, you need more power, either using two uranium rods or singular thorium or fulgurium rods – but you need to mind overvoltage spikes while steering the sub. Bot engineers don't always do a competent job when prioritizing electronic repairs.
Ultimately how much fuel you need depends on the sub, who you are playing with and how you are running missions. There's no simple answer to how much , or especially what kinds, of fuel you should have stored. Always having at least 3 rods should ensure at least getting through the passage way, even if you get in a fight and it goes wrong, but if there's no outpost at the end of that passage, you'll probably need more to reach the next outpost safely... If there are any outposts left in your biome. 8)
If you ever find yourself severely lacking in some materials then concentrate on mining for a round or two, it will cost some fuel but could be just the ticket to get your stocks up. Also loot everything! Deconstruct, don't sell anything until your sub is overflowing with stuff!
This. So long as it's fun, it should be done lol.
Also, if you're in a pinch, you can "borrow" supplies from cargo missions. They need to be crafted into other items or recycled before docking at a station.