So, I will say that the idea of bioships can follow to ways: An asteroid, nature its efficient, not intelligent but energy efficient and we`re talking about constructing a capital ship with organic materials, what would nature do to create such a monster? The answer is simple, a big experiment, because it would be a true advance to have ships that can autorrepair and grow themselves without much effort. You should start by building tunnels, or better EAT the asteroid to use its energy and materials to construct your ship. And when you are done, the ship should start making important organs, a hearth it code for "energy and material distribution system" which is basic for every ship and at the same time you would need to start taking energy, and for that out monster will have to make biological structures outside, these structures will have to be outside to take the energy so they will have to resist the stellar radiation(or use it as a fount of energy) And here comes the artistic option, vegetalia its the solution to the problem since it can support giant doses of radiation, but not just green vegetalia since we need to take all the light spectrum to our energy collector. The player should have the option to place roots on the asteroid surface which ends in colorful solar energy collectors, almost like flowers or mushrooms or maybe both, but if you are looking for a more brutal aesthetic put lots of and lots of roots which ends un spikes that glows with the bacteria they have inside, For the engines there are options, like chemical chambers that produces gases to use them as giant thrusters, since there is no friction in space you can accelerate forever with this system. There are other ways, like a giant organic solar sail with the appearance of the wing of a fly, on this part I cant see much difference between a tech and a bio ship except for the aesthetics. For sensors its easier, in space you can see everything with thermal vision which is something that enters in our known biological world. There could be a part of the asteroid with a giant orb that acts like an actual sensor, or an orb filled with eyes always watching(its a bit creepy) and of course there could be even more sensors, like radiation sensors to detect how "far" is the ship from the nearest sun and the it will use his giant eye to see if that sun have asteroid or other important resources, to create a sensor in a biological way its relatively easy take something that reacts in the presence of another something, then optimize it to a certain function... and there you go, you only have to think it in a chemical way with all the entropy and elements involved. For weapons, we cant have mass drivers, maybe chemical lasers but a laser has the problem of cooling which can be mortal for a bioship. So I see two options here, pods and hive pods. The pods will be charged with inorganic eaters like bacteria or fungus they will act as hull eaters making damage over time, first they will make the ship inefficient or inaccurate and then they will disabled it for the final step of a wonderful explosion. Hive pods are just like the others but these would act as MIRV or small carriers for other creatures specifically engineered to throw into the enemy defenses. To limit the pod making there should be a resource counter so making a pod should consume the resources of the bioship on this way the player should eat their dead enemies on a very natural and savage way to survive. For defenses... well when the bioships feels danger all external energy structures should contract themselves to the interior before they suffer much damage, and then the ship will function with reserves during all the battle, when the enemies are disabled it can pop up again and start eating them or absorbing all they can. Against physical damage we still have the asteroid, it will have to be penetrated, but once penetrated the space radiation will cause mayhem on the delicate systems of the bioship, of course the bio-ship will have defenses against this like a fast repair of the breach and a posterior reinforcement of the breach. For communications, the bioship can use light pulses to communicate, or even messengers pods, to receive messages from radio its possible to make certain organs that can react with precision to radio signals the problem is the translation of such signals, but as long as you can "install" the communication protocols and a direct understanding of digital information And now, the part that should be specifically story driven. The command center, it should be positioned on the center of the asteroid heavily protected, if we`re talking about a pure alien race of bioships it should be a big condensation and complex organization of something similar to a brain, but if we`re talking about a s designed by humans, the "brain" of the ship can be anywhere and can be peripheral because there are humans controlling it behind the console, for their everyday living the "lounge", "medical center" and everything should be in stasis pods that covers all of this necessities on one big room leaving the rest of the space to the living creature. The second way its the way that we al know, the space whales,,, ok not whales, they would be much more like tortoises or in a more aesthetically way giant hammer sharks, but even in this way it would be a very sophisticated environment of pluricelular organism working together just like in the asteroid. For the last part I would add interesting things for biological ships; evolving, repair and reproduction. 1-Evolve its a Basic thing in every organism, but since we`re talking an eternal living bioship, the ship had to improve and adapt on his way so it makes sense that it can evolve while floating in space or even in combat (but in combat it should be in a very violent and spontaneous way.) and to evolve it should use these mecanics. Or it was designed to improved himself by genehackers, adapting with the human help or by giving hum learning capacities. -Assimilation: Simple, eat enemy ships and the total tonelage of the ship will be converted to evolution points, the bigger the haunt the bigger the bounty. -Environment: Some evolutions just need pressure, and since the ship can repair itself you can say that every damage suffered activates certain mutations. That would mean that if you almost died during a battle and you repair the damage, your bioship will have created stronger defenses working like human bones or scars(which is tissue that becomes more resistant to damage when damaged) making you tougher to kill. -Interaction: A bioship don't need to stay in battle every single second, it might need to act as a freighter or as an exploration ship. So, by lamarckism the more you use it in a certain way the more it will improve to accomplish such way efficiently. Of course, if you stay inactive in a certain activity for too long the bioship will have to "train" itself again(but it will be easier) 2-Repair: I mean, ITS BIOLOGICAL, that word has implicit regeneration on it so a bioship should repair all the damaged taken over time and at the same time reinforce the damaged areas as every biothing would do on his place. For repair, there should be logical drawbacks, like you have to divert all your energy on repairs and if they are big they can disable your bioship for a long time, so you cant defend and all your energy structures will be exposed . But the good news is that at certain point the energy used to repairs can be diverted to other areas and the more your evolve such point will come sooner and sooner. 3-Reproduction, ok so you are a biological entity and, which is your main objective in life? Exactly, make copies of yourself. This could be handled at some point when you evolve enough to make seeds of yourself or build a big womb for children and then you will have a potential newman machine. This can be handled in various ways, for example a Hive of asteroids united by strong strings all adding more power to the original bioship that made them. O Have in mind that reproduction don't always mean that the numbers increase, there could be a very dramatic moment when your little asteroid thinggie/whallie has to die because you`re in danger and eating your spawn its the only way to survive. But of course a fleet of interconnected bioships, means that you can specialize your members like this one is for energy, this one is for attack, this one is a matter and energy storage...