Amazing. I think it's a great idea to just get on with this.
Man this is a great idea! That's going to look really great (I love trippy primary colours, as you can tell from all my prototypes).
How about when an agent affects an organelle the organelle flashes or goes red? It'd be nice to have a really obvious alert.
On tactics. Agents are too good if they are "kill juice" where you have figured out the code that kills every mitochonria, for example. Agents are too weak if they don't affect anything (and if it's impossible to know what they will affect). So we're looking for a balance in between these two extremes.
1) All Mitochodira have the same code
2) Have each speicies have it's own codes. So A's mitochondria are 000000 and B's are 110010.
3) Have each microbe have it's own codes, so if your species base is 000011 you're might be any 2 digits different from this.
A) Codes never change.
B) Codes change slowly.
C) The ai adapts fast each generation to being attacked. (this of course could be programmed later)
Up to you how strong you want them, this gives you some options.
Options for player strength:
1) The player gets no info other than by using the agent.
2) The player gets some coarse grain info when creating the agent (this will affect 4 organelles)
3) The players gets fine grain info when creating the agent (this will affect A's mitochondria 50% etc)
4) The player only gets info when they use the agent BUT that info is stored automatically in a database the player can use later to pick codes (you know species B's mitochondria was affected by 110011 etc)
I've been kind of imagining it a bit like magic in rpg's (because I have played a lot of action rpg's and they are fun (Dark Souls FTW)) and basically that agents could work like magic. If you meet an ice golem and you fire a fireball at them then they are done, immediately. However if you meet a rock golem and use a fireball against them it does very little. The wizard / agent user is very powerful in a specialised way. The warrior is good against everything but never has an easy time of it. I think this would transfer quite well to microbe gameplay. If you are a heavy agent user (like you have 4 vaculoles) there are some species you can just instantly dominate, whether they have mellee or not, but there are others who can hunt and kill you with impunity. If we wanted to take the wizard analogy to the limit then good gameplay would be about collecting knowledge about which species were weak to what codes (and knowing a lot of this data was outdated) [a bit like having a dusty old spellbook when no one's seen a dragon for 4 generations, does frost bolt still work?]
However I don't know about realism when it comes to memory. We can't stop the human having memory who is playing so it's not too problematic to give them a database which is auto remembered. Of course this is kind of the realism issue in general, a microbe is just a stimulus responder (and would evolve it's codes by having those who picked bad codes die out) how much are we going to allow the player to circumvent trial and error?
All very interesting. Thanks for starting out on it. [Of course you guys may not like wizard analogy, I've just been working from that because I know it's fun.] There's a good argument for just making what's easiest to program and seeing if that is fun.