Microbial Compounds and Organelles

Subject: Re: Microbial Compounds and Organelles Wed Feb 06, 2013 1:48 pm

Alright, I'm going to take a stab at combining everything we have so far, so it'll be rather heavy on math. I suggest we make this the basic template for a microbe, and then add gameplay over it. For example imposing a limit to how much smaller/lighter than that you're allowed to be, etc.

I'll also try and turn the relations into functions. I'm not sure if this is the right place to post this or not, but you'll tell me if it isn't. Plus I can't be more off-topic than the person who linked to an incredibly soothing theme.

Math:

Our subject will be a perfectly spherical cell with the radius R = 5 µm Dear Lord, I forgot there could be other shapes for microbes. I think amoebas are out of the question if we want to take this approach, or we could just give all shapes the same function but different graphics. This isn't really my domain though so I'll leave it at that.

Spoiler:

Now that we have a new table with all the masses, the next step is to put that in relation with the different organelles:

Spoiler:

Subject: Re: Microbial Compounds and Organelles Thu Feb 07, 2013 1:07 am

Really, really excellent work.
Given the relative proportions you've calculated, we're well o n our way to defining the entire cell metabolism for the game. Don't go crazy calculating out the volumes of different parts of the cell, because those will differ from organism to organism. We don't need to know how big or how many, just what they're made of (continue with relative proportions) and what they do.

Subject: Re: Microbial Compounds and Organelles Thu Feb 07, 2013 11:26 am

Thanks, I'm really enjoying my part in the project so I'm glad to see I'm actually of use. I will definitely try and do this for everything, but I'm not sure what you're referring to exactly when you say relative proportions. I mean because the volumes are variable I can't really say 1 golgi = 5 mitochondria. I'm assuming you a mean to continue giving you information such as "The mass of the cell membrane is half lipids and half proteins" but I would like to just double check first.

Now as for my whole bothering with specific organelle volumes, I'm trying to just gather information from everywhere and somehow patchwork it all so that I have a very average cell prototype with everything defined.
This way I can give you (hopefully approximately correct) constants such as the term I defined as Lipid Density. So that when the player "buys" a mitochondria you know how much it costs based on the size the player decides to make it, simply because we assume that it's all going to be proportional.
I also imagine the numbers could be useful for people to have an idea of "oh that's a mitochondria, it's fairly small, look over here there's a big bloated golgi apparatus"

Really lipids are the only thing I needed a volume for because they're just there for membranes (we should not have bacteria who are able and willing to store triglycerides for energy.

Oh and all organelle functions are here. It's the same file I linked two posts ago, I believe. So if you've read that you should let me know if you'd like any more details on any of them.

Subject: Re: Microbial Compounds and Organelles Sat Feb 09, 2013 12:01 am

Quote :: I'm assuming you a mean to continue giving you information such as "The mass of the cell membrane is half lipids and half proteins" but I would like to just double check first.

That is indeed what I meant

I read your chart a few days ago, now the link seems to not be working- the document isn't showing up. I don't think I had any problems with it though.

All of the volume work you're doing is great, I just want to make sure we're on the same page.

Subject: Re: Microbial Compounds and Organelles Thu Feb 28, 2013 4:03 pm

I can't believe it's almost been a month already. I don't have any new content to offer, I'm still in the middle of my genetics revisions. There isn't much I could have contributed between then and now; there's definitely some things to add, but not very much. My biochem classes have gone really in-depth about nucleic acids and so have consisted of information which is unusable for the game.

We start lipids next week, and then proteins, presumably going into metabolic pathways and whatnot, so I'll try to incorporate an update into the revision of my notes if I have the time. I'll also be sure to lurk a bit beforehand just in case progress has been made without me.

So this post is just to say I'm not entirely gone yet. I believe I can still provide useful information, I just haven't had much time or a real mass of information to make use of in these past three or four weeks.

Subject: Re: Microbial Compounds and Organelles Thu Mar 28, 2013 10:16 pm

Spoiler:

Here is a yEd flowchart for all of the organelles and processes described in the OP here, excluding pseudopodic movement. Please help me extend this by adding new organelles, processes, and connections.

Newcomer Posts : 94 Reputation : 15 Join date : 2013-03-18

Awesome work! This is exactly what I was looking for while building my prototype.

I like the way you put them as Initial/Secondary. It is clear to someone who want to program this. Also like how they are linked to together. I'll definitly come with some question when I'll update my prototype with those.

Nice work! Keep pulling these chart and add number as you can. I really like them and it is easy to implement afterward.

Subject: Re: Microbial Compounds and Organelles Thu Mar 28, 2013 11:11 pm

RodGame wrote:: Awesome work! This is exactly what I was looking for while building my prototype.

I like the way you put them as Initial/Secondary. It is clear to someone who want to program this. Also like how they are linked to together. I'll definitly come with some question when I'll update my prototype with those.

Nice work! Keep pulling these chart and add number as you can. I really like them and it is easy to implement afterward.

I figured this would help a lot. I'll work on describing processes (in terms of input and output compounds) clearly so they're easy to implement, though most of them are probably already on the site somewhere. The forums are a constant reshuffling of information to where it is needed.

Newcomer Posts : 94 Reputation : 15 Join date : 2013-03-18

~sciocont wrote:: I'll work on describing processes (in terms of input and output compounds) clearly so they're easy to implement

Yes, please do that. Transferring concept to game design is really helpful afterward. I would also like a quick description of how you see the process being used in actual gameplay(I.e : How will external digestion be used ? Do you need it to gain new organelle ? Do you need it to eat some particular compound ? What is the difference between having a engulfment prevention or not? Having 1 prevent you from being eaten by anything ?)

As you see, more than Input/Output are needed for gameplay. If you see other aspect given by organelle (Such as compound limit increase by vacuole ? Different movement design depending on movement organelle (same speed in all direction, faster forward..), please but them on paper right there.

~sciocont wrote:: The forums are a constant reshuffling of information to where it is needed.

That's where I think the wiki should come into play. Forum concepts are always moving but still available to everyone. It's hard to tell if a concept from 2011 is still good or not. You need to read all the thread which can be long sometime.

We should work towards having an updated wiki which represent the current true concept and information related to it which link to the forum discussion if you need further investigation to understand the concepts. I know it's not that easy but it would be a good goal to have.

edit : I'd really like to have an easy to access to all those graph being thrown around easily on the wiki. That could be a good start to upgrade it slowly.

Subject: Re: Microbial Compounds and Organelles Sat Mar 30, 2013 12:41 pm

RodGame wrote:: I'd really like to have an easy to access to all those graph being thrown around easily on the wiki. That could be a good start to upgrade it slowly.

I'm sorry, I don't quite understand what you mean here. Do you mean that you want all of the flowcharts being made available on the wiki? That can be done easily.

Subject: Re: Microbial Compounds and Organelles Sat Mar 30, 2013 11:01 pm

This is extremely helpful, i will use this to make MY prototype more realistic so we can get more realistic creatures popping up.

Subject: Re: Microbial Compounds and Organelles Thu Sep 19, 2013 1:59 am

With the recent release of the saving and loading update to the Microbe Stage, we need to get a full list of organelles to implement them into the game. Many organelles and their related processes have been described in the thread, but now we need to take them and list them clearly and extremely specifically, so that it is in a code-able format. Do not assume the computer will know anything that you have not described.

There are several things to describe for each organelle. What does it enable in the cell it is placed in, what does it cost in MP (the maximum MP that can be spent in each editor session is 20), etc.

Here is a starting list just to show you what format to use, not all of these are finished so please help fill them out where possible:

Organelles
---
Mitochondria - X MP
Aerobic Respiration:
1 Sugar + 6 Oxygen = 6 Water + 6 Carbon Dioxide + 38 ATP

Chloroplast – X MP
Photosynthesis:
6 Carbon Dioxide + 6 Water = 6 Oxygen + 1 Sugar
Note: Light intensity factors into the reaction rate of the chloroplast. In a spot of 100% light intensity, the chloroplast will react at maximum reaction rate. At 50% light frequency, the chloroplast will react at only half speed.

Thermoplast – X MP
Note: Heat intensity factors into the reaction rate of the thermoplast. In a spot of 100% heat intensity, the thermoplast will react at maximum reaction rate. At 50% heat intensity, the thermoplast will react at only half speed.

Subject: Re: Microbial Compounds and Organelles Mon Oct 28, 2013 7:08 pm

With the recent work by the coders on the compound system and processing organelles, here is Seregon's documentation on the microbial processes, for use by the programmers.

EDIT: Screw it, the forum won't let me format it the way I want, so here are pictures of it on Microsoft Word.

Spoiler:

Subject: Re: Microbial Compounds and Organelles Tue Oct 29, 2013 7:40 am

NickTheNick wrote:: With the recent work by the coders on the compound system and processing organelles, here is Seregon's documentation on the microbial processes, for use by the programmers.

Thanks i'll put that to good use!
I assume glucose and sugar is the same agent?
Also, the discussion we were having was how to assign input agents if multiple organelles consume the same agent. For example, a single organism capable of Agent Synthesis (that produces what??) and capable of RpAse Synthesis, assuming if all other agents are abundant in the cell, which organelle does a the sparse sugar go to? equally to produce each, according to priority of organelles or how?

Subject: Re: Microbial Compounds and Organelles Tue Oct 29, 2013 7:40 pm

Yes, glucose and sugar are the same. However, note the difference between compounds and agents. A compound is a resource, element, or mixture in the game, like water, iron, textile, or glucose. Agents are chemicals released by cells to affect other cells in a specific way, like damage their membrane, slow them down, etc.

If there is, say, 1 oxygen, and two different organelles that want it, it should just be randomized who gets it.

Subject: Re: Microbial Compounds and Organelles Wed Oct 30, 2013 4:18 am

Difference duly noted!
Randomized, that sounds odd, but i will naturally oblige. What is the reasoning behind randomized instead of equal distribution?

Subject: Re: Microbial Compounds and Organelles Wed Oct 30, 2013 8:41 am

NickTheNick wrote:: A compound is a resource, element, or mixture in the game, like water, iron, textile, or glucose. Agents are chemicals released by cells to affect other cells in a specific way, like damage their membrane, slow them down, etc.

From a programming perspective, it doesn't make much sense to differentiate between agents and compounds like that. Take oxygen for example, which I guess could be classified as "resource" (and element, if you mean it in the chemical way). I don't think we've talked about the specifics yet, but I assume that it will eventually be possible to design microbes that excrete oxygen, so it's also a chemical that is released by cells. Furthermore, oxygen can affect cells in a specific way, namely by filling up their oxygen vacuoles (if any). In other words, oxygen is also an agent.

crovea wrote:: What is the reasoning behind randomized instead of equal distribution?

I can't speak for Nick, but I would also vote for a "random serve" system. There are several approaches for sparse resource distribution. As an example, let's talk about a microbe with 2 organelles. Organelle A wants 1 oxygen for producing 2 RpAse per second and organelle B that wants 2 oxygen for producing 1 glucose per second (it's an alchemist organelle). The microbe receives 1 oxygen per second.

Here are the four approaches I can currently think of:

Equal distribution, scale output: Each second, A and B each receive 0.5 oxygen (would that be ionized oxygen, or radioactive beryllium?). A consumes that oxygen and produces 1 RpAse (half its normal output). B consumes its oxygen also, producing 0.25 glucose (a quarter its normal output).
Equal distribution, wait until there's enough for everyone: A and B only get to process oxygen once there's at least 3 oxygen available. So every 3 seconds, A consumes 1 oxygen and produces 2 RpAse while B consumes 2 oxygen to produce 1 glucose.
Randomized, skip if not enough resources: At each timestep, iterate through the organelles in a random order. If the organelle can't grab enough resources, it does nothing. Better luck next time.
Randomized, reserve resources: At each timestep, iterate through the organelles in a random order. Each organelle moves resources from the microbe's storage into an internal storage. If the internal storage has enough resources, consume them and produce the output.

My personal opinion on those four options:

Option 1 has the obvious flaw that some organelles may be producing miniscule amounts that hardly matter while others work pretty normal.
Option 2 might feel a little strange to the player. The stored amount of resources would always rise to a certain level, then jump to zero again.
Option 3 is my personal favorite, it allows organelles with small resource requirements to keep working while big resource hogs are starved. At the same time, a sparse resource actually stays sparse, never going above the level that the most frugal organelle can consume.
Option 4 can confuse the players because they can't see that internal storage, unless we do some fancy stuff to change the organelle graphics depending on the filling level. That makes it pretty unpredictable which organelles will keep working.

Subject: Re: Microbial Compounds and Organelles Wed Oct 30, 2013 10:35 am

With your option 3, a "resource hog" would never produce then, that would be more confusing for a player to add an producing organelle that would never actually do anything.
On option 4

Nimbal wrote:: That makes it pretty unpredictable which organelles will keep working.

I'm not sure what you mean with "keep working" they would all keep working just with random speed.

The idea i had was to do equal distribution, but more like your option 4 than your option 1, each organelle using oxygen gets 1 oxygen in turns and put it into its internal storage, whenever oxygen is somehow obtained. This would reflect osmosis pretty well (realistic?) like option 1 but without the disadvantage of fractional agents.

Subject: Re: Microbial Compounds and Organelles Wed Oct 30, 2013 10:17 pm

crovea wrote:: Difference duly noted!
Randomized, that sounds odd, but i will naturally oblige. What is the reasoning behind randomized instead of equal distribution?

Actually, I hadn't considered equal distribution. I was suggesting randomization over prioritizing organelles, as I feel as organelle prioritization would need a lot more micromanagement, since an organelle would have to be fully satisfied before any resources would be shared with other organelles.

Nimbal wrote:: From a programming perspective, it doesn't make much sense to differentiate between agents and compounds like that. Take oxygen for example, which I guess could be classified as "resource" (and element, if you mean it in the chemical way). I don't think we've talked about the specifics yet, but I assume that it will eventually be possible to design microbes that excrete oxygen, so it's also a chemical that is released by cells. Furthermore, oxygen can affect cells in a specific way, namely by filling up their oxygen vacuoles (if any). In other words, oxygen is also an agent.

Yes, I was misleading in my answer. To be more accurate in my definitions, an agent is a chemical that does not exist naturally, and can only be produced by cells in an agent vacuole. It is like a microbial counterpart to the poison made in the poison glands of a venomous snake. Oxygen, or any compound for that matter, wouldn't count because none of them can be excreted by a cell from a vacuole, to do something like damage another cell's membrane, slow down their movement organelles, etc. For the most part, we don't even know of any chemicals that cells release that can do this, the agent system is a gameplay thing.

Subject: Re: Microbial Compounds and Organelles Wed Oct 30, 2013 11:43 pm

I like the 2 random options. Here are my thoughts.

Nimbal wrote:: Randomized, skip if not enough resources: At each timestep, iterate through the organelles in a random order. If the organelle can't grab enough resources, it does nothing. Better luck next time.

This option slows down the rate for organelles requiring more resources. (due to its "better luck next time")
Maybe i understood it wrong, but heres something I would do to this option much more game friendly and practical: Allocate any "unused" oxygen to be used in the next timesteps random distribution.

Example:
Say each timestep we get 1 oxygen
Timestep 1:
<1 oxygen to organelle 2 (requiring 2 oxygen to do its reaction)> (random selection)
<Not enough oxygen for reaction>
<1 oxygen put in bank for next timestep>
Timestep 2:
<1 oxygen to organelle 1 (requiring 1 oxygen and 1 oxygen to organelle 2> (again random selection and dist.)
<Organelle 1 reacts! Organelle 2 does not react (not enough oxygen)>
<1 oxygen put in bank for next timestep>
Timestep 3:
<2 oxygen to organelle 2>
<organelle 2 reacts!>

That would be what I think would improve this option. It makes it realistic and randomized at the same time. The oxygen is "still inside the cell" (bank) and has an equal opportunity of meeting the organelle again. (Maybe this is what you guys meant all along and I'm just being redundant haha!)

For:

Nimbal wrote:: Randomized, reserve resources: At each timestep, iterate through the organelles in a random order. Each organelle moves resources from the microbe's storage into an internal storage. If the internal storage has enough resources, consume them and produce the output.

The internal storage method is much more friendly towards organelles that use more resources, since it gives them a guaranteed storage in the event they dont have enough resources. It doesnt seem to realistic, but It may be much more balanced (overall) for the cell. (im not too sure.)

All in all, i would go for the first option i listed with the example. But i do have one concern.
Should the surface area of the organelle (in hexes) also be a factor in the random distribution? So like large jumbo extra super big mega organelle has a 99.9% chance of getting that oxygen compared to miniscule tiny organelle. (exaggerated example)
Hope this sorta made sense!

Subject: Re: Microbial Compounds and Organelles Thu Oct 31, 2013 6:00 am

Psych0Ch3f wrote:: (Maybe this is what you guys meant all along and I'm just being redundant haha!)

Pretty much yep. I just finished the implementation and it's currently working like this!

Psych0Ch3f wrote:: Should the surface area of the organelle (in hexes) also be a factor in the random distribution?

Very interesting idea! Probably a question for the design folks in the misc. thread. I'll leave it as it is for now, should be moderately easy to change if needed tho.

Subject: Re: Microbial Compounds and Organelles Thu Oct 31, 2013 8:59 am

Automatically coupling resource usage to the size of an organelle isn't necessary, I think. The size and shape of organelles can only be changed by editing the script files anyway, and if the designer who implements that change wants the resource usage to go up as well, it can be adjusted manually as well.

Subject: Re: Microbial Compounds and Organelles Thu Oct 31, 2013 7:51 pm

So the weighting of the random distribution should take into account the size of the organelle? That's what im trying to say. The resource usage isn't what I'm talking about. I'm talking about the probability of receiving the resource in the random distribution in each timestep. Think about it. 1 tiny organelle vs 1 jumbo organelle, the jumbo one (regardless of its resource usage) has a higher probability of getting the resource. So shouldnt the random distribution have a weighting towards certain organelles dependant on their size?
Sorry if I'm acting all confused

Subject: Re: Microbial Compounds and Organelles Fri Nov 01, 2013 7:21 am

I understood you chef

Subject: Re: Microbial Compounds and Organelles Fri Nov 01, 2013 12:55 pm

Oh, sorry. I misread your suggestion. But still, the same argument against it applies. Why couple it with the size of an organelle, if we can just as easily (or even easier) make it an independent parameter that designers can tweak?

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