Microbe prototype under Unity

Tarpy wrote:

I can see in this system is that sugar is non-renewable.

This feature was actually already implemented. However I went to test it and it didn't work. Took me a while but it's now fixed. I reduced the radius of Sugar creation on the webplayer so you can see them reappear as you take them(Currently 50 sugar in a 10 radius). I'll put it back to cover the full area on the next build upload. Thanks for the first bug report

A problem comes from the fact that it cost more ATP to move from one sugar to another than you gain from using it. I would need to reduce the ATP cost of movement. However, it is currently 1/frame where key is down which is the minimum. I already consider putting compounds as float(see below), that would solve the problem. Another option would be to make movement every X seconds instead of /frame.

Eventually, both will be implemented I think. A float value of ATP removed each X seconds.

Seregon wrote:

- co2 isn't always bad, and it isn't always expelled by the cell. The obvious example is plants with chloroplasts, which need co2 to perform photosynthesis and produce sugar

I was taking the CO2 as an exemple since it is more harmful to human. Thinking about it I would guess that cell can also be harmed by having too much O2 or too much water in it ? (Also not enough (In relation to the environment?)?)

Since CO2 is an input to Photosynthesis, I didn't put it seperate as a waste. It is a simple Compound as others.

Seregon wrote:

having fractional ATP (or any other compound) is fine

I tought it would be simpler to have them as integer for simplicity but the more I work the simpler it seems to be with fractional compounds. I'll change it in a subsequent build.

Seregon wrote:

So, rather than aiming for an arbitrary amount of each compound in the cell (your 'maximum'), the quantities should regulate towards the environmental concentration (for things like water, co2, o2 etc.).

This is close to what I had in mind. I already have a value for the waterConcentration(As a float between 0.0 and 1.0(0-100%)) Would that make sense for you ?

My question would be how to calculated the concentration in the cell. Would you just do Current Value/Maximum Value ? If so that'd be really simple. However I'm not sure about this idea considering there are no real "Hard Maximum Value". I'd like to keep discussing this concept to implement it.

Seregon wrote:

A similair effect is seen with internal processes. If the concentration of the products of a reaction are high, the rate of that process is slower, and vice versa if the concentration of products is low (and vice versa for inputs).

I was looking at it in the compound thread. This is pretty interesting reading. I'll keep that in mind but won't implement it right away.

Seregon wrote:

Please don't take any of this as criticism, it's not meant to be. I'm just trying to point out issues you may not know about (especially if your not a biologist). Also, I realise your creating this prototype partially as an excersize for yourself, so your welcome to implement it however you like.

No offense taken at all, this was helpful critic post. This is exactly where I wanted this discussion to go. Keep in mind that I have the average Joe knowledge in cellular biology and that I keep learning reading your post. My interest in this topic is growing with each post.

I want to keep the prototype as close to the real project as possible while keeping it enjoyable to implement.

Thanks for the compliment on the proto, and yes you can call me Rod

A few quick answers, then I need to get some sleep. I'll be interested to see what you achieve tonight (no pressure!).

- In my prototypes I did calculate concentration simply as currentValue/maxValue. While this is simple, it gets more interesting when you try to calculate what that maximum capacity is. It depends on the size of the cell, it's organelles, the other compound contents etc., but I haven't looked into this properly yet, so I have no equations atm.
- Note that water is the special case. The volume of water in the cell is (not quite exactly) the volume of the cell itself, every other compound is dissolved in that water volume. This again makes for some slighlty nasty math, which I will work on when I get a chance.
- My ideal when designing the compound system is something where no compound gets any special treatment (i.e.: nothing is hardcoded), allowing compounds, processes etc. to be added to the config xmls without changing the code. I haven't quite reached that point yet, but I'm close, and would be very interested to see if you can achieve something along those lines.
- If you want to do something per step, it should really be per unit time (e.g.: seconds), not per frame, as the framerate is variable. In unity, have a look at deltaTime if you haven't already.

I should have some time to work tonight. I'll probably setup the Organel class. However displaying it on a GUI take so much time. I'll see what I'll come up to!

Seregon wrote:

A few quick answers, then I need to get some sleep. I'll be interested to see what you achieve tonight (no pressure!).

- In my prototypes I did calculate concentration simply as currentValue/maxValue. While this is simple, it gets more interesting when you try to calculate what that maximum capacity is. It depends on the size of the cell, it's organelles, the other compound contents etc., but I haven't looked into this properly yet, so I have no equations atm.

Interesting. Implementation doesn't seems too hard. I'll need help to make something that make sense.

Seregon wrote:

- Note that water is the special case. The volume of water in the cell is (not quite exactly) the volume of the cell itself, every other compound is dissolved in that water volume. This again makes for some slighlty nasty math, which I will work on when I get a chance.

Didn't think about that. I'm interested in seeing work on this topic. If it is too nasty for what it's worth, I'd suggest treating water as other compound.

Seregon wrote:

- My ideal when designing the compound system is something where no compound gets any special treatment (i.e.: nothing is hardcoded), allowing compounds, processes etc. to be added to the config xmls without changing the code. I haven't quite reached that point yet, but I'm close, and would be very interested to see if you can achieve something along those lines.

This is also what I had in mind. It is already pretty close. Only problem I saw was priority(You prefer to do Aerobic Respiration than Anaerobic Respiration if Oxygen is available). Maybe there are no priority at all in real life but I think it'd make sense to have a better control over compounds consumption.

Thinking about it, it could just be a list of Higher-Priority Process straight in the XML. i.e : Anaerobic Respiration(Priority List : Aerobic Respiration). Software will understand that if Aerobic Respiration is Available, Activated and has compounds for it, Anerobic Respiration won't take place.

It's mostly a matter of loading the XML in unity right now, which shouldn't be too hard.

Seregon wrote:

- If you want to do something per step, it should really be per unit time (e.g.: seconds), not per frame, as the framerate is variable. In unity, have a look at deltaTime if you haven't already.

Thanks for the input. I agree, using time would make the game behavior independent from the computer used. I'm already using deltaTime to make Process ticks every seconds. It might be the exact same process to make movement tick.

I would however like to some other options like FixedUpdate. I'll look into it but will make sure everything is second based.

RodGame wrote:

My idea would be that the max value is a aimed value that compounds will try to attain. This would mean oxygen and water absorption and CO2 elimination. For CO2, it would also mean dmg to the cell if its level is too high(Right ?)

So what would be the design of this concept? Do we want a oxygen level in water to influence the rate of oxygen absorption? Do we need some specific organelle for Water/O2 absorption or CO2 expulsion ?

I would like to hear from you guys. I searched for it on the forum without finding exact answers.

Oxygen is required for aerobic, but not anaerobic respiration. In game, you are in a liquid medium that should have a constant level of dissolved oxygen in it, so simply being in the water fills up your oxygen. At the cellular stage, it's very easy for O2 and CO2 to to be dealt with, they just diffuse straight across the cell membrane. There is no specific organelle, but keep the system in place, because more complex organisms will have trouble regulating levels of these gases.

Really, really excellent work here. Brilliant. I actually enjoyed how fast ATP ran out, because it meant that I had to conserve energy in movement, which made the game challenging and fun to play.

~sciocont wrote:

Really, really excellent work here. Brilliant. I actually enjoyed how fast ATP ran out, because it meant that I had to conserve energy in movement, which made the game challenging and fun to play.

Thanks! This is the gameplay I tried to give to the user. I hope to see you around the thread helping on the biologic aspect, always helpful!

------------------------------

Organelle are now added to the prototype!

The concept is based on the first pages of this thread :
https://thrivegame.canadaboard.net/t997p15-microbial-compounds-and-organelles

I admit I haven't finished to read all of it yet, but it gave me the base of the ideas.

I currently added :

Spoiler:

Each Organelle has the following member :

Spoiler:

Currently,

Mitochondria._enabledProcess = "AerobicResp";
Chloroplast._enabledProcess = "Photosynthesis";

------------------------------
Open Question to anyone :

Could you help me make the first list of useful Organelle (Should Nuclei be an Organelle)?
What process are they enabling ?
How do we calculate/choose the maximum number available for each Organelle ?
Some Organelle will have to affect other things than process, such as move speed(cilia, flagellum), compound capacity?(Vacuole) and such... I would be interested in hearing you on this topic : What can organelle give to the cell that isn't a process ?

EDIT :
You can try the new version on the WebPlayer, it's up-to-date. Anyone having problem using it ?

- Organelle system now working. Each organelle can enable 1 and only 1 process. I'll add later for multiple support. You can't really see it because you don't have control of organelle, but aerobic respiration is enabled because of Mitochondria and Photosynthesis is disabled because of lack of Chloroplast. Other ones are hardcoded as enabled to give a bit of gameplay to player for now.

- Added a basic HUD. (Might work poorly on small resolution, tell me if you have problem with it.)
I'll eventually add some info in a Help Windows.
Editor will give the option to add/remove organelle (How would you want it ?)
God Mode will give the option to tweak values that wouldn't be allowed to the normal player.

Here is my list of a few organelles and their uses:

1. Nucleus

The nucleus is probably the most important organelle of any cell. All of the DNA of a cell is stored here, so the nucleus is technically very important for cell reproduction. The player's cell would automatically have a nucleus. In the microbe editor, you can change the size of the nucleus, but you can't remove it from your cell. Also, the nucleus wouldn't be choosable from the organelle section, because there really is no point in having more than one nucleus (although cells with two nuclei actually exist in nature).

2. Membrane

The membrane protects the cell from hazards in the environment, so like the nucleus, it is a very important organelle. The player's cell automatically begins with a membrane. Your cell's health would be the health of the membrane. In the organelle editor, you won't be able to place down more membranes, since you can technically only have one. However, you would be able to adjust some of the traits of your membrane. These traits would be: Thickness, toughness and flexibility. All would have a value from 1 to maybe 10. Here's the effect of each of these:
Thickness- How thick your membrane is, the larger the thickness, the more max health the player's cell has. Downside is it decreases average cell speed and acceleration and membrane flexibility.
Toughness- How much damage can your cell's membrane absorb. The larger the toughness, the more damage is absorbed. Downside is it decreases the average compound intake.
Flexibility- How flexible your cells membrane is. The more flexible, the faster a cell can make sharp turns. Downside is it decreases thickness.
Mitochondria
These are required for converting compounds into ATP. Like nuclei and the cell membrane, every cell starts of with one mitochondria. Every new mitochondria increases the rate at which the players cell converts compounds into ATP.

That's all I got.

Rod, I got just the thread for you.

The OP has a list of all the organelles, as well some important compounds.

Light concentration affects the frequency of photosynthesis processes inside a cell. 0% light means no processing, 50% means half speed, and 100% means full speed ahead.

This is the same with heat and thermoplasts.

From page 7 onwards, Toughtopay makes an appearance, and he has links to his extremely well done tables on organelles and microbes in GoogleDocs. That could help out as well.

Quote :

Could you help me make the first list of useful Organelle (Should Nuclei be an Organelle)?
What process are they enabling ?
How do we calculate/choose the maximum number available for each Organelle ?
Some Organelle will have to affect other things than process, such as move speed(cilia, flagellum), compound capacity?(Vacuole) and such... I would be interested in hearing you on this topic : What can organelle give to the cell that isn't a process ?

Tarpy's imagination of the nucleus agrees with my thoughts. However, I differ on membrane and Mitochondria.
The membrane is important once we get into the cell editor, where the real fun of microbe stage resides. In the cell editor, you build a cytoskeleton, and then connect the membrane in a closed loop around it. Here's a concept image. This overlooked thread should help you out with the prototype.
You can see here How I envision the membrane and cytoskeleton working together to create the form of the cell. Rigidity is all based upon the cytoskeleton and whether or not you have a cell wall (though in real life, the rigidity of a cell membrane is partially controlled by cholesterol). The cell membrane also has a universal thickness and toughness. If it is punctured and not healed immediately, you die.
Mitochondria should be added through endosymbiosis. Before you gain them, you will have only anaerobic respiration.

@NickTheNick
This is the thread I linked in my last post. Thanks for pointing the specifics because I didn't look at page 7. Currently all process are executed at the same interval. I'll change it when I'll add the light concept as you mentioned.


Well, I won't bother with Nuclei right now since it is always there and doesn't serve direct purpose.

I'll add endosymbiosis concept. From my understanding right now, I'll add randomly moving proto-cells that are mitochondria. Colliding with one would mean eating it and would bring a X% change of gaining 1 Mitochondria organelle. Having more would shorten the time between 2 Aerobic respiration ? Allow 2x mitocondria process to be executed at the same instant ?

I had already looked at the thread ~sciocont mentionned a while ago and forgot about it. I'll eventually get to the editor you pointed out. It is however something that would take a bit more time. Is it possible to access the prototype that I think I tried in modDb(Circle where added by mouse wheel click if I remember, a skin was automatically added around it).

Thanks for the feedback, another question, if you look back at the list of process that are currently implemented in the game, how should they be brought availaible ? Aerobic respiration comes from mithocondria. What about AmnioAcid Respiration ? What about AminoAcid Biosynthesis ? Are they available from start or from a give organelle ? This is the kind of inputs I would like from you guys.

Oh, haha, my bad.

The chance of acquiring the organelle upon engulfing it (endocytosis) for mitochondria is 1/1000.
The chance for chloroplasts is 1/2000.
The chance for thermoplasts is also 1/2000.

Did you get anything for chemoplasts scio?

Edit: Also, from what I understand, the standard list of organelles for a cell goes:
Vacuoles
Lysosomes
Nucleus
Cytoskeleton
Golgi Apparatus
Endoplasmic Reticulum

Someome like Scio or Seregon should confirm this first, however.

After a bit of testing the 1 in 2000 thing seems way too rare, i was testing my prototype and if a player had to do this they would be extremely annoyed and probably stop trying.
Should we make these numbers lower , or do you have a better idea..

I agree with untrustedlife, 1/2000 is too small. I get the idea of making it realistic and last a bit but the player will give up before. 1/100 is already small.

But those aren't really important in prototyping. You should use something along the line of 1/10-1/100 for test purpose. I'd like to avoid discussing those number in this thread and stick to implementation of game design. If we want to discuss actual values, we can make another thread.

@NickTheNick
I'd be interested in knowing what all those organelle give to the cell in term of actual game design(i.e : Vacuole = Compound MaxValue + 1000)... That's what I'm asking.

@untrustedlife
Nice to see your prototype is taking form! Would it be possible to see it in action and have access to the code ? Don't be scared of showing your code if you think it's a mess. Everyone will learn from it and give you feedback. You should make another thread along mine to show it off. With 2 prototypes, we should get a really good idea of how to implement it in the actual C++ code!

Quote :

Thanks for the feedback, another question, if you look back at the list of process that are currently implemented in the game, how should they be brought availaible ? Aerobic respiration comes from mithocondria. What about AmnioAcid Respiration ? What about AminoAcid Biosynthesis ? Are they available from start or from a give organelle ? This is the kind of inputs I would like from you guys.

Quote :

Vacuoles
Lysosomes
Nucleus
Cytoskeleton
Golgi Apparatus
Endoplasmic Reticulum

Ok,
vacuoles will do exactly what you think- adding them increases storage of some compound. The best way to implement this initially is to have vacoules hold starch, and be built up when there is an excess of glucose, and depleted when there is not enough. They should be placed using the cell editor and available immediately Lysosomes don't need to be directly implemented- they just break down trash and food for the cell, but aren't big enough for us to notice. The nucleus is mandatory- it just protects the DNA. No upgrades, but you can change where it is. The cytoskeleton is created through the microbe editor. The golgi apparatus and ER can be placed in the editor, and should be able to be upgraded (the ER upgrades increase protein synthesis efficiency, or something along those lines), but right now we don't need to worry too much about them.

Other forms of basic respiration and synthesis (with amino acids, protiens, etc) (excluding exotic forms- more info below) are automatically available but can be upgraded. We may not actually need to do much with them, since they probably won't affect gameplay directly.

Also, I've been playing the prototype for a while, and, though I might be overlooking something, it seems that turning Aerobic respiration on isn't making a difference in my ATP generation. In modern times, Aerobic respiration delivers ~38 ATP per unit of glucose, whereas anaerobic respiration delivers 2 ATP per unit. We can begin Aerobic respiration as much less advantageous, yielding just another 2 ATP (4 total), and just have mitochondria evolve as organelles form that point. This means we can increase the chance of endosymbiosis to something like 1 in 500. A chance not too small to be inaccessible, but small enough that some gameplay time must be invested before you get mitochondria.

This wikipedia page lists other types of respiration. We don't need to include all of them, but it think it might be interesting to put some of them into the game. I'll look into the chemistry behind them.

@~sciocont
This is a clear explanation. It helped me understand a couple of concepts. IMO, things like Lysosomes shouldn't be implemented at all. They are hidden process. We should concentrate on having a small list of organelle/process that have actual gameplay/utilities to limit the knowledge barrier to the average player.

@ untrustedlife
It seems like awesome work. I liked how your prototype seems different than mine and you explored differents area. It will give us a better idea on the actual implementation. Can't wait to have a download. Please make it public as soon as possible.

RodGame wrote:

@~sciocont
This is a clear explanation. It helped me understand a couple of concepts. IMO, things like Lysosomes shouldn't be implemented at all. They are hidden process. We should concentrate on having a small list of organelle/process that have actual gameplay/utilities to limit the knowledge barrier to the average player.

@ untrustedlife
It seems like awesome work. I liked how your prototype seems different than mine and you explored differents area. It will give us a better idea on the actual implementation. Can't wait to have a download. Please make it public as soon as possible.

I added a screenshot showing a small colony of filterers bottom right

RodGame wrote:

@~sciocont
This is a clear explanation. It helped me understand a couple of concepts. IMO, things like Lysosomes shouldn't be implemented at all. They are hidden process. We should concentrate on having a small list of organelle/process that have actual gameplay/utilities to limit the knowledge barrier to the average player.

I agree completely- I want to keep this fairly simple for you guys to program and easy for players to understand- That's why so many organelles are initial.

~sciocont wrote:

RodGame wrote:

@~sciocont
This is a clear explanation. It helped me understand a couple of concepts. IMO, things like Lysosomes shouldn't be implemented at all. They are hidden process. We should concentrate on having a small list of organelle/process that have actual gameplay/utilities to limit the knowledge barrier to the average player.

I agree completely- I want to keep this fairly simple for you guys to program and easy for players to understand- That's why so many organelles are initial.

as long as cells dont become kawaii blobs with kiddy features *cough* SPORE's cell stage *cough*

I downloaded the code and messed with it a bit. Sorry i don't have a github for the code. You can find the compiled program here: link

Things i did:

Decreased the movement cost from 1 to 0.2
Doubled the updates per tick.
Moved the background back so it has the same effect than in the current release.
Made it so sugar spawns around the player, but not too close.
Sugar too far away from the player gets deleted, and then instantly repositioned.

That means that wherever you go, there will be sugar, but it never has more than 50 sugar created.

Code for the sugar deletion and addition: (inside ResManagement)

Code:

// Update is called once per frame
   void Update () {
      GameObject[]sugars = GameObject.FindGameObjectsWithTag("Glucose");
      for (int i = 0;i<sugars.Length;i++){
      GameObject sugar = sugars[i];
         if ((GameObject.FindGameObjectWithTag("Player").transform.position-sugar.transform.position).magnitude>radiusSpawnRes){
            Destroy(sugar);
            nbrSugarInSoup--;
         }      }
      while(nbrSugarInSoup < nbrSugarToCreate)
      {
         CreateRes("Sugar");
      }
   }
         
   // Instantiate a glucose prefab on the map
   void CreateRes(string _resType)
   {
      GameObject _curGameObject;
      Vector3 _resPos = Vector3.zero;
      Vector3 _playerPos = GameObject.FindGameObjectWithTag("Player").transform.position;
      while(_resPos==Vector3.zero||Mathf.Sqrt((_resPos.x-_playerPos.x)*(_resPos.x-_playerPos.x)+(_resPos.z-_playerPos.z)*(_resPos.z-_playerPos.z))<radiusNoSpawnRes){
      _resPos = (Random.insideUnitSphere)*radiusSpawnRes;
      _resPos.x+= _playerPos.x;
      _resPos.z+= _playerPos.z;
      _resPos.y = resGlucose.transform.localScale.y/2;
      }
      _curGameObject = Instantiate(resGlucose, _resPos, Quaternion.identity) as GameObject;
      _curGameObject.tag="Glucose";
      nbrSugarInSoup++;
   }
}

Looks good Daniferrito, I kind of want to try out unity now

Great work!!!

Good job showing it off
Will you do mine next?

untrustedlife wrote:

Good job showing it off
Will you do mine next?

yes what next?

The download is on my post.

I just want to add here that if you have any questions about how to implement something mathematically or in code let me know. I'm pretty good at this sort of thing. Especially with regards to metabolic pathways.

Edit: If you wanted to ask anything about metabolic pathways, regulation, control, etc. I can probably answer those questions too.