Compound system

can you make and post more of these charts, it may come in handy when the creation of cells and their organelles may come about. With the numbers being there and all.

If you don't mind, could I provide them as XML's instead (see above post)? I'm happy to create any more charts like that to make explaining stuff easier, but they're a little too labour intensive to make one for each compound we'll need.

Seregon wrote:

If you don't mind, could I provide them as XML's instead (see above post)? I'm happy to create any more charts like that to make explaining stuff easier, but they're a little too labour intensive to make one for each compound we'll need.

Seregon, I would love to help! Do you think you could PM me the numbers for the different compounds and then I just compose them into a chart? Please PM me.

Seregon wrote:

If you don't mind, could I provide them as XML's instead (see above post)? I'm happy to create any more charts like that to make explaining stuff easier, but they're a little too labour intensive to make one for each compound we'll need.

that is fine, xml isn't too hard to read.

So far these charts look like they're spot on (don't quote me on that).
Great work!

If you prefer XML than I'd suggest doing that because it's a lot quicker and easier indeed.

I myself don't know how to work with XML, Sorry.

Hey this looks great and I really like all the detail that went into it, but I'm a little worried about the amount of calculations it takes, especially if you were going to be doing this for large numbers of cells So I'd like to propose an alternative system that can be used.

Equation: (A modification of the monod equation to account for temperature changes, and cell death)

u_net= (u_m*S/(K_s+S)*e^(-Ea/T)-kd

Variable Descriptions

Spoiler:

The doubling rate of the cell is defined as t=ln(2)/u_net (can be how fast the cell grows)
If the u_net is negative, then the cell is dying.

The energy available to the cell can be u_net/u_mm (might need to change this)

where u_mm is the maximum growth for the "best" substrate or food source.

How to account for multiple food sources and substrate selectivity.

Spoiler:

Cell death rate , kd

Spoiler:

But what about oxygen?

Spoiler:

How this equation can be used for auto evo at the cellular level

Spoiler:

How to keep calculations simple but realistic

Spoiler:

Other issues to look into

Spoiler:

Oh definitions: I defined each 'species' as being separate by a single mutation, which isn't realistic, but I wanted to keep the terminology simple.

I realize you guys have probably already put a ton of work into the cell stage, and that this probably doesn't fit, but I'd just like to mention it in case it might be useful.

Nice ideas there. Remember though, that only the cell you control is affected precisely by these variables. All other cells are run as populations through auto evo and a simpler population dynamics system.

Your idea (gdt) comes close to my initial thoughts on that problem, something I've now started developing in the population dynamics thread. I'm not actually familiar with the monod equation, but it looks like details from this (and other equations) could be very useful.

As Scio said, for most populations we'll be modelling the population, not the individual cells. The exception to this will be your own cell, and possibly (if computation allows) the other cells visible to you in your immediate surroundings. My approach to this is to represent each species as a collection of all the compounds it requires/uses/produces/etc, as well as the average size/energy/etc of its constituent individuals, we then simulate the interactions of these compounds, and their effect on the individual states, at the species level. In the simplest, crudest possible example, if the species has an excess supply of fat, some of this will be stored in its cells, and some will go towards producing larger cell membranes; if there is a deficit of oxygen, aerobic respiration becomes slow/impossible, anaerobic respiration takes place instead, lactic acid (or ethanol, or similiar) is produced and the cell suddenly requires a lot more sugar (or similair) to do what it was doing before.

The major advantage of this system over yours is this (and I only came to this realisation by first attempting what you just did): by representing a species as a collection of compounds, all those compounds are represented equally, we don't need a special variable for oxygen, or energy (atp), they're all simply compounds. What makes each one different is its interactions with other compounds: 6o2 + c6o6h12 -> 6co2 + 6h2o + 38atp. Simply (and I mean that in the most sarcastic way possible) by determining these interactions between compounds we can control how the system behaves, it will effectively attempt to ballance itself (within the constraints of these interactions, as most aren't reversible), and in the process use the available compounds in the available interactions in order to grow its cell/population. Another advantage (solving the problem I think you ran into when trying to account for substrate consumption) is that the system ballances, there should be no loss of compounds between interactions, in effect the system is closed. This is a very crude explanation, and I'll be posting much more detail in the thread linked above at some point (hopefully in the next week or two).

Where things become a lot more complicated is interactions between species, i.e.: what happens when one species predates another? Assuming that x individuals of species A (with total population X) just consumed y individuals of species B (with total population Y), we could simply say that y/Y of each compound in species B is evenly distributed among x individuals of species A (although, within the limits of our representation, they are effectively distributed among the entirety of species A). More than likely it won't be that simple, some of the compounds will be wasted and leak back into the environment, others won't be digestible by A and will be excreted back into the environment (this is already handled by the above system). This is only part of the system which is far from done, and will need a lot more work.

Hopefully that answers your questions. Your ideas are very much appreciated, but your just a little way behind where we are (which is impressive enough, I've been working on this on and off for about 6 months). Where I think you could really help out is determining all the above interactions, as it seems you may already know of some specific equations which I don't.

In the ideal of keeping the simulations as simple as possible (but still keeping to the realistic aspect)
A general form for these reactions is:

Substrates-->(Growth)+Products. This should simplify the need for keeping track of intracellular compounds that wouldn't be seen by the player in the course of normal game-play.

I.E. 36*Food+12*O2-->0.2*X+CO2+[bio-waste].

If we can use this type of reaction for the main simulation and game play it would be great. To get the amount of detail required in the sense you were talking about (I'm not sure where we are exactly on this at the moment) you'd have to have the metabolic flux maps for each species (or simplified versions)

The disadvantage of this method is I can't think of a way at the moment for regulatory constraints (like aerobic vs anaerobic) without writing multiple equations. (unless we relate the coefficients in front of the substrates to the products) (which might work!)

I.E. instead of a*Food+b*O2 --> c*X+d*CO2 it would be a*Food+b*O2-->(b-Z)*X+(RQ)*CO2

where z is the oxygen starvation limit below which the organism X can't survive and starts to die, and RQ is a simply b/N where N is a number to specify the ratio between O2 uptake and CO2 excretion. Obviously we can add more things to the reaction.

I also think these same equations can be used later in the game for cities/planets where X would be population, substrates would be food, material, tech, etc and the products can be things like units, more tech, etc. This could be done in the flux maps simply be adding or removing "reactions" or regulating them.

Additionally, these all turn out to be linear equations. So you can use something like the simplex algorithm (or any linear optimization method) to say hey, "I want to optimize this city for research, growth, product of ___ etc. " and fluxes would be bound by what buildings were in the city/planet. This could also be useful for evolving species by adding/removing reactions, or modifying limits of fluxes.

As I said before, using these simple equations should cut down on the computations the computer needs to run during game play. However for modifying and "evolving" the species having flux maps for them would give you as much detail as you want, help keep everything balanced, and give some insight to the user about how all of this stuff works biologically(I think it would also work nicely later in the game as well for city and planet production)

Where I'm getting this from:

Spoiler:

Hey I kind of lurk here sometimes and I just wanted to give my 2 cents on an actual project to simulate a cell (Since synthetic bio is what I do)
Since it is an actual cell being simulated, it might get toooooooooo complex, but anyway here is the link

http://wholecell.stanford.edu

I can't gather anything from the stuff in the downloads except the virtual machine, but you coders are a lot better then me at that stuff

-Koeng

Koeng wrote:

Hey I kind of lurk here sometimes and I just wanted to give my 2 cents on an actual project to simulate a cell (Since synthetic bio is what I do)
Since it is an actual cell being simulated, it might get toooooooooo complex, but anyway here is the link

http://wholecell.stanford.edu

I can't gather anything from the stuff in the downloads except the virtual machine, but you coders are a lot better then me at that stuff

-Koeng

Thanks for the link, it was pretty interesting to watch. I've also found this E-Coli reaction map showing all the reactions and physical locations/groupings in a typical E-Coli cell. We probably won't do an entire cell simulation as that would take up way to many resources for an average person to play.

Seregon had me write a few compound processes. I've now written the pathways for Fatty Acid metabolism and synthesis. Also done (though still up for changes) are Agent and RpAse synthesis pathways.
Here they are, in the .xml format needed.
For reference:
Fat=C₁₂H₂₆
Oxygen=O₂
Carbon Dioxide=CO₂
Sugar=C₆H₁₂O₆
Water=H₂O
Protein=Amino Acid chain of length n (n=tbd)

Fat Respiration:

Fat Synthesis:

Agent Synthesis:

RpAse Synthesis:

[edit by Seregon] minor fixes to xml code

That looks great. What's more, it actually makes a lot of sense. The format it follows is very similar to the forum format, except with the angular brackets instead of the square ones. Also, it seems really easy to just copy and paste each process, and then just alter the names and quantities.

Using this, I could actually probably get started on writing up some of the processes for the Strategy Mode. Is XML just for the prototype? How easily is it translated into C++ or Lua?

I saw "proteins" in the code and wanted to comment on a few things:D 

I know a lot about systems biology, and seeing that you have the proteins for the code would you like me to dig up some files somewhere and give you EXACT amino acid numbers needed to create the biosynthetic pathway, for lets say, a cell wall? Also the the energy needed ect.

(Also, sorry for asking, but do you guys know anywhere I can learn to put it into the format for XML? If I ever get anymore ideas, I would like to put it into code that you guys can easily use)

EDIT: was looking at website (http://thrivegame.wikidot.com/microbe-stage) and saw reproductase. Would this kinda be like a bunch of enzymes necessary for division? To accumulate enough "reproductase" I really thought of this enzyme in real life. http://en.wikipedia.org/wiki/FtsZ

-Koeng
PS: tryna catch up on everything in microbe stage!

@Nick: Actually, that is xml, and it is the format we had planed to store all the processes in. If we keep with that plan, That would be all there is needed to describe a process.

@Scio - those look great, thank you! The only possible change is that all the syntheses (plural of synthesis?!) should probably require some amount of ATP.

@Koeng - we're simplifying somewhat, and not actually modelling amino acids, as n amino acids are easily interchangable with a protein of length n. That said, if you could get us some accurate numbers for the lengths of some relevant proteins, and better yet, the ATP needed for synthesis, that would be very useful indeed. You should be able to figure out the format by looking at what scio posted, and changing the process name, and the list of input/output compounds and their relative amounts. The organelles needed for most protein syntheses will be the ER, and possibly the golgi.

A quick note on organelles - processes are allowed to require more than one organelle. If they don't require any organelles, then list them as requiring the cytoplasm.

@Seregon- That was stupid of me to forget ATP inputs- they've now been added.
@Koeng- Nice link, this could be helpful, and I'll read through it to see if there's anything we can pick up from it.

Here are a few links I found useful when designing/ thinking about creating a minimal organism

http://subtiwiki.uni-goettingen.de/wiki/index.php/SubtiPathways  
(Probably most helpful, you can find all the cycles and colorful easy to use pathways with ATP and everything)



http://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=sce
(This is the model eukaryote, since I think you guys are thinking of them. This one is a little harder to understand)

Also is there going to be a transition from prokaryotic to eukaryotic? That would be fun because you can go along and handpick all your organelles. Such as to increase photosynthetic capacity, you get infected with a virus (very rare) and you get some of these http://en.wikipedia.org/wiki/Carboxysome
Although it only works when you are a prokaryote. Or if you're staying with eukaryotes, you may want to make it so some organelles are better then others.

EDIT: Working on all the ATP stuff for reproduction

-Koeng

@Scio - I made a few more quick corrections to your xml code, RpAse synthesis now requires an organelle, the ER, and I fixed a quick syntax error - the "<Process ..." line for RpAse synthesis ended in "/>" when it should just be ">". (edited your post).

Seregon wrote:

@Scio - I made a few more quick corrections to your xml code, RpAse synthesis now requires an organelle, the ER, and I fixed a quick syntax error - the "<Process ..." line for RpAse synthesis ended in "/>" when it should just be ">".  (edited your post).

Thanks. Also, it seems forummotion fixed the problem with quotes in the rich editor. /OT