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Offlinescubabuddha
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using agent based modelling to simulate growth of fungi
    #9563306 - 01/07/09 09:33 AM (15 years, 2 months ago)

Hi, i think this is my first venture into the advanced forum, though i've been cultivating for a little while now.  :wave:

anyway, what i'm here for is this: i do agent based modelling (wiki) and it's just struck me that the growth of fungi could be well modeled using this technique. More specifically, the growth of mushroom fungi on agar plates. I won't have much trouble with the simulation loop itself, but i don't know enough about the biology of the process to know what each cell needs to analyze at each clock tick.

A quick example of this modeling technique, called Conway's Game of Life:
consider an infinite grid of squares (standard x-y plane). Each square (agent) has two states--alive or dead. Each square synchronously evaluates its next state based on these rules:
  1. Any live cell with fewer than two live neighbours dies.
  2. Any live cell with more than three live neighbours dies.
  3. Any live cell with two or three live neighbours lives, unchanged.
  4. Any dead cell with exactly three live neighbours will become live again.

It's a very simple rules but it produces very interesting behavior.

What I am aiming to do is create a similar (but more advanced) algorithm for mycelium growth.

What can you tell me about the biology that would be pertinent to this simulation?

Some things that i can think of are frequency of cell division, determining direction, nutrient absorption, etc.


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Invisiblefastfred
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Re: using agent based modelling to simulate growth of fungi [Re: scubabuddha]
    #9564271 - 01/07/09 12:36 PM (15 years, 2 months ago)

There would be quite a lot of factors to consider.  The Conway's game would be a good place to start.  Being a network of cells a lot will depend on it's neighbors. 

So you would have to consider the state of the entire network, food and nutrient availability, pH, temperature, light, CO2 concentration, humidity, and probably a lot more that I'm forgetting.

Just curious, but do you have a specific purpose in modeling fungi?


-FF

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Invisiblefastfred
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Re: using agent based modelling to simulate growth of fungi [Re: scubabuddha]
    #9564421 - 01/07/09 01:07 PM (15 years, 2 months ago)

There would be quite a lot of factors to consider.  The Conway's game would be a good place to start.  Being a network of cells a lot will depend on it's neighbors. 

So you would have to consider the state of the entire network, food and nutrient availability, pH, temperature, light, CO2 concentration, humidity, and probably a lot more that I'm forgetting.

Just curious, but do you have a specific purpose in modeling fungi?


-FF

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Offlinescubabuddha
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Re: using agent based modelling to simulate growth of fungi [Re: fastfred]
    #9564462 - 01/07/09 01:14 PM (15 years, 2 months ago)

Yeah, this model could get very complex very quickly. I'd like to keep this simple at first, to get it working. I can always make it more inclusive. Those are all certainly factors that would contribute to growth rate and direction though. Also, growth on agar plates will be significantly less complicated than in a spawn jar considering that the growth in the third dimension will be considered negligible... for now...

Conway's game of life is a cellular automaton so it could be adapted quite nicely to actual behavior of living cells.

At this point in the project, I'm more interested in how it grows and spreads in ideal conditions, not so much in the factors that will influence how it spreads.

And as for a reason? I enjoy this kind of work AND growing mushrooms :grin:


Here are some more developed questions:
As mycelium grows, does it only grow from the ends of the rhizomorphs? (the way a tree grows from the tips of its branches)

Approximately how often does mycelium duplicate?

What's about a normal colonization rate? (inches or cm per day)

And finally, what are the dimensions of a single mycelium cell (micro or pico meters, presumably)


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OfflineMephistophelian
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Re: using agent based modelling to simulate growth of fungi [Re: scubabuddha]
    #9565862 - 01/07/09 04:54 PM (15 years, 2 months ago)

Fascinating concept you want to design...

I was looking through a catalog of books and your mentions made me think that maybe you were in turn looking at books like I was.

http://www.shroomery.org/forums/showflat.php/Cat/0/Number/9564308/an/0/page/0

They might be able to provide you with more in depth answers, especially those pertaining to the complexity your eventually going to run into (and even alot of basics that could easily be overlooked).


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Master Slants Made Simple

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OfflineEmperor Reishi
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Re: using agent based modelling to simulate growth of fungi [Re: scubabuddha]
    #9570281 - 01/08/09 11:24 AM (15 years, 2 months ago)

I was reading yesterday in the "growing gourmet and medicinal mushrooms"
and they talked about some of this info. The link below is an e-book version. You should check out the stamet's p-value system heading. It talks about cell growth across a petri dish and the size of those cells, ect... which varies quite a bit depending on species.

http://books.google.com/books?id=jH-JI7pAOjAC&dq=the+mushroom+cultivator+pdf&pg=PP1&ots=o1zFe6QxpL&source=in&sig=23-mecIG0Dyez2eayCI4-LX8MLM&hl=en&sa=X&oi=book_result&resnum=11&ct=result#PPA99,M1


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EmperoR ReishI

Looking for:    Live Cultures: Maitake[sclerotia forming], Wood Ear[Auricularia Polytricha],            Prints: **Psilocybe mexicana,                                Reishi [other than red], Bioluminessent                                                                          Cubes & Pan Cyans

Available for trade:    Live cultures: Reishi[ganoderma lucidum], Shiitake[lentinula edodes], Chicken of the woods[Laetiporus                                            sulphureus], Enoki [Flammulina velutipes], Oyster [Pleurotus ostreatus], Lion's Mane [Hericium                                                            erinaceus]

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Invisibleblaine
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Re: using agent based modelling to simulate growth of fungi [Re: Emperor Reishi]
    #9571090 - 01/08/09 01:53 PM (15 years, 2 months ago)

I think to build this in a way that could yield useful information, you'd have to have a number of different tables whose detail I'm not qualified to speculate.

For example, not just whether or not food is in the next cell but if it's a rotting tree stump, is it an alder? In optimum conditions such a stump would offer x amount of food but given that it's sunny, 65 degrees, slightly arid, and some other hungry something has begun working on it...now that's worth 10% of x.

A simplified food model might be to look up the qualities of your the foods on your mycellium's menu. Whether or not this is detailed enough, the Dept of Agriculture has publication HG72-Nutritive Value of Foods (offsite link to usda.gov) that might be a start.

Then you'd need some sort of food preference chart for your mycellium. Sure, mycellium can grow on x but it really thrives on y. And then you've got variations by strains (eg, Stamets' oysters that like hydrocarbons!) and...pure speculation...as mycellium matures, how its nutrition requirements change.

Very interesting but I'm skeptical this could be accomplished without a team of educated (or very well read) people guiding your development process so you're modeling/simulating the real world variables.

Best of luck, though! Hopefully you'll have more to share about this in the future!


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I come from the land of Lizards,
And the Lizards they have died

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