Paris/Cell auto
From 2007.igem.org
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==Spacial simulation== | ==Spacial simulation== | ||
We try with this work to characterize the diffusion of the DAP and the effect on the cells. We have a "tapis bactériens" with germinal cells and some somatic cells.<br> | We try with this work to characterize the diffusion of the DAP and the effect on the cells. We have a "tapis bactériens" with germinal cells and some somatic cells.<br> | ||
| - | + | =='''''We make some hypothesis:'''''== | |
We work with a '''constant population''' (no death and no division), we can imagine that we are a stationary phase or between to division cycle.<br> | We work with a '''constant population''' (no death and no division), we can imagine that we are a stationary phase or between to division cycle.<br> | ||
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The DAP can be under two types intra/extra cellular (DAPi/DAPe)<br> | The DAP can be under two types intra/extra cellular (DAPi/DAPe)<br> | ||
The '''DAP is comsume in bacteria G''' <br><br><br> | The '''DAP is comsume in bacteria G''' <br><br><br> | ||
| - | + | =='''''We have 3 entities in our model'''''== | |
Bact it has a concentration internal of DAP ('''DAPi''') and external ('''DAPe'''). It's a cell in our automaton<br> | Bact it has a concentration internal of DAP ('''DAPi''') and external ('''DAPe'''). It's a cell in our automaton<br> | ||
BactS is a Bact which produce DAPi<br> | BactS is a Bact which produce DAPi<br> | ||
BactG is a Bact which consume DAPi <br><br><br> | BactG is a Bact which consume DAPi <br><br><br> | ||
| - | + | =='''''We produce this set of rules'''''== | |
| + | <br> | ||
For bactS<br> | For bactS<br> | ||
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<br><br><br> | <br><br><br> | ||
| - | + | =='''''Initial state'''''== | |
| + | <br> | ||
We use a 30x30 cells automaton. | We use a 30x30 cells automaton. | ||
All cells are BactG excepted 4 BactS which are placed randomly on the automaton | All cells are BactG excepted 4 BactS which are placed randomly on the automaton | ||
<br><br><br> | <br><br><br> | ||
| - | + | =='''''Parameters'''''== | |
| + | <br> | ||
We have 8 parameters and we can had noise for each of them.<br> | We have 8 parameters and we can had noise for each of them.<br> | ||
'''In BactS:'''<br> | '''In BactS:'''<br> | ||
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<br><br><br> | <br><br><br> | ||
| - | + | =='''''Output'''''== | |
| + | <br> | ||
The output is two animated pictures one showinf the differntiation the other the diffusion of DAPe | The output is two animated pictures one showinf the differntiation the other the diffusion of DAPe | ||
Revision as of 15:39, 20 October 2007
Contents |
Spacial simulation
We try with this work to characterize the diffusion of the DAP and the effect on the cells. We have a "tapis bactériens" with germinal cells and some somatic cells.
We make some hypothesis:
We work with a constant population (no death and no division), we can imagine that we are a stationary phase or between to division cycle.
The differentiation is DAP dependent, it's append when the cell as enough DAP to evolve but not enough to divide.
The DAP is made in bacteria S, the production rate is the difference between the total production and self consummation
The DAP can be under two types intra/extra cellular (DAPi/DAPe)
The DAP is comsume in bacteria G
We have 3 entities in our model
Bact it has a concentration internal of DAP (DAPi) and external (DAPe). It's a cell in our automaton
BactS is a Bact which produce DAPi
BactG is a Bact which consume DAPi
We produce this set of rules
For bactS
- DAPe = DAPe + DAPe_diffused_in_neighborhood + DAPi_diffused_from_the_BactS
- DAPi= DAPi +DAPi_produced - DAPi<_diffused_from_the_BactS
For BactG
- DAPe=DAPe + DAPe_diffused_in_neighborhood - DAPi_diffused_from_the_BactG
- DAPi= DAPi -DAPi_consummate + DAPi_diffused_from_the_BactG
- BactG = if minimal DAPi for differentiation < DAPi < maximal DAPi for differentiation BactS else stay BactG
Initial state
We use a 30x30 cells automaton.
All cells are BactG excepted 4 BactS which are placed randomly on the automaton
Parameters
We have 8 parameters and we can had noise for each of them.
In BactS:
- Dap export
- Dap import
- Dap production
In BactG:
- Dap export
- Dap import
- Dap consummation
- Minimal Dap needed for differentiation
- Maximal Dap needed for differentiation
Output
The output is two animated pictures one showinf the differntiation the other the diffusion of DAPe
