# Team:Edinburgh/Modelling/Signalling

### From 2010.igem.org

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<li><a href="http://2010.igem.org/Team:Edinburgh/Notebook" class="dir">lab notes </a> | <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook" class="dir">lab notes </a> | ||

<ul> | <ul> | ||

- | <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook">collaboration</a></li> | + | <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/Collaboration">collaboration</a></li> |

<li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/BRIDGE">BRIDGE</a></li> | <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/BRIDGE">BRIDGE</a></li> | ||

<li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/Red_light_producer">red light</a></li> | <li><a href="http://2010.igem.org/Team:Edinburgh/Notebook/Red_light_producer">red light</a></li> | ||

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<br> | <br> | ||

- | <p>During the <a href="http://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">intracellular modelling of bacterial BRIDGEs</a>, it became apparent that perturbations alone would not suffice to demonstrate the interactions of light based communication between bacteria. What was needed was modelling of entire colonies of bacteria. The goals of this modelling would be to demonstrate <i>in-silico</i> the light based communication between bacteria that we | + | <p>During the <a href="http://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">intracellular modelling of bacterial BRIDGEs</a>, it became <b>apparent</b> that perturbations alone would not suffice to <b>demonstrate</b> the <b>interactions</b> of light-based communication between bacteria. What was needed was modelling of entire colonies of bacteria. The <b>goals</b> of this modelling would be to <b>demonstrate</b> <i>in-silico</i> the light-based communication between bacteria that we were trying to <b>develop</b>, and to <b>establish</b> whether light-based communication was <b>feasible</b> given the few <i>in-vitro</i> measurements we were able to make.</p> |

- | <p>The ideal | + | <p>The <b>ideal</b> would be to be able to <b>simulate</b> the spontaneous synchronisation of a colony in a random initial state. <b>Realistically</b>, however, this would be a very difficult problem. The computational <b>complexity</b> of simply replicating the intracellular model for lots of individual cells and simulating them all together was <b>prohibitive</b> (especially given the hardware we had available). Also, there were a lot of <b>unknowns</b> that would have to be <b>dealt</b> with:</p> |

<ul> | <ul> | ||

<li>How is the light output from one bacterium converted into signal input by a neighbouring bacterium?</li> | <li>How is the light output from one bacterium converted into signal input by a neighbouring bacterium?</li> | ||

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<br> | <br> | ||

- | <p>The proposed plan | + | <p>The <b>proposed</b> plan was to simplify the intracellular model. The <b>aim</b> would be to produce a model which <b>replicated</b> the three light outputs and <b>reacted</b> to varying levels of three light inputs in exactly the same way as the full <a href="http://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">intracellular model</a>. This was a <b>non-trivial</b> task: first, 'exact' is difficult to <b>define</b> with stochastic modelling - no two simulation runs will be the same. The simplest <b>approach</b> would be to run the simulation repeatedly and <b>compute</b> both the mean and standard deviation for the observables (light output), for each of a number of test profiles (light input). Then we would <b>develop</b> a simplified model which matched the output for each of these profiles. Again, 'matching' would need to be <b>defined</b> as some means of scoring.</p> |

- | simulation runs will be the same. The simplest approach would be to run the simulation repeatedly and compute both the mean and standard deviation for the observables (light output), for each of a number of test profiles (light input). Then we | + | |

- | <p>The development of this model | + | <p>The <b>development</b> of this model would be automated, since there was not the time available to redevelop the simplified intercellular model every time the full <a href="http://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">intracellular model</a> was <b>refined</b> with new experimental data. It was thought that either mathematical <b>analysis</b> or evolutionary model <b>development</b> through genetic algorithms could thus be used to <b>accomplish</b> this; both would <b>entail</b> difficult tasks, but it was thought that genetic algorithms would be within our <b>capabilities</b>.</p> |

- | <p>With a simplified intracellular model, we | + | <p>With the development of a simplified intracellular model, we would be able to think about intercellular <b>communication</b>. This would involve two elements; how to <b>represent</b> the interaction of neighbouring cells over time, and how to <b>transform</b> the light output of one cell into the light input of its neighbours (and itself), taking into account attenuation, multiple conflicting signals, and other factors.</p> |

- | <p>Our proposed solution | + | <p>Our proposed <b>solution</b> was to create a simulation based on both stochastic modelling and cellular automata. For the initial <b>implementation</b> we would make the simplifying <b>assumptions</b> that the cells were non-motile and regularly packed into a two-dimensional hexagonal mesh. Each cell would <b>receive</b> input from its six nearest neighbours (and itself).</p> |

<center><br><br><p><img src="http://2010.igem.org/wiki/images/d/d4/Ed10-Inter1.jpg"></p><br> | <center><br><br><p><img src="http://2010.igem.org/wiki/images/d/d4/Ed10-Inter1.jpg"></p><br> | ||

<p><b>Figure 1:</b> The two-dimensional hexagonal mesh that forms the underlying structure of our proposed intercellular model.</p><br><br></center> | <p><b>Figure 1:</b> The two-dimensional hexagonal mesh that forms the underlying structure of our proposed intercellular model.</p><br><br></center> | ||

- | <p>The stochastic model | + | <p>The stochastic model would hold a <b>representation</b> of a colony laid out in the above hexagonal mesh. Each cell would have an individual representation of the simplified intracellular model. The model would be run stochastically with each cell effectively operating <b>independently</b>. After the elapsing of every time interval delta-t, the values of each of the three light inputs in a cell would be calculated based on the observed light output at that timepoint of the cell itself and its six closest neighbours:</p> |

- | neighbours:</p> | + | |

<br> | <br> | ||

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- | <p>The functions f<sub>red</sub>, f<sub>green</sub>, and f<sub>blue</sub> have yet to be defined, but | + | <p>The functions f<sub>red</sub>, f<sub>green</sub>, and f<sub>blue</sub> have yet to be <b>defined</b>, but would hopefully be based on experimental data.</p> |

- | <p>After updating the input value of all cells in the mesh, stochastic simulation | + | <p>After updating the input value of all cells in the mesh, the stochastic simulation would be resumed. The cycle would then repeat after every delta-t time units. This would thus give us a basis for the simulation of bacterial colony synchronisation.</p><br> |

<br> | <br> | ||

## Revision as of 13:44, 7 October 2010

## Overview: Modelling intercellular bacterial BRIDGEs

During the intracellular modelling of bacterial BRIDGEs, it became **apparent** that perturbations alone would not suffice to **demonstrate** the **interactions** of light-based communication between bacteria. What was needed was modelling of entire colonies of bacteria. The **goals** of this modelling would be to **demonstrate** *in-silico* the light-based communication between bacteria that we were trying to **develop**, and to **establish** whether light-based communication was **feasible** given the few *in-vitro* measurements we were able to make.

The **ideal** would be to be able to **simulate** the spontaneous synchronisation of a colony in a random initial state. **Realistically**, however, this would be a very difficult problem. The computational **complexity** of simply replicating the intracellular model for lots of individual cells and simulating them all together was **prohibitive** (especially given the hardware we had available). Also, there were a lot of **unknowns** that would have to be **dealt** with:

- How is the light output from one bacterium converted into signal input by a neighbouring bacterium?
- What is the distribution of the light sensing molecules in the receiving bacterium?
- How is the light attenuated by distance between the bacteria?
- How is the light attenuated by passing through two cell membranes?
- Will motility of the bacteria be an important factor?
- How much light from other bacteria will be required to not be swamped by the light output of the receiving bacterium itself?
- How will a bacterium cope with multiple conflicting signals from neighbouring bacteria?
- Will the light emission within a single bacterium be homogeneous, or will there be multiple different outputs from different regions within the bacterium?

## The Model

The **proposed** plan was to simplify the intracellular model. The **aim** would be to produce a model which **replicated** the three light outputs and **reacted** to varying levels of three light inputs in exactly the same way as the full intracellular model. This was a **non-trivial** task: first, 'exact' is difficult to **define** with stochastic modelling - no two simulation runs will be the same. The simplest **approach** would be to run the simulation repeatedly and **compute** both the mean and standard deviation for the observables (light output), for each of a number of test profiles (light input). Then we would **develop** a simplified model which matched the output for each of these profiles. Again, 'matching' would need to be **defined** as some means of scoring.

The **development** of this model would be automated, since there was not the time available to redevelop the simplified intercellular model every time the full intracellular model was **refined** with new experimental data. It was thought that either mathematical **analysis** or evolutionary model **development** through genetic algorithms could thus be used to **accomplish** this; both would **entail** difficult tasks, but it was thought that genetic algorithms would be within our **capabilities**.

With the development of a simplified intracellular model, we would be able to think about intercellular **communication**. This would involve two elements; how to **represent** the interaction of neighbouring cells over time, and how to **transform** the light output of one cell into the light input of its neighbours (and itself), taking into account attenuation, multiple conflicting signals, and other factors.

Our proposed **solution** was to create a simulation based on both stochastic modelling and cellular automata. For the initial **implementation** we would make the simplifying **assumptions** that the cells were non-motile and regularly packed into a two-dimensional hexagonal mesh. Each cell would **receive** input from its six nearest neighbours (and itself).

**Figure 1:** The two-dimensional hexagonal mesh that forms the underlying structure of our proposed intercellular model.

The stochastic model would hold a **representation** of a colony laid out in the above hexagonal mesh. Each cell would have an individual representation of the simplified intracellular model. The model would be run stochastically with each cell effectively operating **independently**. After the elapsing of every time interval delta-t, the values of each of the three light inputs in a cell would be calculated based on the observed light output at that timepoint of the cell itself and its six closest neighbours:

_{red}= f

_{red}(output

_{cell}; (output

_{neighbour - i}: i = 1::6))

input

_{green}= f

_{green}(output

_{cell}; (output

_{neighbour - i}: i = 1::6))

input

_{blue}= f

_{blue}(output

_{cell}; (output

_{neighbour - i}: i = 1::6))

The functions f_{red}, f_{green}, and f_{blue} have yet to be **defined**, but would hopefully be based on experimental data.

After updating the input value of all cells in the mesh, the stochastic simulation would be resumed. The cycle would then repeat after every delta-t time units. This would thus give us a basis for the simulation of bacterial colony synchronisation.