Difference between revisions of "Team:Manchester/Collaborations"

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<h1 class="title11">Collaboration</h1>
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<h1 class="title11">Collaborations</h1>
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<div class="navbutton column onethird_size">
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    <b>Contents</b>
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      <ol style="text-align:left"> 
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        <a href="#gothen"><li style="text-align:left">iGEM Chalmers Gothenburg</li></a>
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        <a href="#virginia"><li style="text-align:left">iGEM Virginia</li></a>
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        <a  href="#paris"><li style="text-align:left">iGEM Paris Saclay</li></a>
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      </ol>
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<h1 class="subtitle1">Chalmers Gothenburg </h1>
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<h1 id="gothen" style="clear:both;padding-left:10%;margin-bottom:0; padding-top: 20px;" class="subtitle1">iGEM Chalmers Gothenburg </h1>
  
 
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     <p style="font-size:17px;">The work on this page may not represent the final modelling used by Chalmers Gothenburg but it represents the final model that was built by the University of Manchester iGEM team in collaboration with the Chalmers Gothenburg iGEM team at the point the collaboration was concluded, any edits and changes beyond this were solely the work of the Chalmers Gothenburg team. Work that was not completed by our team included finding of parameters for the equations etc the only work completed in collaboration was the actual model itself.
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     <p style="font-size:17px;">We helped the Chalmers Gothenburg team with their initial steps of model building. The description below illustrates the model that was built by the Manchester iGEM team, which got the Chalmers team started. Any edits and changes beyond this were solely the work of the Chalmers Gothenburg team, such as finding of parameters for the equations. We also discussed our method of obtaining accurate descriptions of plausible parameter values for ensemble modelling, but this aspect was not incorporated in the final model, due to time constraints.
 
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<b>The final model used by Chalmers Gothenburg can be seen <a href="https://2016.igem.org/Team:Chalmers_Gothenburg/Model" target="_blank">here</a></b>
 
<b>The final model used by Chalmers Gothenburg can be seen <a href="https://2016.igem.org/Team:Chalmers_Gothenburg/Model" target="_blank">here</a></b>
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The model consists of two organisms in co-culture, each dependant on one another for an essential substrate, ie without one the other would be unable to survive. The model predicts the concentration of the 2 organisms as well as the acetate which is the main product of the system.
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The model consists of two organisms in co-culture, each dependant on one another for an essential substrate, i.e. without one the other would be unable to survive. The model predicts the growth of the two organisms as well as the concentration acetate which is the main product of the system.
  
 
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The system was modelled using the following differential equations:
 
The system was modelled using the following differential equations:
 
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Substrate limited specific cell growth (Monad equation)
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Substrate-limited specific cell growth <a href="https://en.wikipedia.org/wiki/Monod_equation" target="_blank">(Monod equation)</a>:
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$$r_g = \mu_{max} \frac{Sx_v}{K_s + S}$$
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$$r_g = x_v \mu_{max} \frac{S}{K_s + S}$$
  
 
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Cell death. First order with respect to viable cell concentration
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Cell death. First order with respect to viable cell concentration:
 
$$r_d = k_d x_v$$
 
$$r_d = k_d x_v$$
  
 
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Product formation (Luedeking–Piret equation)
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Product formation (Luedeking–Piret equation).
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Product produced  in cell growth and in cell maintenance
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Product produced  in cell growth and in cell maintenance:
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$$r_p = \alpha r_g +\beta x_v \qquad , \text{ where } r_x = r_g - r_v$$
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$$r_p = \alpha r_g +\beta x_v $$
  
 
$$x_v = \int r_x dt \qquad , \text{ where } r_x = r_g - r_v$$
 
$$x_v = \int r_x dt \qquad , \text{ where } r_x = r_g - r_v$$
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$$r_s = r_{s_x} + r_{s_p} + r_{s_m}$$
 
$$r_s = r_{s_x} + r_{s_p} + r_{s_m}$$
  
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that is, the sum of rate of substrate utilisation in cell sythensis, maintenance and product formation
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that is, the sum of rate of substrate utilisation in cell synthesis, maintenance and product formation
  
 
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Note: each equation occurs twice, once for each cell and these are just the generic forms.
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Note: each equation occurs twice, once for each cell, with cell type-specific parameter values; the equations shown are just the generic forms.
 
Side reactions in the system were not considered at this stage.
 
Side reactions in the system were not considered at this stage.
  
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<h1 style="clear:both;padding-top:100px;" class="subtitle1">Virginia </h1>
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<h1 style="clear:both;padding-top:50px;padding-left:10%;" class="subtitle1">iGEM Virginia </h1>
  
 
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<h1 style="clear:both;padding-top:50px;" class="subtitle1">Paris Saclay </h1>
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<h1 style="clear:both;padding-top:50px;padding-left:10%;" class="subtitle1">iGEM Paris Saclay </h1>
  
 
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<a class="projectlink" href="https://2016.igem.org/Team:Manchester/Achievement"><< Achievement Overview</a>
 
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Latest revision as of 02:17, 20 October 2016

Manchester iGEM 2016


Collaborations

Contents
  1. iGEM Chalmers Gothenburg
    2.
  2. iGEM Virginia
    3.
  3. iGEM Paris Saclay
    4.

iGEM Chalmers Gothenburg



We helped the Chalmers Gothenburg team with their initial steps of model building. The description below illustrates the model that was built by the Manchester iGEM team, which got the Chalmers team started. Any edits and changes beyond this were solely the work of the Chalmers Gothenburg team, such as finding of parameters for the equations. We also discussed our method of obtaining accurate descriptions of plausible parameter values for ensemble modelling, but this aspect was not incorporated in the final model, due to time constraints.

The final model used by Chalmers Gothenburg can be seen here

figure 1

The model consists of two organisms in co-culture, each dependant on one another for an essential substrate, i.e. without one the other would be unable to survive. The model predicts the growth of the two organisms as well as the concentration acetate which is the main product of the system.

The system was modelled using the following differential equations:

Substrate-limited specific cell growth (Monod equation): $$r_g = x_v \mu_{max} \frac{S}{K_s + S}$$
Cell death. First order with respect to viable cell concentration: $$r_d = k_d x_v$$
Product formation (Luedeking–Piret equation). Product produced in cell growth and in cell maintenance: $$r_p = \alpha r_g +\beta x_v $$ $$x_v = \int r_x dt \qquad , \text{ where } r_x = r_g - r_v$$
The substrate uptake: $$r_s = r_{s_x} + r_{s_p} + r_{s_m}$$ that is, the sum of rate of substrate utilisation in cell synthesis, maintenance and product formation

A MATLAB script was produced to solve the system of equations.

Note: each equation occurs twice, once for each cell, with cell type-specific parameter values; the equations shown are just the generic forms. Side reactions in the system were not considered at this stage.


Reference: McNeil, B. and Harvey, L. (2008). Practical fermentation technology. Chichester, England: Wiley.

iGEM Virginia



We took part in the biocontainment survey conducted by Virginia iGEM 2016 and were granted a collaboration badge for our help

iGEM Paris Saclay



We filled a form on Responsible Research and Innovation (RRI) as conducted by Paris Saclay iGEM 2016 and were granted a collaboration badge for our help

paris saclay batch
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