Difference between revisions of "Team:Manchester/Collaborations"

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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2016.igem.org/Judging/Medals">team collaboration silver medal criterion</a>. </p>
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Evaluated_Pages/Instructions"> Instructions for Evaluated Pages </a>.</p>
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Sharing and collaboration are core values of iGEM. We encourage you to reach out and work with other teams on difficult problems that you can more easily solve together.
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<h4> Which other teams can we work with? </h4>
 
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You can work with any other team in the competition, including software, hardware, high school and other tracks. You can also work with non-iGEM research groups, but they do not count towards the iGEM team collaboration silver medal criterion.
 
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In order to meet the silver medal criteria on helping another team, you must complete this page and detail the nature of your collaboration with another iGEM team.
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<h1 class="title11">Collaborations</h1>
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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 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;">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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  <br /><br />
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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>
 
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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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<br /><br />
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The system was modelled using the following differential equations:
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      <br /><br />
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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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$$r_g =  x_v \mu_{max} \frac{S}{K_s + S}$$
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      <br />
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Cell death. First order with respect to viable cell concentration:
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$$r_d = k_d x_v$$
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    <br />
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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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$$r_p = \alpha r_g +\beta x_v $$
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$$x_v = \int r_x dt \qquad , \text{ where } r_x = r_g - r_v$$
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      <br />
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The substrate uptake:
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$$r_s = r_{s_x} + r_{s_p} + r_{s_m}$$
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that is, the sum of rate of substrate utilisation in cell synthesis, maintenance and product formation
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<br /><br />
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A MATLAB script was produced to solve the system of equations.
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<br /><br />
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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.
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Side reactions in the system were not considered at this stage.
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    <br /><br /><br />
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Reference:  McNeil, B. and Harvey, L. (2008). Practical fermentation technology. Chichester, England: Wiley.
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    </p>
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<!---------------------------------------------------------------br------------------------------------------------------>
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<div id="virginia" class="column half_size">
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<h1 style="clear:both;padding-top:50px;padding-left:10%;" class="subtitle1">iGEM Virginia </h1>
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    <p style="font-size: 17px;" >We took part in the biocontainment survey conducted by <a href="https://2016.igem.org/Team:Virginia" target="_blank">Virginia iGEM 2016</a> and were granted a collaboration badge for our help </p>
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<a href="https://2016.igem.org/Team:Virginia/Collaborations" target="_blank"></a>
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Here are some suggestions for projects you could work on with other teams:
 
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<li> Improve the function of another team's BioBrick Part or Device</li>
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<li> Debug a construct </li>
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<h1 style="clear:both;padding-top:50px;padding-left:10%;" class="subtitle1">iGEM Paris Saclay </h1>
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<li> Model or simulating another team's system </li>
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<li> Test another team's software</li>
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<li> Help build and test another team's hardware project</li>
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<li> Mentor a high-school team</li>
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    <p style="font-size: 17px;" >We filled a form on Responsible Research and Innovation (RRI) as conducted by <a href="https://2016.igem.org/Team:Paris_Saclay" target="_blank">Paris Saclay iGEM 2016</a> and were granted a collaboration badge for our help </p>
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    <img class="batchparis" src="https://static.igem.org/mediawiki/2016/f/fa/T--Manchester--Paris_Saclay_survey_batch.png" alt="paris saclay batch" />
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<div class="floatleft1 project">
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<a class="projectlink" href="https://2016.igem.org/Team:Manchester/Achievement"><< Achievement Overview</a>
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{{Manchester/CSS/footer}}

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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