Latest revision as of 03:44, 18 October 2014

Modelling Homepage

Our team believes that the key to synthetic biology is to use engineering-based models and designs to improve the development of biochemical systems. Therefore, the engineers in our team have worked with the biochemists every step of the way to design initial project ideas, analyse in detail the expected response of the system, and interpret the results of the various types of experiments that we have run.

This means that, unlike some teams in the past, our modelling is interspersed with our biochemistry information to give a feel of the real interactions that have taken place between the specialities in our team. To aid the viewer, all modelling sections have pink header bubbles, all of the biochemistry sections have light blue header bubbles.

We have also worked very closely with the policy and practices team and influential figures in industry to look at exactly how this project could be implemented in the real world. Included in this has been the 3D CAD (computer aided design) of the expected product and the 3D printing and circuit building of the biosensor unit.

Click on the links below to find out more!

Characterising a genetic network
We used stochastic and deterministic genetic circuit modelling to help the wet-lab team in characterising a previously unknown genetic circuit. Find out more here...

Optimising a genetic network
We used these genetic circuit models to predict the fluoresence of the system as a response to thousands of different combinations of inputs. This allowed us to optimise the input levels and advise the biochemists on the construction of the system so that we could develop the best possible system in the amount of time available. See what we found out...

Analysing the native bacterium
We constructed a model based on Michaelis-Menten kinetics that could inform us how much DCM the native bacterium would be able to degrade and also what the pH change of the system would be. This further convinced us to use synthetic biology to solve the problem of chlorinated waste disposal. See how we did it here...

Analysing microcompartments mathematically
We used spacial modelling to determine an estimate of various parameters to do with the microcompartments. We then gave this information to the biochemists to help them analyse their results with expressing microcompartments in E. coli and P. putida.

Analysing the benefits of microcompartments
On this page we explain in detail how our stochastic diffusion models work and then provide in-depth information on how we then used these carefully analyse of the benefits of microcompartments for our system.

Creating models of iGEM Melbourne's star peptide
We embarked on a major collaboration project with Melbourne iGEM team. Part of this collaboration involved helping this team by modelling the benefit of using their star peptide system in a bacterium and how that could control reaction rates. To do this we drew on the extensive knowledge that we have gained of stochastically modelling diffusion-driven systems.

Realising the biosensor
On the advice of industry experts, we produced concept designs of our whole system using CAD. We built the biosensor using the latest 3D printing technologies and we designed and built a very cheap circuit that can detect low levels of GFP fluorescence to go inside the biosensor. This part is really exciting...

Bioremediation realisation
Discover how we envisage our project becoming a real world product and see the CAD models that have allowed us to demonstrate our idea to industry experts.

Biopolymer containment
Find out how we modelled the processes that control the diffusion of DCM and reaction products through the biopolymer containment beads, and how this modelling played an integral part in calculating the optimum bead thickness for our system.

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 </div>
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+<div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:-35px;">
-In the emerging field of synthetic biology, iGEM is growing as a source of ambitious and imaginative ideas which have the potential to offer great benefits to human society and our environment. The number of successful iGEM start-ups clearly demonstrates that the competition gives teams the opportunity to get involved in much more than just a summer project; students have the chance to come up with a solution which has a positive impact in the  real world.
 <br>
-In fact, many projects are conceived in the hope of doing just this, often with a specific unresolved social problem in mind. iGEM draws inspiration from the world and the challenges it faces, and contributes back potential solutions.
+<h1 style="color:#777777">Our team believes that the key to synthetic biology is to use engineering-based models and designs to improve the development of biochemical systems. Therefore, the engineers in our team have worked with the biochemists every step of the way to design initial project ideas, analyse in detail the expected response of the system, and interpret the results of the various types of experiments that we have run.
 <br><br>
-<h1blue>
+This means that, unlike some teams in the past, our modelling is interspersed with our biochemistry information to give a feel of the real interactions that have taken place between the specialities in our team. To aid the viewer, all modelling sections have pink header bubbles, all of the biochemistry sections have light blue header bubbles.
-"Quote from EA about usefulness of our project/bioremediation/synthetic biology generally, the fact that it could actually help the problem etc…”
-</h1blue>
-<h1blue2>
-(British Environment Agency)
-</h1blue2>
 <br><br>
-Our work with the Environment Agency, which inspired us to explore bioremediation as an option for dealing with the pressing environmental concern cause by chlorinated solvent pollution, brought home just how great an impact our own project might have on the in cleaning up this issue. Chlorinated solvents are indispensable to many manufacturing, professional, and even everyday household activities, yet no environmentally acceptable method of disposal currently exists. Our research has led us to believe that bioremediation is a genuinely viable option for addressing this challenge, a position which the Environment Agency has supported. We realized that what began as an iGEM project may well be worth developing further than the months we had to complete the competition.
+We have also worked very closely with the policy and practices team and influential figures in industry to look at exactly how this project could be implemented in the real world. Included in this has been the 3D CAD (computer aided design) of the expected product and the 3D printing and circuit building of the biosensor unit.
 <br><br>
-With this in mind, for the policy and practices element of our project we decided to ask…
+Click on the links below to find out more!</h1>
+<br>
 </div>
-<br><br><br><br><br><br><br><br><br><br><br><br><br>
-<br><br><br><br><br><br><br><br><br><br>
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-<h1grey align="center">HOW CAN AN IGEM PROJECT CHANGE THE WORLD?</h1grey>
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-For the policy and practices element of the competition, our team has researched how iGEM projects grow from ideas into real world solutions. What are the challenges face teams who want to develop their projects beyond the jamboree? What can be done to help them realise the potential benefits of their ideas for society? And what should we be aiming to achieve by all this?
-<br><br>
-Our team identified what we believe are the key considerations for teams to take into account.
-</div>
+<a href="https://2014.igem.org/Team:Oxford/biosensor_characterisation#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
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-<h1blue3>The Goal….</h1blue3>
 <br>
-<h2blue3>Many teams are inspired by their search for a synbio solution to a problem or challenge faced by the world. For our team, the need for a way of address the environmental problems caused by chlorinated solvents was clear. Find out more here...</h2blue3>
+<h1blue3>Characterising a genetic network</h1blue3>
+<br>
+<h2blue3>We used stochastic and deterministic genetic circuit modelling to help the wet-lab team in characterising a previously unknown genetic circuit. Find out more here...
+</h2blue3>
+<br><br>
 </div></a>
@@ Line 593: / Line 61: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_environmental_impact"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/biosensor_optimisation#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
 <img src="https://static.igem.org/mediawiki/2014/4/43/Oxford_Realisation2.png" style="float:right;position:relative; width:6%;margin-right:3%;" />
+<br>
-<h1red>Practicality….</h1red>
+<h1red>Optimising a genetic network</h1red>
 <br>
-<h2red>How can the idea be implemented and delivered in the real world? Our engineers used design software and 3D printing to think about how we might realise DCMation and the environments in which the biosensor and bioremediation technique might be used.</h2red>
+<h2red>We used these genetic circuit models to predict the fluoresence of the system as a response to thousands of different combinations of inputs. This allowed us to optimise the input levels and advise the biochemists on the construction of the system so that we could develop the best possible system in the amount of time available. See what we found out...</h2red>
+<br><br>
 </div></a>
@@ Line 615: / Line 83: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_intellectual_property"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/how_much_can_we_degrade?#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
-<img src="https://static.igem.org/mediawiki/2014/c/c7/Oxford_IP.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<img src="https://static.igem.org/mediawiki/2014/6/65/Oxford_dm4_.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<br>
-<h1purple>Intellectual Property….</h1purple>
+<h1purple>Analysing the native bacterium</h1purple>
 <br>
-<h2purple>Determining the ownership of the intellectual property of a project is crucial for any team hoping to develop their ideas beyond the Jamboree. Our report looks at how the iGEM community can navigate this controversial and difficult issue. </h2purple>
+<h2purple>We constructed a model based on Michaelis-Menten kinetics that could inform us how much DCM the native bacterium would be able to degrade and also what the pH change of the system would be. This further convinced us to use synthetic biology to solve the problem of chlorinated waste disposal. See how we did it here...</h2purple>
+<br><br>
 </div></a>
@@ Line 635: / Line 103: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_communication"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/what_are_microcompartments?#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
-<img src="https://static.igem.org/mediawiki/2014/c/c5/Oxford_Communication.png" style="float:right;position:relative; width:10%;margin-right:3%;" />
+<img src="https://static.igem.org/mediawiki/2014/2/27/Oxford_q.png" style="float:right;position:relative; width:10%;margin-right:3%;" />
+<br>
-<h1orange>Communication….</h1orange>
+<h1orange>Analysing microcompartments mathematically</h1orange>
 <br>
-<h2orange>Determining the ownership of the intellectual property of a project is crucial for any team hoping to develop their ideas beyond the Jamboree. Our report looks at how the iGEM community can navigate this controversial and difficult issue. </h2orange>
+<h2orange>We used spacial modelling to determine an estimate of various parameters to do with the microcompartments. We then gave this information to the biochemists to help them analyse their results with expressing microcompartments in E. coli and P. putida.</h2orange>
+<br><br>
 </div></a>
@@ Line 654: / Line 122: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_public_engagement"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/why_do_we_need_microcompartments?#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
-<img src="https://static.igem.org/mediawiki/2014/c/c6/Oxford_public.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<img src="https://static.igem.org/mediawiki/2014/6/6f/Oxford_analyse_micro2.png" style="float:left;position:relative; width:10%;margin-right:3%;" />
+<br>
-<h1blue3>Public Participation….</h1blue3>
+<h1blue3>Analysing the benefits of microcompartments</h1blue3>
 <br>
 <h2blue3>
-Determining the ownership of the intellectual property of a project is crucial for any team hoping to develop their ideas beyond the Jamboree. Our report looks at how the iGEM community can navigate this controversial and difficult issue.
+On this page we explain in detail how our stochastic diffusion models work and then provide in-depth information on how we then used these carefully analyse of the benefits of microcompartments for our system.
 </h2blue3>
+<br><br>
 </div></a>
@@ Line 678: / Line 146: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_igem_europe"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/alternatives_to_microcompartments#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
-<img src="https://static.igem.org/mediawiki/2014/e/e5/Oxford_europe.png" style="float:right;position:relative; width:10%;margin-right:3%;" />
+<img src="https://static.igem.org/mediawiki/2014/2/20/Oxford_shake.png" style="float:right;position:relative; width:10%;margin-right:3%;" />
+<br>
-<h1green>The iGEM Competition….</h1green>
+<h1green>Creating models of iGEM Melbourne's star peptide </h1green>
 <br>
 <h2green>
-iGEM has been steadily expanding since its beginnings in 2004, climbing from 5 to over 200 teams in the last 10 years. As the first ever Oxford team, we are more than a little late to the party! Our team has researched the growing contribution made by the rest of Europe to the competition, of which we hope to become a part from 2014 onwards!
+We embarked on a major collaboration project with Melbourne iGEM team. Part of this collaboration involved helping this team by modelling the benefit of using their star peptide system in a bacterium and how that could control reaction rates. To do this we drew on the extensive knowledge that we have gained of stochastically modelling diffusion-driven systems.
 </h2green>
+<br><br>
 </div></a>
@@ Line 701: / Line 169: @@
+<a href="https://2014.igem.org/Team:Oxford/biosensor_realisation#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
+<img src="https://static.igem.org/mediawiki/2014/4/43/Oxford_Realisation2.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<br>
+<h1red>Realising the biosensor</h1red>
+<br>
+<h2red>On the advice of industry experts, we produced concept designs of our whole system using CAD. We built the biosensor using the latest 3D printing technologies and we designed and built a very cheap circuit that can detect low levels of GFP fluorescence to go inside the biosensor. This part is really exciting...</h2red>
+<br><br>
+</div></a>
@@ Line 713: / Line 189: @@
+<a href="https://2014.igem.org/Team:Oxford/realisation_bioremediation#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
+<img src="https://static.igem.org/mediawiki/2014/4/43/Oxford_Realisation2.png" style="float:right;position:relative; width:6%;margin-right:3%;" />
+<br>
+<h1orange>Bioremediation realisation</h1orange>
+<br>
+<h2orange> Discover how we envisage our project becoming a real world product and see the CAD models that have allowed us to demonstrate our idea to industry experts.</h2orange>
+<br><br>
+</div></a>
@@ Line 730: / Line 214: @@
+<a href="https://2014.igem.org/Team:Oxford/biopolymer_containment#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
+<img src="https://static.igem.org/mediawiki/2014/4/43/Oxford_Realisation2.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<br>
+<h1blue3>Biopolymer containment</h1blue3>
+<br>
+<h2blue3> Find out how we modelled the processes that control the diffusion of DCM and reaction products through the biopolymer containment beads, and how this modelling played an integral part in calculating the optimum bead thickness for our system.</h2blue3>
+<br><br>
+</div></a>
+<br>
-<div class="white_news_block">
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-<a href="https://2014.igem.org/Team:Oxford/P&P_igem_europe">
-<img src="https://static.igem.org/mediawiki/2014/9/92/Oxford_P%26P7.png" style="float:right;position:relative; width:12%;" /></a>
-<br><br><br><br><br><br><br><br><br>
-</div>
-</div>
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Team:Oxford/Modelling

From 2014.igem.org

Latest revision as of 03:44, 18 October 2014