Difference between revisions of "Team:USTC-Software/Model"

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<h1> Modeling</h1>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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          <h1 class="text-center">Model</h1>
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          <h3>Biological Models</h3>
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          <h4>Flux Balance Analysis</h4>
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          <div class="passage">Flux Balance Analysis (FBA) is a mathematical method for simulating metabolism in
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            metabolic networks. It is based on linear programming to calculate fluxes when the model is stable.
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            <br>
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            Assuming S is a matrix, which contains all reactions in a model. In this matrix, metabolites consumed take
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            negative coefficients, and metabolites produced then take positive ones. Furthermore, v is a vector that
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            represents the flux of all reactions. When the system is steady, it satisfies:
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            $$
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            \textbf{S}\textbf{v}=0
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            $$
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              <img alt="" src="https://static.igem.org/mediawiki/2019/d/d8/T--USTC-Software--colla_biomaster.png">
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              <p>Figure 1: UESTC biomaster</p>
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            Our team quickly contacted with the UESTC team to ask if we could make good
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            use of the data. They satisfied our request without hesitation. After getting their data, we build our
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            project on it. Through the way of developing the project, we also contributed our biobricks to their project
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            which they might need. Their project was updated as well. During the process of our communication, both of
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            our
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            project were upgraded.
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              <img alt="" src="https://static.igem.org/mediawiki/2019/3/3f/T--USTC-Software--colla_tongji.jpg">
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              <p>Figure 2: Communicating with UESTC</p>
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<h3> Gold Medal Criterion #3</h3>
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Convince the judges that your project's design and/or implementation is based on insight you have gained from modeling. This could be either a new model you develop or the implementation of a model from a previous team. You must thoroughly document your model's contribution to your project on your team's wiki, including assumptions, relevant data, model results, and a clear explanation of your model that anyone can understand.  
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<br><br>
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The model should impact your project design in a meaningful way. Modeling may include, but is not limited to, deterministic, exploratory, molecular dynamic, and stochastic models. Teams may also explore the physical modeling of a single component within a system or utilize mathematical modeling for predicting function of a more complex device.
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<h3>Best Model Special Prize</h3>
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To compete for the <a href="https://2019.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2019.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the Gold Medal criterion #3 and the Best Model prize with this page.
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You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
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<h3> Inspiration </h3>
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Here are a few examples from previous teams:
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<li><a href="https://2018.igem.org/Team:GreatBay_China/Model">2018 GreatBay China</a></li>
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<li><a href="https://2018.igem.org/Team:Leiden/Model">2018 Leiden</a></li>
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<li><a href="https://2016.igem.org/Team:Manchester/Model">2016 Manchester</a></li>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">2016 TU Delft</li>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">2014 ETH Zurich</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">2014 Waterloo</a></li>
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Revision as of 05:44, 20 October 2019

Model

Biological Models

Flux Balance Analysis

Flux Balance Analysis (FBA) is a mathematical method for simulating metabolism in metabolic networks. It is based on linear programming to calculate fluxes when the model is stable.

Assuming S is a matrix, which contains all reactions in a model. In this matrix, metabolites consumed take negative coefficients, and metabolites produced then take positive ones. Furthermore, v is a vector that represents the flux of all reactions. When the system is steady, it satisfies: $$ \textbf{S}\textbf{v}=0 $$

Figure 1: UESTC biomaster

Our team quickly contacted with the UESTC team to ask if we could make good use of the data. They satisfied our request without hesitation. After getting their data, we build our project on it. Through the way of developing the project, we also contributed our biobricks to their project which they might need. Their project was updated as well. During the process of our communication, both of our project were upgraded.

Figure 2: Communicating with UESTC