Difference between revisions of "Team:Virginia/Model"

Line 5: Line 5:
 
<h1> Modeling</h1>
 
<h1> Modeling</h1>
  
−
<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>
+
<p0>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.</p0>
  
 
</div>
 
</div>
Line 11: Line 11:
  
 
<div class="column full_size">
 
<div class="column full_size">
−
<h1> Metabolic Modeling</h1>
+
<h2> Metabolic Modeling</h2>
  
−
<p> Recent advances in computational biology include <b>whole-genome metabolic networks</b>. They describe the flow of metabolites within a particular organism. Using constraint-based methods allows to make quantitative predictions about the phenotype while eliminating many of the complex parameters. Of particular interest to our project is <b>flux balance analysis (FBA)</b>, which allows to predict the optimal steady-state biomass flux, which is directly correlated with cell growth rate and is the most likely observed phenotype. One major advantage of FBA is that it does not require knowledge of enzymatic parameters. </p>
+
<p0> Recent advances in computational biology include <b>whole-genome metabolic networks</b>. They describe the flow of metabolites within a particular organism. Using constraint-based methods allows to make quantitative predictions about the phenotype while eliminating many of the complex parameters. Of particular interest to our project is <b>flux balance analysis (FBA)</b>, which allows to predict the optimal steady-state biomass flux, which is directly correlated with cell growth rate and is the most likely observed phenotype. One major advantage of FBA is that it does not require knowledge of enzymatic parameters. </p0>
  
−
<p> One of the primary questions for the project is this: <b>will the synthetic <i>P. denitrificans</i> strain grow better than the unmodified one in presence of ammonia?</b> To answer this question, we performed comparative analysis of the two strains using FBA on the whole-genome metabolic models. The analysis pipeline involved a slew of open-source computational tools, which we will describe below.</p>
+
<p0> One of the primary questions for the project is this: <b>will the synthetic <i>P. denitrificans</i> strain grow better than the unmodified one in presence of ammonia?</b> To answer this question, we performed comparative analysis of the two strains using FBA on the whole-genome metabolic models. The analysis pipeline involved a slew of open-source computational tools, which we will describe below.</p0>
  
 
<center><img src="https://static.igem.org/mediawiki/2017/7/78/Virginia--mod_pipeline.png" alt="" usemap="#map1500485992320" style="width:812px;height:271px"></center>
 
<center><img src="https://static.igem.org/mediawiki/2017/7/78/Virginia--mod_pipeline.png" alt="" usemap="#map1500485992320" style="width:812px;height:271px"></center>
Line 22: Line 22:
 
<a href="https://2017.igem.org/Team:Virginia/Model/ModelSEED"><h1>ModelSEED</h1></a>
 
<a href="https://2017.igem.org/Team:Virginia/Model/ModelSEED"><h1>ModelSEED</h1></a>
  
−
<p>1</p>
+
<p0>1</p0>
  
 
</div>
 
</div>

Revision as of 19:56, 20 July 2017


Modeling

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.

Metabolic Modeling

Recent advances in computational biology include whole-genome metabolic networks. They describe the flow of metabolites within a particular organism. Using constraint-based methods allows to make quantitative predictions about the phenotype while eliminating many of the complex parameters. Of particular interest to our project is flux balance analysis (FBA), which allows to predict the optimal steady-state biomass flux, which is directly correlated with cell growth rate and is the most likely observed phenotype. One major advantage of FBA is that it does not require knowledge of enzymatic parameters. One of the primary questions for the project is this: will the synthetic P. denitrificans strain grow better than the unmodified one in presence of ammonia? To answer this question, we performed comparative analysis of the two strains using FBA on the whole-genome metabolic models. The analysis pipeline involved a slew of open-source computational tools, which we will describe below.
Image HTML map generator

ModelSEED

 1

Gold Medal Criterion #3

To complete for the gold medal criterion #3, please describe your work on this page and fill out the description on your judging form. To achieve this medal criterion, you must convince the judges that your team has gained insight into your project from modeling. You may not convince the judges if your model does not have an effect on your project design or implementation.

Please see the 2017 Medals Page for more information.

Best Model Special Prize

To compete for the Best Model prize, please describe your work on this page and also fill out the description on the judging form. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.

You must also delete the message box on the top of this page to be eligible for the Best Model Prize.

Inspiration

Here are a few examples from previous teams: