Difference between revisions of "Team:KU Leuven/Modeling"

 
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                 <div class="summary">
 
                 <div class="summary">
 
                     <p>
 
                     <p>
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                         The fascinating properties of pattern creating bacteria may be translated into
+
                         The fascinating properties of pattern creating bacteria can be translated into
−
                         the language of mathematics. In this subsection we are investigating the
+
                         the language of mathematics. In this subsection we investigate the
−
                         equations behind the behaviour of the genetically modified organisms created in
+
                         equations behind the behavior of the genetically modified organisms created in
−
                         the wetlab. We do so using a layered approach. Colony level modeling employs
+
                         the wetlab. For this purpose, a layered approach seems appropriate. Colony level modeling employs
 
                         partial differential equations to describe large cell groups which are treated
 
                         partial differential equations to describe large cell groups which are treated
 
                         as a continuum. Internal level models describe the interactions that happen
 
                         as a continuum. Internal level models describe the interactions that happen
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                             <div class="subtext">
 
                             <div class="subtext">
 
                                 <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Top">
 
                                 <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Top">
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                                     <h2>Colony level</h2>
+
                                     <h2>Colony</h2>
 
                                     <p>
 
                                     <p>
−
                                         Our colony layer model relies on a Keller-Segel type system of differential
+
                                         Our colony layer model relies on a Keller-Segel type system of partial differential
 
                                         equations. These equations are simulated using finite differences.
 
                                         equations. These equations are simulated using finite differences.
 
                                        
 
                                        
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                             <div class="subtext">
 
                             <div class="subtext">
 
                                 <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Hybrid">
 
                                 <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Hybrid">
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                                     <h2>Hybrid model</h2>
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                                     <h2>Hybrid</h2>
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                                     <p>Our hybrid model merges both colony and internal level to define the cell-cell
+
                                     <p>The hybrid model represents an intermediate level of detail in between the colony level model and the internal model. Bacteria are treated as individual agents, while chemical species are modeled using partial differential equations. </p>
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                                    interactions of our pattern forming cells. </p>
+
 
                                 </a>
 
                                 </a>
 
                             </div>
 
                             </div>
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                             <div class="subtext">
 
                                 <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Internal">
 
                                 <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Internal">
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                                     <h2>Internal model</h2>
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                                     <h2>Internal</h2>
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                                     <p>Our internal model aims to simulate the internal dynamics of every cell with a system of
+
                                     <p>Our internal model aims to simulate the internal dynamics of every cell with a system of ordinary differential equations. </p>
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                                    ordinary differential equations. </p>
+
 
                                 </a>
 
                                 </a>
 
                             </div>
 
                             </div>
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                             <div class="subtext">
 
                             <div class="subtext">
 
                                 <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Toulouse">
 
                                 <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Toulouse">
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                                     <h2>Toulouse model</h2>
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                                     <h2>FBA (Toulouse)</h2>
 
                                     <p>
 
                                     <p>
 
                                         As a part of our modeling cooperation we exchanged models with the Toulouse
 
                                         As a part of our modeling cooperation we exchanged models with the Toulouse
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                         <div class="subimgm">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Top">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Top">
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                                 <b>Colony level</b>
+
                                 <b>Colony</b>
 
                                 <img
 
                                 <img
 
                                     src="https://static.igem.org/mediawiki/2015/6/6a/KU_Leuven_Wiki_Button_-_Colony_level2.png"
 
                                     src="https://static.igem.org/mediawiki/2015/6/6a/KU_Leuven_Wiki_Button_-_Colony_level2.png"
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                         <div class="subimgm">
 
                         <div class="subimgm">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Hybrid">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Hybrid">
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                             <b>Hybrid model</b>
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                             <b>Hybrid</b>
 
                             <img
 
                             <img
 
                                 src="https://static.igem.org/mediawiki/2015/0/02/KU_Leuven_Wiki_Button_-_Hybrid_model2.png"
 
                                 src="https://static.igem.org/mediawiki/2015/0/02/KU_Leuven_Wiki_Button_-_Hybrid_model2.png"
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                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Hybrid">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Hybrid">
 
                                 <p>
 
                                 <p>
−
                                     Coming soon
+
                                     Our hybrid model merges both colony and internal level to define the cell-cell
−
                                     <br/>
+
                                     interactions of our pattern forming cells.
 
                                 </p>
 
                                 </p>
 
                             </a>
 
                             </a>
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                         <div class="subimgm">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Internal">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Internal">
−
                             <b>Internal model</b>
+
                             <b>Internal</b>
 
                             <img
 
                             <img
 
                                 src="https://static.igem.org/mediawiki/2015/4/47/KU_Leuven_Wiki_Button_-_Internal_model2.png"
 
                                 src="https://static.igem.org/mediawiki/2015/4/47/KU_Leuven_Wiki_Button_-_Internal_model2.png"
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                         <div class="subtextm">
 
                         <div class="subtextm">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Internal">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Internal">
−
                                 <p>
+
                                 <p>Our internal model aims to simulate the internal dynamics of every cell with a system of ordinary differential equations.
−
                                    Coming soon
+
−
                                    <br/>
+
 
                                 </p>
 
                                 </p>
 
                             </a>
 
                             </a>
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                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Toulouse">
 
                             <a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Toulouse">
−
                             <b>Toulouse model</b>
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                             <b>FBA (Toulouse)</b>
 
                             <img src="https://static.igem.org/mediawiki/2015/b/b1/KU_Leuven_Wiki_Button_Flux2.png"
 
                             <img src="https://static.igem.org/mediawiki/2015/b/b1/KU_Leuven_Wiki_Button_Flux2.png"
 
                                 width="100%">
 
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  </div>
 
                 <div id="kuleuven">
 
                 <div id="kuleuven">
 
                     <a href="http://www.kuleuven.be/english"><img alt="bioSCENTer"
 
                     <a href="http://www.kuleuven.be/english"><img alt="bioSCENTer"
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                     <a href="http://www.filterservice.be/"><img alt="Machery Nagel"
 
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Latest revision as of 09:37, 20 October 2015

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Modeling

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The fascinating properties of pattern creating bacteria can be translated into the language of mathematics. In this subsection we investigate the equations behind the behavior of the genetically modified organisms created in the wetlab. For this purpose, a layered approach seems appropriate. Colony level modeling employs partial differential equations to describe large cell groups which are treated as a continuum. Internal level models describe the interactions that happen within single cells. Finally the hybrid model merges the two approaches into a final description of our pattern forming cells.





Colony

Our colony layer model relies on a Keller-Segel type system of partial differential equations. These equations are simulated using finite differences.

Hybrid

The hybrid model represents an intermediate level of detail in between the colony level model and the internal model. Bacteria are treated as individual agents, while chemical species are modeled using partial differential equations.

Internal

Our internal model aims to simulate the internal dynamics of every cell with a system of ordinary differential equations.

FBA (Toulouse)

As a part of our modeling cooperation we exchanged models with the Toulouse team. This is the flux balance analysis they performed for us.
Read more
Read more
Read more
Read more
Colony

Our colony layer model relies on a Keller-Segel type system of differential equations. These equations are simulated using finite differences.

Hybrid

Our hybrid model merges both colony and internal level to define the cell-cell interactions of our pattern forming cells.

Internal

Our internal model aims to simulate the internal dynamics of every cell with a system of ordinary differential equations.

FBA (Toulouse)

As a part of our modeling cooperation we exchanged models with the Toulouse team. This is the flux balance analysis they performed for us.

Contact

Address: Celestijnenlaan 200G room 00.08 - 3001 Heverlee
Telephone: +32(0)16 32 73 19
Email: igem@chem.kuleuven.be