Team:Evry/Modeling

From 2012.igem.org

(Difference between revisions)
Line 3: Line 3:
<h1>Modeling a tadpole: a multi-level approach</h1>
<h1>Modeling a tadpole: a multi-level approach</h1>
<br>
<br>
-
Our aim is to understand the trajectory of the auxin molecules in the tadpole's organism. More precisely, we will try to link what we see in the tadpole to what is happening in it's organs to what is happening in it's cells.
+
<h2>Modeling a system on a complete organism</h2>
-
Therefore, we will model this trajectory by a multi-level approach:<br>
+
<br>
-
<br><br>
+
<p>This year, our team decided to tackle a challenging project: creating de-novo a new hormonal system in a vertebrate organism. In the modeling part of our work, we were interested in modeling the entire genetic and transport system in the host organism in order to undersatnd the system better as well as to give indications to guide the development of the system in the wet part of our work.</p>
 +
<br>
 +
<p>Modeling a system at the organism level is not an easy task at all. Various approaches and hypothesis have to be used depending on the scale you want to look at the system from. In our work, we used the entire combination of classical synthetic biology modeling techniques to look at the system from the organism to the molecular level, using analytical and modeling techniques involving biochemical models, diffusion and transport models using simultaneously and in conjunction Ordinary Differential Equations (ODEs), Partial Differential equations (PDEs and Agent Based simulations (AB).
 +
<br>
-
<img src= https://static.igem.org/mediawiki/2012/a/a8/FrenchTouch.jpg style="width:100px">
 
-
<img src=https://static.igem.org/mediawiki/2012/a/a0/Fl%C3%A8che_loupe.png style="width:100px">
 
-
<img src=https://static.igem.org/mediawiki/2012/c/c1/Frog_organs.JPG style="width:150px">
 
-
 
-
<img src=https://static.igem.org/mediawiki/2012/0/08/Fl%C3%A8che_microscope.png style="width:100px">
 
-
<img src=https://static.igem.org/mediawiki/2012/5/58/Frogcells_skin.jpg style="width:150px">
 
-
<img src=https://static.igem.org/mediawiki/2012/f/f8/Microscope_electronique.png style="width:125px">
 
-
<img src=https://static.igem.org/mediawiki/2012/4/47/Dna.gif style="width:150px">
 
-
<ul>
 
<br>
<br>
 +
<h2>Preparing the work of the future generations on iGEMers working on complex organism</h2>
<br>
<br>
-
<li>First we will link what we'll see during the experiments to the transport of auxin through each organ.  
+
<p>When writing down our work, we have made an especial effort for our models and hypothesis to be very understandable, in order help the work of the future generation of iGEMers working on tadpoles, and on multicellular organisms in general. You can access general informations on the models by clicking on the ODE, PDE and AB simulations on the image below, and all the instructions are provided for you to run our simulations either on your own computer or directely in your web browser (!) using the full power of the Java Applets created using the Netlogo program.</p>
-
</li>
+
<p>We hope our work will be useful for other to learn, enjoy and create new models for their projects in the future!</p>
-
<li>Then we'll "zoom" at each organ in order to study the interaction among it's cells and the auxin molecules.
+
 
-
</li>
+
 
-
<li>Finally we'll model the expression of genes in the cells that create and use the auxin.
+
<h2>Summaries of our models</h2>
-
</li>
+
 
-
</ul>
+
<p>This schematic represents the different parts of the models we have created, as well as general information on the modeling methods used in these models. Clicks on the different elements of this image to access read the different models:</p>
 +
 
 +
<img src="Schematic modeling.png" width="840" height="555" border="0" usemap="#map" />
 +
<map name="map">
 +
<!-- #$-:Image map file created by GIMP Image Map plug-in -->
 +
<!-- #$-:GIMP Image Map plug-in by Maurits Rijk -->
 +
<!-- #$-:Please do not edit lines starting with "#$" -->
 +
<!-- #$VERSION:2.3 -->
 +
<!-- #$AUTHOR:Cyrille Pauthenier -->
 +
<area shape="rect" coords="210,105,765,225" href="Global_Model" />
 +
<area shape="rect" coords="195,240,330,480" href="Auxin_diffusion" />
 +
<area shape="rect" coords="405,300,540,465" href="auxin_pde" />
 +
<area shape="rect" coords="630,285,810,450" href="auxin_production" />
 +
<area shape="rect" coords="15,120,135,240" href="ODE" />
 +
<area shape="rect" coords="15,240,135,375" href="PDE" />
 +
<area shape="rect" coords="15,375,135,495" href="AB" />
 +
<area shape="rect" coords="330,405,360,435" href="AB" />
 +
<area shape="rect" coords="330,450,360,480" href="PDE" />
 +
<area shape="rect" coords="540,450,570,480" href="PDE" />
 +
<area shape="rect" coords="765,450,810,495" href="ODE" />
 +
<area shape="rect" coords="765,195,810,240" href="ODE" />
 +
<area shape="rect" coords="315,510,645,555" href="Model_integration" />
 +
</map>
 +
<div id="citation_box">
 +
<p id="references">References:</p>
 +
<ol>
 +
<li><i> An introduction to agent-based modeling: Modeling natural, social and engineered complex systems with NetLogo</i>, Wilensky, U., & Rand, W. (in press), Cambridge, MA: MIT Press</li>
 +
</ol>
 +
</div>
</html>
</html>

Revision as of 15:29, 2 September 2012

Modeling a tadpole: a multi-level approach


Modeling a system on a complete organism


This year, our team decided to tackle a challenging project: creating de-novo a new hormonal system in a vertebrate organism. In the modeling part of our work, we were interested in modeling the entire genetic and transport system in the host organism in order to undersatnd the system better as well as to give indications to guide the development of the system in the wet part of our work.


Modeling a system at the organism level is not an easy task at all. Various approaches and hypothesis have to be used depending on the scale you want to look at the system from. In our work, we used the entire combination of classical synthetic biology modeling techniques to look at the system from the organism to the molecular level, using analytical and modeling techniques involving biochemical models, diffusion and transport models using simultaneously and in conjunction Ordinary Differential Equations (ODEs), Partial Differential equations (PDEs and Agent Based simulations (AB).

Preparing the work of the future generations on iGEMers working on complex organism


When writing down our work, we have made an especial effort for our models and hypothesis to be very understandable, in order help the work of the future generation of iGEMers working on tadpoles, and on multicellular organisms in general. You can access general informations on the models by clicking on the ODE, PDE and AB simulations on the image below, and all the instructions are provided for you to run our simulations either on your own computer or directely in your web browser (!) using the full power of the Java Applets created using the Netlogo program.

We hope our work will be useful for other to learn, enjoy and create new models for their projects in the future!

Summaries of our models

This schematic represents the different parts of the models we have created, as well as general information on the modeling methods used in these models. Clicks on the different elements of this image to access read the different models:

References:

  1. An introduction to agent-based modeling: Modeling natural, social and engineered complex systems with NetLogo, Wilensky, U., & Rand, W. (in press), Cambridge, MA: MIT Press

Retrieved from "http://2012.igem.org/Team:Evry/Modeling"