Team:UPO-Sevilla/Project/Basic Flip Flop/Multiagent System/Overview

From 2011.igem.org

(Difference between revisions)
 
(2 intermediate revisions not shown)
Line 2: Line 2:
<html>
<html>
 +
 +
<script type="text/javascript">
 +
            ddmenuactual = 1;
 +
            $("#menuPBasic").addClass("TopMenuSelected");
 +
</script>
 +
         
                     <div id="principal">
                     <div id="principal">
                         <div class="main">
                         <div class="main">
Line 40: Line 46:
                             </div>
                             </div>
-
                             <h2>Extending the model</h2>
+
                              
-
 
+
-
                            <p>This model could become more complicated adding more and more details of the real biological system, but it would increase the complexity of it and so the ability of making simulations in a reasonable time. Some of the improvements that could be implemented without making the program much more complex is the strength of the SD or adding a cycle life to the ribosomes and the RNA polymerases. A more interesting improvement and still plausible could be representing the growth of the bacterium while the time goes by and the sharply decrease of the size to the half after the binary fission.</p>
+
-
+
-
 
+
-
                            <h2>Bibliography</h2>
+
-
 
+
-
                            <p>
+
-
<li> Christopher P.Fall, Eric S.Marland, John M. Wagner and John J. Tyson. Computational Cell Biology. United States of America: Springer, 2002.</li>
+
-
 
+
-
<li> Guo, Shan Sundararaj and An Chi. CyberCell Database. 2006. http://redpoll.pharmacy.ualberta.ca/CCDB/index.html.</li>
+
-
 
+
-
<li> Kaczanowska M, Rydén-Aulin M. "Ribosome biogenesis and the translation process in Escherichia coli. ." Microbiol Mol Biol Rev., 2007 :                    Sep71(3):p.478 right column 1st paragraph.</li>
+
-
 
+
-
<li>Leyton-Browm, Yoav Shoham and Kevin. Multiagent Systems: Algorithmic, Game-theoretic and Logical Foundations. 2009, 2010.</li>
+
-
 
+
-
<li>Timothy S. Gardner, Charles R. Cantor, James J. Collins. "Construction of a genetic toggle switch in Escherichia coli." Nature, 2000: 339-342.</li>
+
-
<li> Wilensky, Uri. NetLogo. 199-2011. http://ccl.northwestern.edu/netlogo/.</li>
+
-
 
+
-
<li> Zoltan Szallasi, Jörg Stelling, and Vipul Periwal. System Modeling in Cellular Biology: From concepts to nuts and bolts. Cambridge, Massachusetts: MIT press, 2010.</li>
+
-
 
+
-
                          </p>
+
Line 67: Line 52:
                         </div>
                         </div>
                         <div class="left">
                         <div class="left">
-
                               </html>{{:Team:UPO-Sevilla/leftTemplateProject}}<html>
+
                               </html>{{:Team:UPO-Sevilla/leftTemplateProjectBasic}}<html>
 +
 
 +
                              <script type="text/javascript">
 +
                                          $("#menuVBMOverview").addClass("menuSelected");
 +
                              </script>
                         </div>
                         </div>
</html>
</html>
{{:Team:UPO-Sevilla/footTemplate}}
{{:Team:UPO-Sevilla/footTemplate}}

Latest revision as of 22:05, 27 October 2011

Grey iGEM Logo UPO icon

Multiagent System based modeling

Spatial simulation of a bacteria

We have also developed a spatial simulation of the basic flip-flop by considering the interaction between the different components in the interior of a bacterium using NetLogo. This kind of model allows to analyze some parameters not considered in the simulations based on the differential equations governing the concentrations of diverse elements, like the spatial (volumetric) variation of these concentrations. Moreover, we wanted to provide a friendly program that allows the researcher to study the influence of several parameters in the global behavior of the system.

About NETLOGO

NetLogo is a programmable modeling environment for simulating natural and social phenomena. It was authored by Uri Wilensky in 1999 and has been in continuous development ever since at the Center for Connected Learning and Computer-Based Modeling.

NetLogo is particularly well suited for modeling complex systems developing over time. Modelers can give instructions to hundreds or thousands of "agents" all operating independently. This makes it possible to explore the connection between the micro-level behavior of individuals and the macro-level patterns that emerge from the interaction of many individuals.

Simulating the bistable

To run the simulation you have to download the NetLogo environment from his web page and open after the file biestable-simulation.nlogo (download here)

Multiagent System Simulation. General View

Simulation General View

Retrieved from "http://2011.igem.org/Team:UPO-Sevilla/Project/Basic_Flip_Flop/Multiagent_System/Overview"