Team:Heidelberg/Modeling/Chemotaxis

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(Difference between revisions)

Latest revision as of 22:54, 29 October 2008

Chemotaxis - Killing Model

Our detailed documentation "Spatially Resolved Modeling of Colicin-Induced Killing and Chemotactic Sensing in Escherichia Coli." includes the following information:

Introduction into the biological sytem
Chemotaxis model
Parameter estimation
Numerical methods
Results
Conclusions

You can download the documentation on Spatially Resolved Modeling of Colicin-Induced Killing and Chemotactic Sensing in Escherichia Coli. Further we have made a summary of the complete modeling group for non-mathematicians.

Simulation movies

Below is a list of simulation movies. Specific parameters can be taken from our documentation. All simulations are in ogg vorbis format (see http://www.vorbis.com for help).

movie 1 (3D, 2D)
- 4-PDE system
- killer cells positioned in corner
- prey evenly distributed
movie 2 (3D, 2D)
- 5-PDE system
- killer cells positioned in corner
- prey evenly distributed
movie 3 (3D, 2D)
- 5-PDE system
- killer cells positioned in corner
- prey evenly distributed
- 1/1000 AI-2 production rate
movie 4 (3D, 2D)
- 5-PDE system
- killer cells positioned in corner
- prey evenly distributed
- 8-fold chemotactic activity towards AI-2
movie 5 (3D, 2D)
- 5-PDE system
- killer cells evenly distributed
- prey positioned in center

@@ Line 464: / Line 464: @@
-==Chemotaxis - Killing Model==
+== Chemotaxis - Killing Model ==
-Our detailed documentation "Model for Sensing Network and the Production of Colicins as the Killing Mechanism" includes the following information:
+Our detailed documentation "Spatially Resolved Modeling of Colicin-Induced Killing and Chemotactic Sensing in ''Escherichia Coli''." includes the following information:
 * Introduction into the biological sytem
 * Chemotaxis model
@@ Line 473: / Line 473: @@
 * Conclusions
-You can download the documentation here and the summary of the modeling project can be downloaded [[Media:Summary.pdf|here]].
+You can download the documentation on [[Media:Documentation_Sensing_Colicin.pdf|Spatially Resolved Modeling of Colicin-Induced Killing and Chemotactic Sensing in ''Escherichia Coli'']]. Further we have made a [[Media:Summary.pdf|summary]] of the complete modeling group for non-mathematicians.
 === Simulation movies ===
-Below is a list of simulation movies. Specific parameters can be taken from our documentation. 3D movies show the dynamics of all components of the system, while 2D movies show only the distribution of the bacterial strains. The 2D movies are ideally for seeing the killer cells spread over the area, while killing the prey strain.
+Below is a list of simulation movies. Specific parameters can be taken from our documentation. All simulations are in ogg vorbis format (see http://www.vorbis.com for help).
-* movie 1 (<a href="https://static.igem.org/mediawiki/2008/6/6d/HD_4PDE_3D.ogg">3D</a>, <a href="https://static.igem.org/mediawiki/2008/6/6d/HD_4PDE_2D.ogg">2D</a>)
+* movie 1 ([https://static.igem.org/mediawiki/2008/7/7f/HD_4PDE_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/6/6d/HD_4PDE_2D.ogg '''2D'''])
 ** 4-PDE system
 ** killer cells positioned in corner
 ** prey evenly distributed
-* movie 1 (3D, 2D)
+* movie 2 ([https://static.igem.org/mediawiki/2008/f/f8/HD_5PDE_a_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/8/8a/HD_5PDE_a_2D.ogg '''2D'''])
 ** 5-PDE system
 ** killer cells positioned in corner
-* movie 3 (3D, 2D)
+** prey evenly distributed
+* movie 3 ([https://static.igem.org/mediawiki/2008/2/2f/HD_5PDE_a_0-01AI2_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/1/10/HD_5PDE_a_0-01AI2_2D.ogg '''2D'''])
 ** 5-PDE system
 ** killer cells positioned in corner
 ** prey evenly distributed
 ** 1/1000 AI-2 production rate
-* movie 4 (3D, 2D)
+* movie 4 ([https://static.igem.org/mediawiki/2008/1/15/HD_5PDE_a_4-fold-chemotaxis_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/9/9b/HD_5PDE_a_4-fold-chemotaxis_2D.ogg '''2D'''])
 ** 5-PDE system
 ** killer cells positioned in corner
 ** prey evenly distributed
-** 4-fold chemotactic activity towards AI-2
+** 8-fold chemotactic activity towards AI-2
-* movie 5 (3D, 2D)
+* movie 5 ([https://static.igem.org/mediawiki/2008/8/81/HD_5PDE_b_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/1/11/HD_5PDE_b_2D.ogg '''2D'''])
 ** 5-PDE system
 ** killer cells evenly distributed
 ** prey positioned in center