Team:KULeuven/Model/Filter

From 2008.igem.org

(Difference between revisions)
(Parameters)
Line 91: Line 91:
[[Image:Filter_CellDesigner.png|800px|center|filter]]
[[Image:Filter_CellDesigner.png|800px|center|filter]]
-
[[Image:Sim_filter_1.png|800px|center|filter]]
 
==== Matlab ([https://static.igem.org/mediawiki/2008/c/ce/Filter_Matlab.zip SBML file])====
==== Matlab ([https://static.igem.org/mediawiki/2008/c/ce/Filter_Matlab.zip SBML file])====
Line 99: Line 98:
[[Image:Filter_Matlab.jpg|center]]
[[Image:Filter_Matlab.jpg|center]]
-
{| align="center"
+
 
-
|[[Image:Sim_filter_short.jpg|450px]]
+
=== Simulations ===
-
|[[Image:Sim_filter_long.jpg|450px]]
+
 
-
|}
+
[[Image:Sim_filter_1.png|800px|center|filter]]
 +
 
=== Sensitivity Analysis ===
=== Sensitivity Analysis ===
[[Image:Sens Filter.png|center]]
[[Image:Sens Filter.png|center]]

Revision as of 10:13, 14 August 2008

  dock/undock dropdown  

Pictogram filter.png

Contents

Filter

Position in the system

Describing the system

Filter BioBrick.jpg

ODE's

Parameters

Parameter values Filter
Name Value Comments Reference
Degradation rates
dpT7_tag 0.00155 s-1 tag added to speed up degradation of otherwise too stable T7 polymerase [http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation link]
dmRNA_RIBOKEY 0.00462 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dclosed_mRNA_T7 0.00462 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dopen_mRNA_T7 0.00231 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dopen_mRNA_T7_complex 0.00231 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
Equilibrium constants
Keq_1 0,015 [M] closed and open mRNA
Keq_2 0.0212 [M] closed and key (binded with ribokey) complex mRNA
Transcription rates
kmRNA_RIBOKEY Input dependent
kmRNA_T7 0,0011 s-1

Remark: The key-lock system can be enhanced to 0.3%-14% (todo: Jonas/Dries)

Models

CellDesigner (SBML file)

filter

Matlab (SBML file)

Matlab diagram for the filter system:

Filter Matlab.jpg


Simulations

filter


Sensitivity Analysis

Sens Filter.png