Team:KULeuven/Modeling

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Revision as of 08:36, 12 September 2011

KULeuven iGEM 2011

overview Freeze Antifreeze Cell Death

Modeling Overview

1. Describing the whole system

To make predictions for are plasmid transformed E.coli, a structured segregated model is designed in Simbiology. A graphical representation of the model was build in the block diagram editor . Afterwards reaction equations and parameters were added. We designed one model for the whole system and 3 models for 3 subsystems. The 3 subsystems are antifreeze, freeze and cell death. For more information about these 3 subsystems, we refer to the extended project description and the 3 modelling pages. Refer to detailed project description: https://2011.igem.org/Team:KULeuven/Details

PARAMETER TABLE

2. Full Model

There are in total 5 different kinetic equations we used in the model Transcription equation For most promoters, hill kinetics is used, it is a way of quantitatively describing cooperative binding processes, it was developed for hemoglobin in 1913. A Hill coefficient (n) is a measure for the cooperativity. Translation equation RNA degradation Protein degration Assimiliation

@@ Line 144: / Line 144: @@
 <h3>Modeling Overview</h3>
-<br><h2>Introduction
+<br><h2>1. Describing the whole system</h2>
 To make predictions for are plasmid transformed E.coli, a structured segregated model is designed in Simbiology. A graphical representation of the model was build in the block diagram editor . Afterwards reaction equations and parameters were added.
-Description
 We designed one model for the whole system and 3 models for 3 subsystems. The 3 subsystems are antifreeze, freeze and cell death. For more information about these 3 subsystems, we refer to the extended project description and the 3 modelling pages.
-Refer to detailed project description: https://2011.igem.org/Team:KULeuven/Details
+Refer to detailed project description: https://2011.igem.org/Team:KULeuven/Details<br><br>
-Ordinary differential equations
-.pdf
+<br><p>PARAMETER TABLE
-(use simbiology2latex toolbox of igem kuleuven 2008 to become formula and ask Sarah to convert the latex-file to pdf)
-There are in total 5 different kinetic equations we used in the model:
+<br><h2>2. Full Model </h2>
-Transcription equation:
+There are in total 5 different kinetic equations we used in the model
+Transcription equation
 For most promoters, hill kinetics is used, it is a way of quantitatively describing cooperative binding processes, it was developed for hemoglobin in 1913. A Hill coefficient (n) is a measure for the cooperativity.
-Translation equation:
+Translation equation
-RNA degradation:
+RNA degradation
-Protein degration:
+Protein degration
-Assimiliation:
+Assimiliation
-Full model
-.Jpg full model
+<br><h2>3. Simulations </h2>
-Parameter table
-When no accurate parameters where found in literature we used these estimated values:
-Transcription parameter
-Translation parameter
-RNA degradation parameter
-Protein degradation parameter
-Simulations
+<br><br>
-Sensitivity analysis
+<br><h2>4. Sensitivity analysis</h2>
 <br><br>