Team:KULeuven/Model/Overview

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Revision as of 09:18, 17 August 2008

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Introduction

As an introduction to modeling we've made a small presentation for the workout sessions of the first meeting. This presentation handles the following items:

some definitions
the difference between white box and black box models with an example
focus on the role of ODE's
the need for modeling
some modeling tools
and iGEM modeling

This presentation is mainly based on the wiki of ETH Zürich 2006/2007.

Why modeling?

Modeling steps

Position in the system

For each of the subsystems (compartments) we started with the idea of what it was supposed to do, considering it as a black-box system (as described in the project page). ...

Describing the system

We first searched for existing components which could be able to perform the requested task ... (todo: ODE/parameters)

Models

We implemented these subsystems in both Celldesigner (todo:link) and the MATLAB Symbiology Toolbox (todo:link).

Simulation(s)

...

Sensitivity Analysis

Good modeling practice requires that the modeler provides an evaluation of the confidence in the model, possibly assessing the uncertainties associated with the modeling process and with the outcome of the model itself. Uncertainty and Sensitivity Analysis offer valid tools for characterizing the uncertainty associated with a model. Uncertainty analysis (UA) quantifies the uncertainty in the outcome of a model. Sensitivity Analysis has the complementary role of ordering by importance the strength and relevance of the inputs in determining the variation in the output. Sensitivity analysis lets you calculate the time-dependent sensitivities of all the species states with respect to species initial conditions and parameter values in the model.

A sensitivity analysis is needed e.g. when some of the parameter values are not known. The true value of a parameter is unimportant when the most essential species states are insensitive to the unknown parameter. Only for the sensitive unknown parameters are experiments needed to determine their true values. In our project we have been able to find hypothetical values for all used parameters, but a sensitivity analyses is nevertheless always valuable to detect critical parameters. These are the parameter values on which our project critically depends and which should be analyzed/characterized as exact as possible.

Important notes

The idea of a pulsgenerator as reset mechanism has been cancelled for the following reasons:
- it takes too long before the proposed system generates a pulse-like event
- the pulse itself is too long
- a constant lactonase production sequence generates enough lactonase to reset the timer
More information about this problem and the solution can be found on Reset-page.

@@ Line 1: / Line 1: @@
 {{:Team:KULeuven/Tools/Header}}
+__NOTOC__
 === Introduction ===
@@ Line 16: / Line 18: @@
 [[Image:WhyWeNeedComputer.png|280px|center]]
-=== Modeling steps & important notes===
+=== Modeling steps===
-* The idea of a pulsgenerator as reset mechanism has been cancelled for the following reasons:
+==== Position in the system ====
-** it takes too long before the proposed system generates a pulse-like event
-** the pulse itself is too long
-** a constant lactonase production sequence generates enough lactonase to reset the timer
-* More information about this problem and the solution can be found on [https://2008.igem.org/Team:KULeuven/Model/Reset Reset]-page.
+For each of the subsystems (compartments) we started with the idea of what it was supposed to do, considering it as a black-box system (as described in the [https://2008.igem.org/Team:KULeuven/Project project page]). ...
-=== Sensitivity Analysis ===
+==== Describing the system ====
+We first searched for existing components which could be able to perform the requested task ... (todo: ODE/parameters)
+==== Models ====
+We implemented these subsystems in both Celldesigner (todo:link) and the MATLAB Symbiology Toolbox (todo:link).
+==== Simulation(s) ====
+...
+==== Sensitivity Analysis ====
 Good modeling practice requires that the modeler provides an evaluation of the confidence in the model, possibly assessing the uncertainties associated with the modeling process and with the outcome of the model itself. Uncertainty and Sensitivity Analysis offer valid tools for characterizing the uncertainty associated with a model. Uncertainty analysis (UA) quantifies the uncertainty in the outcome of a model. Sensitivity Analysis has the complementary role of ordering by importance the strength and relevance of the inputs in determining the variation in the output. Sensitivity analysis lets you calculate the time-dependent sensitivities of all the species states with respect to species initial conditions and parameter values in the model.
 A sensitivity analysis is needed e.g. when some of the parameter values are not known. The true value of a parameter is unimportant when the most essential species states are insensitive to the unknown parameter. Only for the sensitive unknown parameters are experiments needed to determine their true values. In our project we have been able to find hypothetical values for all used parameters, but a sensitivity analyses is nevertheless always valuable to detect critical parameters. These are the parameter values on which our project critically depends and which should be analyzed/characterized as exact as possible.
+=== Important notes ===
+* The idea of a pulsgenerator as reset mechanism has been cancelled for the following reasons:
+** it takes too long before the proposed system generates a pulse-like event
+** the pulse itself is too long
+** a constant lactonase production sequence generates enough lactonase to reset the timer
+* More information about this problem and the solution can be found on [https://2008.igem.org/Team:KULeuven/Model/Reset Reset]-page.