Team:ETH Zurich/Modeling/Overview

 {|style="background:#FFFFFF ; border:3.5px solid #60AFFE; padding: 1em; margin: auto ; width:98.5% "

Overview on the modelling framework
This page is meant to give an introduction to the overall modelling framework we have constructed in order to assess feasibility analysis, temporal scale details and other parameter estimations with regard of our project setup. As introduced in the Project Overview section, four main components can be identified in the devised mechanism. Accordingly, we divided the modeling framework in four modules that address different challenges. The first module is concerned with the analysis of restriction enzymes and their cutting pattern on E.coli genome. The second module predicts the cell's response to the selection pressure and the forced genome reduction from a system point of view (that is, using a genome scale model). The third module addresses issues related to the sensitivity and setting of the chemostat mechanism. The fourth and final module presents the model of the genetic switch circuit used to control the restriction enzymes expression. In the table below, you can find a birds-eye view on the four modules, with the most important aspects highlighted. Since we believe that a model is only useful when it answers specific and well-posed questions, this is the first aspect we report in the summary view. Second, we briefly report about the modeling method applied. Finally, we summarize the results we obtained. By clicking on each module's title, you can browse the specific module pages containing all the detailed information, such as plots, modelling assumptions and data sources. Note that it is possible to download from our Downloading Page all the data and code (MATLAB source) that we used and wrote in order to generate our results.


 * }