From 2013.igem.org
(Difference between revisions)
|
|
| Line 9: |
Line 9: |
| | <div style="margin-left:50px;margin-right:50px;float:left;display:inline-block;"> | | <div style="margin-left:50px;margin-right:50px;float:left;display:inline-block;"> |
| | <br> | | <br> |
| - | <p align="justify">Modeling will play an important role in the iGEM project. Our total system is rather complex and requires careful tuning in order for it to work. This tuning cannot be done in the lab due to time constraints, so the modeling will be used to derive conditions on strengths of promoters and binding sites in order for the system to work. This way the correct implementation can be done in the lab, saving effort and time. | + | <p align="justify"> Modelling is our bridge between science and engineering. Using the scientific knowledge on our system, we can describe how the system will act and interact. Combining our mathematical model(s) with our lab results will lead to an as much realistic as possible description of our constructs and its possibilities. This description can then be used for predicting what will happen when you control the system using a specific parameter. Modelling offers the first answers to the questions posed when one engineers.</p> |
| - | The modeling will first focus on the timer, then the SUMO fusion and finally the kill switch. These parts will be introduced below and details on these parts will be added later on in the project.
| + | |
| - | </p>
| + | |
| - | <br>
| + | |
| - | <b><font color="#330000" size="3">Timer</font></b>
| + | |
| - | <p align="justify" margin: 20px >The most important aspect here is the modeling of the ‘time delay’: What is the difference in time between inducing and the output. In our case we have two outputs, a small delay must also be present between those two.
| + | |
| - | <br>
| + | |
| - | | + | |
| - | <center>
| + | |
| - | <img src="https://static.igem.org/mediawiki/2013/1/1a/Timer_simple.png" height=300px>
| + | |
| - | </center>
| + | |
| - | | + | |
| - | | + | |
| - | <br>
| + | |
| - | At the moment only one output is currently modeled, the ULP-1 protease. Results of this simulation are shown in Figure 1, here the time delay is about … minutes. Next to add is the interaction with the peptide tagged with SUMO and the ULP-1 protease. The second output will be added later (the kill switch cassette).
| + | |
| - | </p>
| + | |
| - | <br>
| + | |
| - | <b><font color="#330000" size="3">SUMO fusion</font></b>
| + | |
| - | <p align="justify" margin: 20px >The peptide is expressed with a SUMO tag added to it, expressing the protease will cleave of the SUMO. It is important to accurately know this cleavage rate in order to describe the rate of ‘free’ peptide production.
| + | |
| - | <br>
| + | |
| - | <br>
| + | |
| - | <b><font color="#330000" size="3">Kill switch</font></b>
| + | |
| - | <p align="justify" margin: 20px >
| + | |
| - | The kill switch contains two important parts the expression of holin and the antiholin. These two are important tuning parameters to make the system stable and robust. It will be essential to make sure that the ‘free’ peptide reaches a steady state before lysis of the cell. Making sure of this yields the most efficient system, lysis before the cleavage is done yields less active peptides. The tuning parameters will be the respective RBS and the const. promoter, a thorough sensitivity analysis will be performed on this model to derive the optimal conditions and robustness.
| + | |
| - | | + | |
| - | <br> | + | |
| | | | |
| | | | |
| | </html> | | </html> |
Revision as of 13:55, 16 August 2013
Modeling
Modelling is our bridge between science and engineering. Using the scientific knowledge on our system, we can describe how the system will act and interact. Combining our mathematical model(s) with our lab results will lead to an as much realistic as possible description of our constructs and its possibilities. This description can then be used for predicting what will happen when you control the system using a specific parameter. Modelling offers the first answers to the questions posed when one engineers.
"
