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Team:UNIPV-Pavia/Modeling
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The purposes of writing mathematical models for gene networks can be: | The purposes of writing mathematical models for gene networks can be: | ||
*'''Prediction''': a good and well identificated model can be used in simulations to predict real system behavior. In particular we could be interested in system output in response to never seen inputs. In this way, the system can be tested 'in silico', without performing real experiments 'in vitro' or 'in vivo'. | *'''Prediction''': a good and well identificated model can be used in simulations to predict real system behavior. In particular we could be interested in system output in response to never seen inputs. In this way, the system can be tested 'in silico', without performing real experiments 'in vitro' or 'in vivo'. | ||
| - | *'''Parameter identification''': we already wrote that it is very important to estimate all the parameters involved in the model, in order to perform realistic simulations. Another goal that can be reached with parameter identification is 'network summarization', in fact estimated parameters can be used as 'behavior indexes' for the network (or a part of it). These indexes can be very useful for synthetic biologists to choose and compare BioBrick standard parts for | + | *'''Parameter identification''': we already wrote that it is very important to estimate all the parameters involved in the model, in order to perform realistic simulations. Another goal that can be reached with parameter identification is 'network summarization', in fact estimated parameters can be used as 'behavior indexes' for the network (or a part of it). These indexes can be very useful for synthetic biologists to choose and compare BioBrick standard parts for genetic circuits design, just like electronic engineers choose, for example, a Zener diode, knowing its Zener voltage. |
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Revision as of 10:43, 28 September 2008
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Mathematical modeling page
In this section we explain two dynamic models that can be used to describe the gene networks in our project. After a brief overview about the motivation of a mathematical model, we will illustrate the general formulas we used, we will show the complete ODE models for Mux and Demux gene networks, and then we will report results of some simulations performed with Matlab and Simulink.
Why writing a mathematical model?
The purposes of writing mathematical models for gene networks can be:
- Prediction: a good and well identificated model can be used in simulations to predict real system behavior. In particular we could be interested in system output in response to never seen inputs. In this way, the system can be tested 'in silico', without performing real experiments 'in vitro' or 'in vivo'.
- Parameter identification: we already wrote that it is very important to estimate all the parameters involved in the model, in order to perform realistic simulations. Another goal that can be reached with parameter identification is 'network summarization', in fact estimated parameters can be used as 'behavior indexes' for the network (or a part of it). These indexes can be very useful for synthetic biologists to choose and compare BioBrick standard parts for genetic circuits design, just like electronic engineers choose, for example, a Zener diode, knowing its Zener voltage.
