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Team:LCG-UNAM-Mexico/Simulation
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<span class="bodyText">With the aim of predicting the behavior of the system, the biochemical reactions were implemented in the SimBiology package of MATLAB, using the previously <a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Parameters">defined parameters</a>. Simulations were run for different values of the initial concentration of AHL and Ni<sub>total</sub> (Ni<sub>int</sub> + Ni<sub>ext</sub>) which are the metabolites that we can directly manipulate in our experiments. A parameter scan was also run for some parameters to understand their influence on the system.</span><br> | <span class="bodyText">With the aim of predicting the behavior of the system, the biochemical reactions were implemented in the SimBiology package of MATLAB, using the previously <a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Parameters">defined parameters</a>. Simulations were run for different values of the initial concentration of AHL and Ni<sub>total</sub> (Ni<sub>int</sub> + Ni<sub>ext</sub>) which are the metabolites that we can directly manipulate in our experiments. A parameter scan was also run for some parameters to understand their influence on the system.</span><br> | ||
| - | <span class="bodyText">In order to gain insights into the system dynamics to elucidate the conditions needed to get the desired behavior, we performed a series of analyses on it: | + | <span class="bodyText">In order to gain insights into the system dynamics to elucidate the conditions needed to get the desired behavior, we performed a series of analyses on it: Sensitivity analysis allowed us to identify critical parameters that needed to be defined on the most stringent way. Basis for the (right) null and left null space were calculated to obtain information about the general network behavior. Steady-states were calculated by numerical integration of the non-linear ODEs system. Finally the Jacobian of the system was calculated around the steady-states. All simulations and analyses were implemented and performed on MATLAB.</span> |
<p> <span class="style2"><a name="SimulationParameterScan"></a>Simulation and parameter scan</span><br> | <p> <span class="style2"><a name="SimulationParameterScan"></a>Simulation and parameter scan</span><br> | ||
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Revision as of 14:04, 29 October 2008
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With the aim of predicting the behavior of the system, the biochemical reactions were implemented in the SimBiology package of MATLAB, using the previously defined parameters. Simulations were run for different values of the initial concentration of AHL and Nitotal (Niint + Niext) which are the metabolites that we can directly manipulate in our experiments. A parameter scan was also run for some parameters to understand their influence on the system. In order to gain insights into the system dynamics to elucidate the conditions needed to get the desired behavior, we performed a series of analyses on it: Sensitivity analysis allowed us to identify critical parameters that needed to be defined on the most stringent way. Basis for the (right) null and left null space were calculated to obtain information about the general network behavior. Steady-states were calculated by numerical integration of the non-linear ODEs system. Finally the Jacobian of the system was calculated around the steady-states. All simulations and analyses were implemented and performed on MATLAB. Simulation and parameter scan Sensitivity analysis Definir brevemente de que se trata, mostrar análisis a diferentes tiempos. Señalar los resultados que esperábamos y los que no Stoichiometric matrix Definir la información que contiene la matriz estequimétrica. Steady-states Definir estado estacionario, decir algo de la complejidad del problema y justificar la estrategia elegida (aproximación numérica) Presentar la solución ontenida. Jacobian Definición general del jacobiano (link a wikipedia o mathworld?). Definición en redes bioquímicas.
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