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<div class="sec white" id="methods"> | <div class="sec white" id="methods"> | ||
<div> | <div> | ||
− | < | + | <h2>ESTIMATION METHODS</h2> |
− | <p>We used two different approaches for parameter estimation from experimental data | + | <p>We used two different approaches for parameter estimation from experimental data:</p> |
− | < | + | <h3>MEIGO</h3> |
− | < | + | <p>MEIGO is an open source global optimization <a href="http://gingproc.iim.csic.es/meigo.html">toolbox</a> that provides several solvers for different applications. In our project we used the <i>Cooperative enhanced Scatter Solver (CeSS)</i> from the MATLAB version of the toolbox. Parameters were estimated by fitting ODE simulations to the experimental data using a least-square error function.</p> |
+ | <h3>INSIGHT</h3> | ||
+ | <p> | ||
+ | </p> | ||
</div> | </div> | ||
</div> | </div> |
Revision as of 08:30, 19 October 2016
PARAMETERS
ESTIMATION METHODS
We used two different approaches for parameter estimation from experimental data:
MEIGO
MEIGO is an open source global optimization toolbox that provides several solvers for different applications. In our project we used the Cooperative enhanced Scatter Solver (CeSS) from the MATLAB version of the toolbox. Parameters were estimated by fitting ODE simulations to the experimental data using a least-square error function.
INSIGHT
Parameter constant for the NO module
Name | Description | Unit | range values | value Estimation | method of Evaluation | Source |
---|---|---|---|---|---|---|
knor_no | NorR NOproduction rate | nM-1min-1 | 0.001 - 10 | 0,0011183 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
k_nor_no | NorR NOdissociation rate | nM-1min-1 | 0.01 - 10 | 0,0363665 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
knorV1 | DNorR NO2binding rate | nM-1min-1 | 0.01 - 1 | 0,0014788 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
k_norV1 | DNorR NO2unbinding rate | nM-1min-1 | 0.01 - 1 | 0,00081 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
knorV2 | DNorR NO2binding rate | nM-1min-1 | 0.01 - 10 | 0,00185016 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
k_norV2 | DNorR NO2unbinding rate | nM-1min-1 | 0.01 - 1 | 7.1 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
knorV3 | DNorR NO2binding rate | nM-1min-1 | 0.01 - 10 | 0,986026 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
k_norV3 | DNorR NO2unbinding rate | nM-1min-1 | 0.01 - 10 | 6.1 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
knorprod | NorR constitutive production rate | nM-1min-1 | 0.01 - 10 | 0,958777 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
dnor | NorR degradation rate | nM-1min-1 | 0.01 - 1 | 89,159 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
dnor_no | NorR NOdegradation rate | nM-1min-1 | 0.01 - 1 | 46,678 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
kdnor | DNorR dimerization constant | nM-1min-1 | 0.01 - 1 | 75698,5 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
k_dnor | DNorR dissociation rate | nM-1min-1 | 0.01 - 1 | 1,91699 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
kmrna | mRNA production rate for pnorV promoter | nM-1min-1 | 0.01 - 1 | 3438,47 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
dmrna | mRNA degradation rate | min-1 | 0.01 - 1 | 0,0199458 | MEIGO metaheuristic evaluation from plate reader | Computed from parameter estimation |
Parameter constant for the AHL module
Name | Description | Unit | range values | value Estimation | method of Evaluation | Source |
---|---|---|---|---|---|---|
kesarProd | EsaR constitutive production rate | nM-1min-1 | 0.01 - 10 | 3,24412 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
desar | DEsaR degradation rate | min-1 | 0.01 - 1 | 0,0152529 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
kl | promoter leakiness | nM-1min-1 | 0.01 - 10 | 0,00242729 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
k5 | DEsaR production rate | nM-1min-1 | 0.01 - 1 | 0,01 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
k_5 | DEsaR dissociation rate | nM-1min-1 | 0.01 - 10 | 0,65492 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
k6 | DEsaR AHL production rate | nM-1min-1 | 0.01 - 10 | 0,0100102 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
k_6 | DEsaR AHL dissociation rate | nM-1min-1 | 0.01 - 10 | 0,719465 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
k7 | AHL to Pesar promoter binding rate | nM-1min-1 | 0.01 - 1 | 0,4878 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
k_7 | AHL to Pesar promoter unbinding rate | nM-1min-1 | 0.01 - 1 | 0,0383841 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
kmrna | mRNA production rate for Pconst+esaboxes promoter | nM-1min-1 | 0.01 - 1 | 0,0121775 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
dmrna | mRNA degradation rate | min-1 | 0.01 - 1 | 0,0142082 | MEIGO metaheuristic evaluation from FACS Datas | Computed from parameter estimation |
Parameter constant for the AHL module
Name | Description | Unit | range values | value Estimation | method of Evaluation | Source |
---|---|---|---|---|---|---|
klac_pyr | NorR NOproduction rate | nM-1min-1 | 0.01 - 10 | 0.1 | Litterature | Source |
k_lac_pyr | NorR NOdissociation rate | nM-1min-1 | 0.01 - 10 | 1.5 | Litterature | Source |
kdlldr | DNorR NO2binding rate | nM-1min-1 | 0.01 - 1 | 0.1 | Litterature | Source |
k_dlldr | DNorR NO2unbinding rate | nM-1min-1 | 0.01 - 1 | 8.1 | Litterature | Source |
kgoff | DNorR NO2binding rate | nM-1min-1 | 0.01 - 10 | 0.1 | Litterature | Source |
k_goff | DNorR NO2unbinding rate | nM-1min-1 | 0.01 - 1 | 7.1 | Litterature | Source |
kdlldr_lac | DNorR NO2binding rate | nM-1min-1 | 0.01 - 10 | 0.1 | Litterature | Source |
k_dlldr_lac | DNorR NO2unbinding rate | nM-1min-1 | 0.01 - 10 | 6.1 | Litterature | Source |
kgoff_lac | NorR constitutive production rate | nM-1min-1 | 0.01 - 10 | 3 | Litterature | Source |
k_goff_lac | NorR degradation rate | nM-1min-1 | 0.01 - 1 | 0.1 | Litterature | Source |
dlld | NorR NOdegradation rate | nM-1min-1 | 0.01 - 1 | 1 | Litterature | Source |
kllddProd | DNorR dimerization constant | nM-1min-1 | 0.01 - 1 | 1 | Litterature | Source |
klldrProd | DNorR dissociation rate | nM-1min-1 | 0.01 - 1 | 10 | Litterature | Source |
kl | DEsaR production rate | nM-1min-1 | 0.01 - 10 | 1.5 | Litterature | Source |
nlact | DNorR NO2binding rate | nM-1min-1 | 0.01 - 1 | 0.1 | Litterature | Source |
Klact | DEsaR degradation rate | nM-1min-1 | 0.01 - 1 | 8.1 | Litterature | Source |