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Pre-print:

GZM_InducibleTF

Modeling inducible transcriptional regulators, GEM & ZPM, dose-response.

Code asociated to Gómez-Schiavon, Dods_et al. (2020; ACS Synthetic Biology) and Dods, Gómez-Schiavon et al. (2020; bioRxiv).

Main files:

  • FN_SS_MODELNAME.m: Finding steady state solution the output (formula) for the specific model (e.g. FN_SS_SimpleHill.m for simple hill model; see options below) given a set of biophysical paramers (e.g. formula), inducer concentration (formula), and total transcription factor concentration (formula).
  • FN_FitError.m: Calculate the sum of square errors between model's steady state (formula) and observed data (formula), given a set of biophysical paramers (e.g. formula), inducer concentration (formula), and total transcription factor concentration (formula).
  • FN_FitMRW.m: Find the set of parameters that best fit the data.
  • RUN_FitMRW.m: Determine model, conditions, and parameters to be fitted, and call FN_FitMRW.m.

MODEL: Simple Hill model

FN_SS_SimpleHill.m

formula

formula

MODEL: Hill + Basal model

FN_SS_HillxBasal.m

formula

formula

MODEL: Mechanistic model

FN_SS_Mechanistic.m

formula

formula

formula

formula

formula

MODEL: Expanded Hill model

* NOTE: Also refered as allosteric

FN_SS_Allosteric.m

formula

formula

formula

formula

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Modeling inducible transcriptional regulators, GEM & ZPM, dose-response.

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