README.md

GZM_InducibleTF

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

Code asociated to Dods, Gómez-Schiavon et al. (2020; bioRxiv).

Main files:

• FN_SS_MODELNAME.m: Finding steady state solution the output () 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. ), inducer concentration (), and total transcription factor concentration ().
• FN_FitError.m: Calculate the sum of square errors between model's steady state () and observed data (), given a set of biophysical paramers (e.g. ), inducer concentration (), and total transcription factor concentration ().
• 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

MODEL: Hill + Basal model

FN_SS_HillxBasal.m

MODEL: Mechanistic model

FN_SS_Mechanistic.m

MODEL: Expanded Hill model

* NOTE: Also refered as allosteric

FN_SS_Allosteric.m