Models

Bayesian model for inference of the activity of transcription factors from targets' mRNA levels. A standalone C sharp package (runs on linux and mac under MONO).

Code for joint probabilistic inference of transcription factor behaviour and gene-transcription factor as well as metabolite-transcription factor interaction based on genome and metabolite data.

Mathematical model for TPI kinetics, GAP and DHAP saturation, and inhibition with 3PG and PEP.

The zip file contains two executable Matlab functions.

File named 'fnct_gen_tfcompmod.m' generates a Simbiology model based on the following interactions: R + X <-> RX -> R + X + Px R + Y <-> RY -> R + Y + Py R + Z <-> RZ -> R + Z + Pz Y + Pz -> Pz Px -> Py -> Pz ->

We assume much higher reaction speeds of sigma factor RNApol binding/unbinding compared to protein expression. Protein expression can therefore be represented by Michaelis-Menten like kinetic ...