A script from SS2009 "Einführung in die Theoretische Systembiologie" (in German).
We will cover several topics from this lecture in the course M4447.
A jupyter notebook "Growth Forms.ipynb" with linear, exponential and logistic growth. It contains the integration of the differential equation and the plot.
A summary of the calculation with the modified logistic growth equation.
Three jupyter notebooks with the implemented 2-compartment-model "2Compartment_Model.ipynb", and with the 2-compartment-model with steady state solution "2Compartment-Model steadystate.ipynb", and with the 2-compartment-model with Michael Menten-kinetics "2Comparment_Model_MichaelMenten.ipynb".
Another jupyter notebook with a 3-compartment-model "3Compartment_Model with steadystate.ipynb".
Calculation of the stationary points of the 2-compartment-model with Michaelis Menten-kinetics "Stat_2CModel.pdf".
PS-Model: Calculations of stationary points and their stability in theory "PS-Model.pdf" and as a jupyter notebook "PS-Model.ipynb".
Implementation of the Lotka-Volterra-Model: "LV-Model.ipynb".
Implementation of the 5-compartment-model: "5Compartment-Model.ipynb".
Jupyter notebook for the 2-compartment-model with autocatalysis "2Compartment-Model_autocatalytic.ipynb".
Implementation of the genetic-switch-model: "genetic switches.ipynb".
Jupyter notebook with the four dynamic behaviors (variation of the predator death rate) of the predator-prey-model with Holling Typ II predation and logistic growth of the prey "PP-Model with Holling-Typ2- Predation.ipynb".
Implementation of the Fitzhugh-Model with nullclines, stationary points and phase plot: "Fitzhugh-Model.ipynb".
Part I of the Morris-Lecar-Model with nullclines and steadystate: "ML-Model Part 1.ipynb".
Part 2 of the Morris-Lecar-Model with nullclines and steadystate:"ML-Model Part 2.ipynb".
Literature
A seminal synthetic biology paper, in which the genetic toggle switch was built in E.coli: Gardner2000.pdf
A comprehensive treatise of the Morris-Lecar model by Rinzel and Ermentrout: Rinzel1998.pdf
