BISE

Course: Biological Experiments In Silico

Department/Abbreviation: KBF/BISE

Year: 2020

Guarantee: 'doc. RNDr. Dušan Lazár, Ph.D.'

Annotation: Obtaining basic general knowledge about in silico biology, i.e., about studying of biological organisms and processes by means of computer modelling and simulations.

Course review:
- Introduction (mathematics in biology, purpose of modelling, motivating example - AIDS/HIV research) - Basic mathematics (linear, exponential and other functions, differential equations) - Descriptive models and basic data analysis (linear and exponential regressions, ?2 method) - Estimation of model parameters (different methods) - Model validation and verification (Kullback-Liebler divergence, Occam's razor principle, Akike information criterion) - Chemical reaction kinetics and its modelling (types of reactions, reaction order, law of mass action, master equations, Markov chain) - Michaelis-Menten and Hill enzymatic kinetics - Transition state rate theory and rate of electron tunneling - Modelling of oscillating chemical/biological systems (phase space, criteria for oscillations, Lotka-Voltera model, Brusselator, Belousov-Zhabotinsky reaction, Oregonator, glycolysis in yeast, photosynthetic oscillations) - Metabolic control analysis (assumptions, control and response coefficients, elasticity, summation and connectivity theorems, biological examples) - Examples of complex models - modeling of photosynthetic processes (different models)