Building mathematical models of biological systems with modelbase, a Python package for semi-automatic ODE assembly and construction of isotope-specific models

Abstract

The modelbase package is a free expandable Python package for building and analysing dynamic mathematical models of biological systems. Originally it was designed for the simulation of metabolic systems, but it can be used for virtually any deterministic chemical processes. modelbase provides easy construction methods to define reactions and their rates. Based on the rates and stoichiometries, the system of differential equations is assembled automatically. modelbase minimises the constraints imposed on the user, allowing for easy and dynamic access to all variables, including derived ones, in a convenient manner. A simple incorporation of algebraic equations is, for example, convenient to study systems with rapid equilibrium or quasi steady-state approximations. Moreover, modelbase provides construction methods that automatically build all isotope-specific versions of a particular reaction, making it a convenient tool to analyse non-steady state isotope-labelling experiments.

Application of the Theory of New Information Operators in Conducting Research in the Field of Information Technologies

“…Today many problems are being solved in cases when the input information about a function is a set of traces of the function on planes, set of traces of the function on lines or a set of values of the function in the points. It has been proven that different views on data can give new results in digital signal and image processing, in space, computed tomography, seismic tomography and non-destructive testing [3], [4]. By understanding the principles of building new information operators, professionals in other scientific areas may consider a possibility of solving their problems by using other types of data.…”