RT Journal Article SR Electronic T1 Building mathematical models of biological systems with modelbase, a Python package for semi-automatic ODE assembly and construction of isotope-specific models JF bioRxiv FD Cold Spring Harbor Laboratory SP 362954 DO 10.1101/362954 A1 O. Ebenhöh A1 M. van Aalst A1 N.P. Saadat A1 T. Nies A1 A. Matuszyńska YR 2018 UL http://biorxiv.org/content/early/2018/07/05/362954.abstract AB 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.AbbreviationsCBBCalvin-Benson-BasshamNMRNuclear Magnetic ResonanceODEOrdinary Differential EquationsPAMPulse Amplitude ModulationPPPPentose-PhosphateSBMLSystems Biology Markup LanguageUMLUnified Modeling Language