Abstract
BackgroundComputational mathematical models of biological and biomedical
systems have been successfully applied to advance our understanding of
various regulatory processes, metabolic fluxes, effects of drug
therapies, and disease evolution and transmission. Unfortunately,
despite community efforts leading to the development of SBML and the
BioModels database, many published models have not been fully exploited,
largely due to a lack of proper documentation or the dependence on
proprietary software. To facilitate the reuse and further development of
systems biology and systems medicine models, an open-source toolbox that
makes the overall process of model construction more consistent,
understandable, transparent, and reproducible is desired.Results and
discussionWe provide an update on the development of modelbase, a free,
expandable Python package for constructing and analysing ordinary
differential equation-based mathematical models of dynamic systems. It
provides intuitive and unified methods to construct and solve these
systems. Significantly expanded visualisation methods allow for
convenient analysis of the structural and dynamic properties of models.
After specifying reaction stoichiometries and rate equations modelbase
can automatically assemble the associated system of differential
equations. A newly provided library of common kinetic rate laws reduces
the repetitiveness of the computer programming code. modelbase is also
fully compatible with SBML. Previous versions provided functions for the
automatic construction of networks for isotope labelling studies. Now,
using user-provided label maps, modelbase v1.2.3 streamlines the
expansion of classic models to their isotope-specific versions. Finally,
the library of previously published models implemented in modelbase is
growing continuously. Ranging from photosynthesis to tumour cell growth
to viral infection evolution, all these models are now available in a
transparent, reusable and unified format through
modelbase.ConclusionWith this new Python software package, which is
written in currently one of the most popular programming languages, the
user can develop new models and actively profit from the work of others.
modelbase enables reproducing and replicating models in a consistent,
tractable and expandable manner. Moreover, the expansion of models to
their isotopic label-specific versions enables simulating label
propagation, thus providing quantitative information regarding network
topology and metabolic fluxes.
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