modelbase is a python package to help you build and analyze dynamic mathematical models of biological systems. It has originally been designed for the simulation of metabolic systems, but can be used for virtually any processes, in which some substances get converted into others.
modelbase incorporates an easy construction method to define 'reactions'. A rate law and the stoichiometry need to be specified, and the system of differential equations is assembled automatically.
modelbase allows 'algebraic modules', which are useful to implement rapid equilibrium or quasi steady-state approximations. In the simplest instance, they allow easy incorporation of conserved quantities.
modelbase also allows a simple construction of isotope-specific models. This class contains a constructor method that automatically construct all isotope specific versions of a particular reaction. Very cool - check it out!
Versions 1.0 and 0.4.0 introduced changes not compatible with the previous official release 0.2.5. API changes are summarised in this notebook
Version 0.4.5 was the prior stable version
Version 0.2.5 is the official release for the submission of the mansucript "Building mathematical models of biological systems with modelbase, a Python package for semi-automatic ODE assembly and construction of isotope-specific models" to the Journal of Open Research Software.
See changelog.md for details on changes of earlier versions.
If you quickly want to test out modelbase, or do not require assimulo support, install modelbase via
pip install modelbase
To enable assimulo support, the easiest way is to install modelbase via conda. We also recommend using the conda-forge channels.
# recommended to avoid package clashes
conda config --add channels conda-forge
# Create a new environment (not necessary, but recommended)
conda create -n mb39 python=3.9
conda install -c conda-forge modelbase
The official documentation is hosted here on gitlab.
If you experience issues using the software please contact us through our issues page.
All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome. See our contribution guide for more information.
If you use this software in your scientific work, please cite this article:
van Aalst, M., Ebenhöh, O. & Matuszyńska, A. Constructing and analysing dynamic models with modelbase v1.2.3: a software update. BMC Bioinformatics 22, 203 (2021)
FAQs
A package to build metabolic models
We found that modelbase demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 5 open source maintainers collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
Security News
PyPI confirms no security flaws were exploited in the Ultralytics supply chain attack and highlights improvements for safer package publishing.
Security News
Research
The Socket Research Team breaks down a malicious wrapper package that uses obfuscation to harvest credentials and exfiltrate sensitive data.
Research
Security News
Attackers used a malicious npm package typosquatting a popular ESLint plugin to steal sensitive data, execute commands, and exploit developer systems.