Mathematical Modeling Python Packages

biosimulators-utils

Utilities for building standardized command-line interfaces for biosimulation software packages

kisao

Ontology of algorithms for analyzing biological models, their parameters, and their outputs

axiomize

Reproducible scientific modeling engine and agent skill pack: versioned Model IR with mandatory units, dimensional and numerical validation, calibration, uncertainty analysis, and portable export (SBML, CellML, Modelica) via CLI, REST and MCP. Install: pip install axiomize.

axiomize-quantum-skills-2-0

Scientific modeling engine (versioned Model IR, dimensional validation, uncertainty) plus quantum-inspired multi-branch reasoning. Python, MCP and REST. MIT.

biosimulators-pyneuroml

pyNeuroML simulation program via BioSimulators-compliant command-line interface and Docker container

biosimulators-opencor

OpenCOR simulation program via BioSimulators-compliant command-line interface and Docker container

simbiology-mcp

An MCP server providing AI assistants with access to MATLAB SimBiology for modelling, simulating, and analyzing biological systems

biosimulators-rbapy

RBApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

phi47

Scientific Python framework for finite complex lattices, deterministic numerical kernels, integration proxies, and reproducible experiments.

lp-comp

Python library for coordinated planning in two-level systems, finding compromise solutions between a Center and Elements using mathematical models & a GUI.