A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
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Updated
May 28, 2024 - Python
A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
python Parameter EStimation TOolbox
A python library for metabolic networks sampling and analysis
A Python package for analyses of Boolean and semi-quantitative Boolean networks.
Semantic Capture of Relationships In Biological Literature (scribl)
Patient-Specific Modeling in Python
Python package to study microbial communities using metabolic modeling.
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
CBMPy is a Python based platform for constraint based modelling and analysis.
PyBioPAX: A python implementation of the BioPAX object model
An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
PySCeS biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
Registry of containerized biosimulation tools that support a standard command-line interface
Synthesis and Reprogramming of Most Permissive Boolean Networks
Estimation of extracellular fluxes and growth rate
The biologist's Boolean attractor landscape mapper, building Waddington landscapes from Boolean networks.
AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
A Python Framework for Modeling and Analysis of Signaling Systems
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