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opencobra
cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

62K 560 234
pybel
pybel

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

16K 138 32
biosimulators
biosimulators-utils

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

9K 4 6
PEtab-dev
petab

Python package for working with PEtab files

8K 16 7
gyorilab
indra

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.

8K 209 77
spatial-model-editor
sme

Spatial Model Editor python bindings

8K 19 8
dweindl
sbmlmath

SBML MathML ↔ SymPy

5K 9 1
indralab
pybiopax

PyBioPAX: A python implementation of the BioPAX object model

5K 27 6
micom-dev
micom

Microbial community modeling based on cobrapy.

4K 127 23
napistu
napistu

The core library of the Napitsu project supporting the creation, transformation, and network-based interrogation of biological pathways

4K 1 0
biosimulators
biosimulators-test-suite

Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators

3K 7 2
ecell
ecell4-base

A software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell. E-Cell has multi-algorithm, multi-timescale and multi-spatial-representation as its central feature.

3K 62 22
SED-ML
kisao

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

3K 12 0
icb-dcm
pypesto

python Parameter EStimation TOolbox

3K 270 48
SystemsBioinformatics
cbmpy

CBMPy: https://systemsbioinformatics.github.io/cbmpy/ is a platform for constraint based modelling. It implements popular FBA analyses, model editing and supports the latest SBML3FBC standards.

2K 20 4
charlesrocabert
metevolsim

MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.

2K 5 0
biosimulators
biosimulators-copasi

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

2K 2 3
CiaranWelsh
pycotools

A Python Toolbox for COPASI

2K 6 4
biosimulators
biosimulators-tellurium

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

1K 2 2
biomass-dev
biomass

A Python Framework for Modeling and Analysis of Signaling Systems

1K 29 13
PEtab-dev
petab-select

Model selection for PEtab

1K 14 1
pybel
pybel-tools

A PyBEL extension for analyzing BEL graphs

1K 5 5
biosimulators
biosimulators-amici

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

1K 3 1
biosimulators
biosimulators-pysces

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

1K 2 0
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