BioSimulators

All

40 repositories

SimpleProcessBigraphRuntime
Public
A simple project demonstrating how to take a process bigraph input file, and run simulations / workflows utilizing a simple registry
Python
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MIT License
•0•0•0•2•Updated Jul 1, 2025Jul 1, 2025
Biosimulators_COPASI
Public
COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
docker simulation systems-biology computational-biology dynamical-modeling sbml copasi sed-ml biochemical-networks combine-archive
Python
•
MIT License
•3•2•6•2•Updated Jun 19, 2025Jun 19, 2025
Biosimulators_smoldyn
Public
Smoldyn biochemical network stochastic simulation program via BioSimulators-compliant python interface.
Python
•0•0•0•3•Updated Jun 19, 2025Jun 19, 2025
Biosimulators
Public
Registry of containerized biosimulation tools that support a standard command-line interface
docker systems-biology computational-biology reuse reproducibility combine sbml mathematical-model sbo sed-ml
Python
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MIT License
•0•13•14•7•Updated Jun 18, 2025Jun 18, 2025
Biosimulators_utils
Public
Utilities for building standardized command-line interfaces for biosimulation software packages
systems-biology computational-biology combine mathematical-modeling sed-ml omex biosimulators kisao python simulation
Python
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MIT License
•6•4•39•7•Updated May 23, 2025May 23, 2025
compose-server
Public
This repo is intended to replace both the bio-check and bio-compose-server repos. The aforementioned repos will be archived.
Python
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Apache License 2.0
•0•0•0•1•Updated Mar 12, 2025Mar 12, 2025
bio-compose-server
Public archive
Backend for BioCompose: a microservices-based data service leveraging Kubernetes for efficient orchestration of bio-chemical simulation comparisons.
Python
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Apache License 2.0
•1•1•0•0•Updated Feb 4, 2025Feb 4, 2025
Biosimulators_tellurium
Public
tellurium biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
docker simulation systems-biology computational-biology dynamical-modeling sbml tellurium sed-ml biochemical-networks combine-archive
Python
•
MIT License
•2•2•1•3•Updated Jan 8, 2025Jan 8, 2025
bio-check
Public archive
A microservices-based data service leveraging Kubernetes for efficient orchestration of bio-chemical simulation comparisons.
Python
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Apache License 2.0
•1•1•0•1•Updated Jan 7, 2025Jan 7, 2025
bsvs
Public
A high-level Python client for the Biological Simulation Verification Service REST API.
Python
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Apache License 2.0
•0•0•0•0•Updated Dec 23, 2024Dec 23, 2024
bio-compose
Public archive
Create, execute, and introspect reproducible composite simulations of dynamic biological systems.
Jupyter Notebook
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Apache License 2.0
•0•0•0•1•Updated Dec 22, 2024Dec 22, 2024
Biosimulators_test_suite
Public
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
docker systems-biology computational-biology mathematical-modelling sbml cellml sed-ml biochemical-networks combine-archive omex-metadata
Python
•
MIT License
•2•7•22•7•Updated Nov 22, 2024Nov 22, 2024
Biosimulators_MASSpy
Public
MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container
systems-biology computational-biology reaction-network metabolism combine sbml mathematical-model sed-ml numerical-simulation omex
Python
•
MIT License
•0•1•2•0•Updated Oct 31, 2024Oct 31, 2024
Biosimulators_PySCeS
Public
PySCeS biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
simulation systems-biology computational-biology combine sbml mathematical-model sed-ml omex biochemical-network biosimulators
Python
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MIT License
•0•2•2•0•Updated Oct 18, 2024Oct 18, 2024
Biosimulators_simularium
Public
Converting Biosimulators spatial simulation outputs into a Simularium-compliant format.
Jupyter Notebook
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MIT License
•0•1•0•0•Updated Aug 23, 2024Aug 23, 2024
OMEX-archive-editor
Public
Jupyter Notebook
•0•0•0•8•Updated May 21, 2024May 21, 2024
Biosimulators_AMICI
Public
AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
simulation systems-biology computational-biology combine sbml mathematical-model sed-ml omex biosimulators
Python
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MIT License
•1•3•4•0•Updated Apr 22, 2024Apr 22, 2024
biosimulator-processes
Public archive
Core implementations of simulator processes using the process-bigraph Process API
Jupyter Notebook
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Apache License 2.0
•1•1•0•0•Updated Mar 6, 2024Mar 6, 2024
Smoldyn
Public
Smoldyn is a particle-based biochemical simulator for modeling molecular diffusion, surface interactions, and chemical reactions
C++
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GNU General Public License v3.0
•13•0•0•0•Updated Jan 31, 2024Jan 31, 2024
biosimulators-smoldyn
Public
Smoldyn is a particle-based biochemical simulator for modeling molecular diffusion, surface interactions, and chemical reactions
C++
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GNU General Public License v3.0
•13•0•0•0•Updated Dec 11, 2023Dec 11, 2023
Biosimulators_tutorials
Public
Tutorials for BioSimulators
tutorial systems-biology computational-biology combine sbml mathematical-modeling sed-ml numerical-simulation omex biosimulations
Jupyter Notebook
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MIT License
•0•2•1•2•Updated May 1, 2023May 1, 2023
sphinx-pretty-searchresults
Public
Fork of "Sphinx: pretty search results" adding a necessary os import statement
Python
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MIT License
•5•0•0•0•Updated Dec 6, 2022Dec 6, 2022
xvfb-action
Public
Fork of GabrielBB/xvfb-action
JavaScript
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MIT License
•22•0•0•0•Updated Oct 9, 2022Oct 9, 2022
edamontology
Public
EDAM is an ontology of bioscientific data analysis and data management.
Shell
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Creative Commons Attribution Share Alike 4.0 International
•59•0•0•0•Updated Mar 29, 2022Mar 29, 2022
.github
Public
Profile for the BioSimulators organization
MIT License
•0•0•0•0•Updated Mar 3, 2022Mar 3, 2022
Biosimulators_XPP
Public
XPP mathematical simulation program via BioSimulators-compliant command-line interface and Docker container
combine mathematical-model xpp sed-ml numerical-simulation omex biosimulators kisao
Python
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MIT License
•1•0•4•0•Updated Feb 28, 2022Feb 28, 2022
Biosimulators_GillesPy2
Public
GillesPy2 biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
docker simulation systems-biology computational-biology stochastic-simulation-algorithm dynamical-modeling sbml sed-ml biochemical-networks combine-archive
Python
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MIT License
•1•2•2•0•Updated Feb 25, 2022Feb 25, 2022
Biosimulators_BioNetGen
Public
BioNetGen biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
docker simulation systems-biology stochastic-simulation-algorithm dynamical-modeling rule-based-modeling bionetgen sed-ml biochemical-networks combine-archive
Python
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MIT License
•3•1•3•0•Updated Feb 25, 2022Feb 25, 2022
Biosimulators_COBRApy
Public
COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
docker systems-biology computational-biology cobrapy sbml flux-balance-analysis constraint-based-modeling fba sed-ml biochemical-networks
Python
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MIT License
•0•2•2•0•Updated Feb 23, 2022Feb 23, 2022
Biosimulators_CBMPy
Public
CBMPy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
systems-biology computational-biology combine sbml flux-balance-analysis fba sed-ml omex biosimulators
Python
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MIT License
•0•0•3•0•Updated Feb 23, 2022Feb 23, 2022