BioSimulations

All

23 repositories

.github
Public
GitHub profile for the BioSimulations organization
MIT License
•0•0•0•1•Updated Aug 2, 2025Aug 2, 2025
status
Public
📈 Uptime monitor and status page for BioSimulations, powered by @upptime
uptime-monitor status-page upptime
Markdown
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MIT License
•1•0•1•0•Updated Aug 2, 2025Aug 2, 2025
biosim-client
Public
library for accessing biosimulations APIs.
Python
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MIT License
•0•0•2•11•Updated Aug 1, 2025Aug 1, 2025
compose-api
Public
Python
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Other
•0•0•1•3•Updated Jul 31, 2025Jul 31, 2025
biosim-server
Public
Server for the Biological Simulation Verification Service (BSVS)
Python
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Apache License 2.0
•0•1•0•9•Updated Jul 31, 2025Jul 31, 2025
biosimulations
Public
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
simulation biology modeling biological-simulations standards vega reproducibility biosimulation sbml sed-ml
TypeScript
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MIT License
•14•41•112•14•Updated Jul 27, 2025Jul 27, 2025
process-bigraph-lang
Public
Domain Specific Language and Language Server for Process Bigraphs
Python
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MIT License
•0•0•0•7•Updated Jul 1, 2025Jul 1, 2025
biosimulations-runutils
Public
Automation tools for running and comparing biosimulations from OMEX archives.
Python
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MIT License
•0•0•0•4•Updated Jun 19, 2025Jun 19, 2025
deployment
Public
Kubernetes Configuration for BioSimulations
argo argocd biosimulations kubernetes gitops
Shell
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MIT License
•1•3•6•11•Updated Jun 17, 2025Jun 17, 2025
biomodels-qc
Public
Quality control tool for the BioModels repository of biochemical models
testing quality-control validation systems-biology computational-model biomodels numerical-simulation
Python
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MIT License
•0•0•1•1•Updated May 21, 2025May 21, 2025
biosimulations-modeldb
Public
Command-line program and scheduled GitHub action for publishing the ModelDB model repository to BioSimulations
systems-biology computational-biology electrophysiology neuron combine modeldb xpp sed-ml omex biosimulations
MATLAB
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MIT License
•0•0•2•5•Updated Mar 13, 2025Mar 13, 2025
biosimulations-bigg
Public
Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations
systems-biology computational-biology metabolism combine sbml flux-balance-analysis fba cell-biology sed-ml omex
Python
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MIT License
•0•1•3•5•Updated Mar 12, 2025Mar 12, 2025
eslint-plugin-exclude-strings
Public
TypeScript
•0•0•0•8•Updated Dec 15, 2023Dec 15, 2023
static
Public
Repository for holding static files hosted at https://static.biosimulations.org
CSS
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Apache License 2.0
•0•0•0•1•Updated Dec 15, 2023Dec 15, 2023
hsds
Public
Cloud-native, service based access to HDF data
Python
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Apache License 2.0
•58•0•0•0•Updated Apr 4, 2023Apr 4, 2023
nestjs-bullmq
Public
TypeScript
•
MIT License
•11•0•1•1•Updated Apr 4, 2023Apr 4, 2023
material-file-input
Public
File input for Angular Material form-field
TypeScript
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MIT License
•66•0•0•0•Updated Apr 4, 2023Apr 4, 2023
nx-python
Public
🐍 Plugin for using Python in an Nx Workspace
TypeScript
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MIT License
•11•0•0•0•Updated Apr 4, 2023Apr 4, 2023
hdf-rest-api
Public
Python
•5•0•0•0•Updated Apr 4, 2023Apr 4, 2023
biosimulations-rulehub
Public
Repository of rule-based models implemented with the BioNetGen model language (BNGL) and command-line program for publishing RuleHub to BioSimulations
systems-biology computational-biology combine bionetgen sed-ml omex biosimulations rulehub bngl
Python
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MIT License
•3•1•0•0•Updated Apr 4, 2023Apr 4, 2023
cellml-validation
Public
A suite of CellML files used to test validation methods
Python
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Other
•1•0•0•0•Updated Apr 3, 2023Apr 3, 2023
biosimulations-physiome
Public
Command-line application for publishing the Physiome model repository of physiological models to the BioSimulations repository for simulation projects
systems-biology computational-biology combine pmr cellml sed-ml omex physiome-model-repository
JavaScript
•0•0•7•0•Updated May 16, 2022May 16, 2022
Owl2Json
Public
A very simple Java program to produce a JSON file from an ontology IRI
Java
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MIT License
•0•0•0•0•Updated Oct 4, 2021Oct 4, 2021