https://github.com/bluebrain/circuit-model-suite
https://github.com/bluebrain/circuit-model-suite
Last synced: 6 months ago
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- Host: GitHub
- URL: https://github.com/bluebrain/circuit-model-suite
- Owner: BlueBrain
- Created: 2022-06-07T14:08:43.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2024-06-04T06:04:07.000Z (about 2 years ago)
- Last Synced: 2025-01-19T23:38:39.250Z (over 1 year ago)
- Size: 33.2 KB
- Stars: 3
- Watchers: 6
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Circuit Model Suite
A suite to build, analyze and visualize circuits.
- [Neurodamus](#neurodamus) - BBP Simulation Control application for NEURON.
- [CoreNeuron](#coreneuron) — Optimised simulator engine for NEURON.
- [Snap](#snap) — Blue Brain Simulation and Neural network Analysis Productivity layer.
- [BlueETL](#blueetl) - Multiple simulations analysis tool.
- [ConnectomeUtilities](#connectomeutilities) — Complex network representation and analysis layer.
- [ConnectomeManipulator](#connectomemanipulator) - A connectome manipulation framework for SONATA circuits .
- [Functionalizer](#functionalizer) - Create a functional connectome from physical connections between cells.
- [Brayns](#brayns) — Visualizer for large-scale and interactive ray-tracing of neurons.
- [libsonata](#libsonata) — C++ / Python reader for SONATA circuit files.
- [BioExplorer](#bioexplorer) - Extract and analyze scientific data for visualization and interactive exploration.
## [Neurodamus](https://github.com/BlueBrain/Neurodamus)
Useful links:
[GitHub repo](https://github.com/BlueBrain/neurodamus),
[Documentation](https://github.com/BlueBrain/neurodamus#readme).
**BBP Simulation Control application for NEURON**
Neurodamus is a BBP Simulation Control application for the NEURON simulator. The Python implementation offers a comprehensive Python API for fine tunning of the simulation, defined by a configuration file in SONATA format.
## [CoreNeuron](https://github.com/BlueBrain/CoreNeuron)
Useful links:
[GitHub repo](https://github.com/BlueBrain/CoreNeuron),
[Documentation](https://github.com/BlueBrain/CoreNeuron#readme).
**Optimised simulator engine for NEURON**
CoreNEURON is a compute engine for the NEURON simulator optimized for both memory usage and computational speed. Its goal is to simulate large cell networks with small memory footprint and optimal performance.
## [Snap](https://github.com/BlueBrain/snap)
Useful links:
[GitHub repo](https://github.com/BlueBrain/snap),
[Documentation](https://bluebrainsnap.readthedocs.io/).
**Blue Brain Simulation and Neural network Analysis Productivity layer (Blue Brain SNAP)**
Blue Brain SNAP is a Python library for accessing BlueBrain circuit models represented in SONATA format.
## [BlueETL](https://github.com/BlueBrain/blueetl)
Useful links:
[GitHub repo](https://github.com/BlueBrain/blueetl),
[Documentation](https://blueetl.readthedocs.io/).
Core transformations:
[GitHub repo](https://github.com/BlueBrain/blueetl-core),
[Documentation](https://blueetl-core.readthedocs.io/).
**Multiple simulations analysis tool**
## [ConnectomeUtilities](https://github.com/BlueBrain/ConnectomeUtilities)
Useful links:
[GitHub repo](https://github.com/BlueBrain/ConnectomeUtilities)
**Complex network representation and analysis layer**
It simplifies running topological analyses on detailed models of networks by providing a bridge between existing analyses and the model representation.
## [ConnectomeManipulator](https://github.com/BlueBrain/connectome-manipulator)
Useful links:
[GitHub repo](https://github.com/BlueBrain/connectome-manipulator)
**Connectome manipulation framework for SONATA circuits**
The framework allows for rapid connectome manipulations of biophysically detailed network models in SONATA format, the standard for large-scale network models. Manipulations can be targeted to entire models, specific sub-networks, or even single neurons, ranging from insertion or removal of specific motifs to complete rewiring based on stochastic connectivity models at various levels of complexity.
## [Functionalizer](https://github.com/BlueBrain/functionalizer)
Useful links:
[GitHub repo](https://github.com/BlueBrain/functionalizer)
**Create a functional connectome from physical connections between cells**
Functionalizer is a tool for filtering the output of a touch detector (the "touches") according to morphological models, given in in the form of recipe prescription as described in the SONATA extension.
## [Brayns](https://github.com/BlueBrain/Brayns)
Useful links:
[GitHub repo](https://github.com/BlueBrain/Brayns),
[Documentation](https://github.com/BlueBrain/Brayns#readme).
**Visualizer for large-scale and interactive ray-tracing of neurons**
Brayns is a minimalistic visualizer that can perform ray-traced rendering of neurons. It provides an abstraction of the underlying rendering engines so that the best possible acceleration libraries can be used for the relevant hardware.
## [libsonata](https://github.com/BlueBrain/libsonata)
Useful links:
[GitHub repo](https://github.com/BlueBrain/libsonata),
[Documentation](https://github.com/BlueBrain/libsonata#readme).
**C++ / Python reader for SONATA circuit files**
## [BioExplorer](https://github.com/BlueBrain/BioExplorer)
**The Blue Brain BioExplorer is a tool for scientists to extract and analyze scientific data for visualization and interactive exploration**
Exploration relies on building software that combines data integration, analysis and interactive visualization to build, modify and navigate through large scientific datasets. For this, Blue Brain built and open-sourced the Blue Brain BioExplorer. It was originally developed to answer key scientific questions related to the Coronavirus as a use case and to deliver a visualization tool. Today, the BioExplorer allows to reconstruct, visualize, explore, and describe in detail the structure and function of highly-detailed biological structures such as molecular systems, neurons, astrocytes, blood vessels, and more. You can see the first application of the BioExplorer in [A Machine-Generated View of the Role of Blood Glucose Levels in the Severity of COVID-19](https://www.frontiersin.org/articles/10.3389/fpubh.2021.695139/full?utm_source=F-NTF&utm_medium=EMLX&utm_campaign=PRD_FEOPS_20170000_ARTICLE) study.
Useful links:
[GitHub repo](https://github.com/BlueBrain/BioExplorer),
[Documentation](https://bluebrain.github.io/BioExplorer/).